Starting phenix.real_space_refine on Mon Aug 10 05:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ram_19019/08_2026/8ram_19019.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 235 5.16 5 C 26796 2.51 5 N 7515 2.21 5 O 8315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42965 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11020 Classifications: {'peptide': 1400} Link IDs: {'PTRANS': 65, 'TRANS': 1334} Chain breaks: 5 Chain: "B" Number of atoms: 8839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8839 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 50, 'TRANS': 1062} Chain breaks: 6 Chain: "C" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2078 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain: "D" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1270 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain breaks: 1 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: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 343 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "N" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "O" Number of atoms: 5523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5523 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 28, 'TRANS': 661} Chain breaks: 2 Chain: "P" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 624 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 13, 'rna3p': 15} Chain breaks: 1 Chain: "T" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 786 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Y" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "Z" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3397 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 12, 'TRANS': 416} Chain breaks: 5 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "M" 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 809 SG CYS A 107 75.786 134.401 146.520 1.00100.93 S ATOM 833 SG CYS A 110 73.822 138.268 147.636 1.00104.38 S ATOM 1276 SG CYS A 167 74.829 136.127 149.806 1.00113.42 S ATOM 504 SG CYS A 67 58.707 133.379 101.910 1.00 95.72 S ATOM 579 SG CYS A 77 62.567 131.731 100.277 1.00 84.02 S ATOM 19396 SG CYS B1163 69.061 144.765 108.056 1.00 83.57 S ATOM 19414 SG CYS B1166 70.230 143.155 111.235 1.00 79.89 S ATOM 19539 SG CYS B1182 66.464 142.958 110.101 1.00 89.37 S ATOM 19558 SG CYS B1185 67.973 146.180 111.415 1.00 96.43 S ATOM 20506 SG CYS C 86 78.853 103.484 43.180 1.00 67.90 S ATOM 20523 SG CYS C 88 75.992 103.408 45.638 1.00 74.05 S ATOM 20556 SG CYS C 92 76.043 100.855 42.812 1.00 63.03 S ATOM 20579 SG CYS C 95 78.539 100.525 45.541 1.00 60.57 S ATOM 28101 SG CYS I 7 101.842 74.103 159.313 1.00132.44 S ATOM 28316 SG CYS I 32 99.783 74.449 163.375 1.00135.56 S ATOM 28643 SG CYS I 75 127.576 61.250 126.667 1.00108.82 S ATOM 28665 SG CYS I 78 127.189 57.522 126.203 1.00111.29 S ATOM 28881 SG CYS I 103 124.568 59.827 124.771 1.00101.64 S ATOM 28901 SG CYS I 106 124.827 59.438 128.549 1.00103.68 S ATOM 29073 SG CYS J 7 98.330 85.093 64.006 1.00 48.45 S ATOM 29096 SG CYS J 10 99.916 85.790 60.622 1.00 48.94 S ATOM 29376 SG CYS J 45 102.005 84.454 63.518 1.00 49.87 S ATOM 29382 SG CYS J 46 99.457 82.205 61.752 1.00 51.11 S ATOM 30506 SG CYS L 31 58.103 78.150 77.972 1.00 75.58 S ATOM 30526 SG CYS L 34 56.576 74.822 76.797 1.00 78.58 S ATOM 30630 SG CYS L 48 54.344 77.781 77.789 1.00 79.94 S ATOM 30653 SG CYS L 51 56.297 75.795 80.385 1.00 82.03 S ATOM 30855 SG CYS M 25 69.045 102.203 158.861 1.00194.46 S ATOM 30880 SG CYS M 28 66.658 105.085 158.324 1.00198.85 S ATOM 31035 SG CYS M 49 70.369 105.800 158.824 1.00191.50 S ATOM 31058 SG CYS M 52 68.362 104.596 161.742 1.00196.94 S Time building chain proxies: 8.25, per 1000 atoms: 0.19 Number of scatterers: 42965 At special positions: 0 Unit cell: (169.05, 207.9, 182.7, 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 9 29.99 S 235 16.00 P 94 15.00 Mg 1 11.99 O 8315 8.00 N 7515 7.00 C 26796 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: 3.97 Conformation dependent library (CDL) restraints added in 1.8 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 107 " 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 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " 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 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " 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 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " Number of angles added : 36 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9690 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 63 sheets defined 39.4% alpha, 17.8% beta 34 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.087A pdb=" N THR A 46 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.554A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.571A pdb=" N MET A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.841A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 504 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 574 through 580 removed outlier: 3.806A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (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 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.916A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) 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 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.963A 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 915 through 920 removed outlier: 3.719A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.569A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1163 through 1165 No H-bonds generated for 'chain 'A' and resid 1163 through 1165' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 4.231A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1259 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.521A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.738A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1405 through 1416 removed outlier: 3.608A pdb=" N LEU A1409 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.086A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.758A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.861A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (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 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 removed outlier: 4.181A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.287A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.722A pdb=" N ALA B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 435 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.704A pdb=" N GLY B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.128A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.522A pdb=" N GLY B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.643A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.708A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.016A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 813 removed outlier: 4.444A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.168A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.435A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 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 69 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.563A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 removed outlier: 3.978A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 76 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.537A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.535A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 3 through 27 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.503A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.513A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) 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 124 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.126A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) 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 21 through 35 Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'H' and resid 128 through 134 removed outlier: 4.349A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.483A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 55 through 62 removed outlier: 4.141A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.601A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'O' and resid 1096 through 1110 Processing helix chain 'O' and resid 1113 through 1122 removed outlier: 3.544A pdb=" N GLN O1122 " --> pdb=" O GLU O1118 " (cutoff:3.500A) Processing helix chain 'O' and resid 1136 through 1140 Processing helix chain 'O' and resid 1149 through 1176 Proline residue: O1159 - end of helix Processing helix chain 'O' and resid 1203 through 1210 Processing helix chain 'O' and resid 1232 through 1239 removed outlier: 3.614A pdb=" N PHE O1236 " --> pdb=" O SER O1232 " (cutoff:3.500A) Processing helix chain 'O' and resid 1268 through 1274 Processing helix chain 'O' and resid 1288 through 1301 Processing helix chain 'O' and resid 1302 through 1304 No H-bonds generated for 'chain 'O' and resid 1302 through 1304' Processing helix chain 'O' and resid 1306 through 1313 Processing helix chain 'O' and resid 1322 through 1334 Processing helix chain 'O' and resid 1336 through 1349 Processing helix chain 'O' and resid 1362 through 1377 Processing helix chain 'O' and resid 1412 through 1425 removed outlier: 3.704A pdb=" N SER O1425 " --> pdb=" O LEU O1421 " (cutoff:3.500A) Processing helix chain 'O' and resid 1449 through 1453 Processing helix chain 'O' and resid 1456 through 1466 Processing helix chain 'O' and resid 1535 through 1562 Processing helix chain 'O' and resid 1570 through 1573 Processing helix chain 'O' and resid 1574 through 1581 Processing helix chain 'O' and resid 1591 through 1595 removed outlier: 3.818A pdb=" N CYS O1595 " --> pdb=" O ALA O1592 " (cutoff:3.500A) Processing helix chain 'O' and resid 1596 through 1602 Processing helix chain 'O' and resid 1603 through 1606 removed outlier: 3.615A pdb=" N TYR O1606 " --> pdb=" O PRO O1603 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1603 through 1606' Processing helix chain 'O' and resid 1626 through 1632 Processing helix chain 'O' and resid 1637 through 1646 removed outlier: 3.534A pdb=" N ARG O1641 " --> pdb=" O SER O1637 " (cutoff:3.500A) Processing helix chain 'O' and resid 1658 through 1668 removed outlier: 4.274A pdb=" N PHE O1664 " --> pdb=" O SER O1660 " (cutoff:3.500A) Proline residue: O1665 - end of helix Processing helix chain 'O' and resid 1719 through 1736 Processing helix chain 'O' and resid 1752 through 1767 Processing helix chain 'O' and resid 1768 through 1773 removed outlier: 3.660A pdb=" N ILE O1771 " --> pdb=" O GLY O1768 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS O1773 " --> pdb=" O MET O1770 " (cutoff:3.500A) Processing helix chain 'O' and resid 1779 through 1784 Processing helix chain 'O' and resid 1805 through 1809 removed outlier: 4.272A pdb=" N LEU O1808 " --> pdb=" O VAL O1805 " (cutoff:3.500A) Processing helix chain 'O' and resid 1810 through 1820 removed outlier: 3.638A pdb=" N MET O1814 " --> pdb=" O ASP O1810 " (cutoff:3.500A) Processing helix chain 'O' and resid 1831 through 1837 removed outlier: 4.062A pdb=" N SER O1837 " --> pdb=" O SER O1833 " (cutoff:3.500A) Processing helix chain 'O' and resid 1837 through 1850 Processing helix chain 'O' and resid 1865 through 1876 removed outlier: 3.725A pdb=" N GLN O1869 " --> pdb=" O ASN O1865 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 20 Processing helix chain 'Y' and resid 25 through 33 Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Y' and resid 52 through 55 Processing helix chain 'Y' and resid 56 through 62 Processing helix chain 'Y' and resid 81 through 87 Processing helix chain 'Z' and resid 1 through 6 removed outlier: 4.090A pdb=" N LEU Z 6 " --> pdb=" O ARG Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 43 Processing helix chain 'Z' and resid 68 through 77 removed outlier: 3.604A pdb=" N ILE Z 72 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 93 No H-bonds generated for 'chain 'Z' and resid 91 through 93' Processing helix chain 'Z' and resid 94 through 100 Processing helix chain 'Z' and resid 179 through 188 removed outlier: 3.802A pdb=" N GLN Z 188 " --> pdb=" O LEU Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 218 through 220 No H-bonds generated for 'chain 'Z' and resid 218 through 220' Processing helix chain 'Z' and resid 682 through 684 No H-bonds generated for 'chain 'Z' and resid 682 through 684' Processing helix chain 'Z' and resid 739 through 742 Processing helix chain 'Z' and resid 748 through 750 No H-bonds generated for 'chain 'Z' and resid 748 through 750' Processing helix chain 'Z' and resid 841 through 843 No H-bonds generated for 'chain 'Z' and resid 841 through 843' Processing helix chain 'Z' and resid 859 through 864 removed outlier: 3.617A pdb=" N ASN Z 863 " --> pdb=" O ASP Z 859 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.697A pdb=" N GLY A 20 " --> pdb=" O THR B1213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 7.331A pdb=" N ALA A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.559A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.651A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.304A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 removed outlier: 3.534A pdb=" N TRP A 572 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.608A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.810A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 4.006A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1147 through 1151 Processing sheet with id=AB8, first strand: chain 'A' and resid 1442 through 1445 removed outlier: 3.797A pdb=" N ASP A1442 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 91 through 97 removed outlier: 6.144A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.691A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.888A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.662A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.670A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.606A pdb=" N VAL B 589 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.479A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.622A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.678A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.032A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 11.054A pdb=" N ARG O1188 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR C 100 " --> pdb=" O ARG O1188 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA O1190 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN C 102 " --> pdb=" O ALA O1190 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 1194 through 1202 current: chain 'C' and resid 42 through 54 removed outlier: 4.100A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 96 through 104 current: chain 'O' and resid 1242 through 1253 removed outlier: 4.780A pdb=" N ASP O1215 " --> pdb=" O VAL O1247 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET O1286 " --> pdb=" O LEU O1216 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL O1218 " --> pdb=" O LYS O1284 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS O1284 " --> pdb=" O VAL O1218 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA O1220 " --> pdb=" O CYS O1282 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N CYS O1282 " --> pdb=" O ALA O1220 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N SER O1182 " --> pdb=" O ALA O1202 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA O1202 " --> pdb=" O SER O1182 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE O1184 " --> pdb=" O SER O1200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER O1200 " --> pdb=" O ILE O1184 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 1194 through 1202 current: chain 'C' and resid 42 through 54 removed outlier: 4.100A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.470A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.661A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.288A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.825A pdb=" N LYS G 73 " --> pdb=" O ASP G 55 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP G 55 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 38 through 39 removed outlier: 6.898A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.612A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.580A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 95 through 98 removed outlier: 6.319A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.473A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AF6, first strand: chain 'O' and resid 1439 through 1441 removed outlier: 6.461A pdb=" N ILE O1406 " --> pdb=" O ILE O1565 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER O1567 " --> pdb=" O ILE O1406 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE O1408 " --> pdb=" O SER O1567 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL O1587 " --> pdb=" O ILE O1612 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL O1614 " --> pdb=" O VAL O1587 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE O1589 " --> pdb=" O VAL O1614 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER O1353 " --> pdb=" O MET O1613 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N TYR O1649 " --> pdb=" O PHE O1352 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU O1354 " --> pdb=" O TYR O1649 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 1653 through 1654 removed outlier: 3.545A pdb=" N GLN O1654 " --> pdb=" O LYS O1675 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'O' and resid 1775 through 1777 removed outlier: 6.508A pdb=" N GLU O1789 " --> pdb=" O SER O1824 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TRP O1826 " --> pdb=" O GLU O1789 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE O1791 " --> pdb=" O TRP O1826 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU O1828 " --> pdb=" O ILE O1791 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE O1793 " --> pdb=" O LEU O1828 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N HIS O1830 " --> pdb=" O ILE O1793 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY O1829 " --> pdb=" O PHE O1700 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA O1854 " --> pdb=" O TYR O1697 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE O1699 " --> pdb=" O ALA O1854 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA O1856 " --> pdb=" O PHE O1699 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP O1701 " --> pdb=" O ALA O1856 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 1707 through 1709 Processing sheet with id=AG1, first strand: chain 'Y' and resid 11 through 13 Processing sheet with id=AG2, first strand: chain 'Y' and resid 44 through 45 Processing sheet with id=AG3, first strand: chain 'Y' and resid 70 through 72 removed outlier: 3.905A pdb=" N LEU Y 47 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER Z 51 " --> pdb=" O GLU Z 65 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N ILE Z 14 " --> pdb=" O LYS Z 87 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS Z 87 " --> pdb=" O ILE Z 14 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N GLY Z 16 " --> pdb=" O SER Z 85 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER Z 85 " --> pdb=" O GLY Z 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG Z 18 " --> pdb=" O TYR Z 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 114 through 116 removed outlier: 5.727A pdb=" N VAL Z 129 " --> pdb=" O LYS Z 142 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS Z 142 " --> pdb=" O VAL Z 129 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN Z 131 " --> pdb=" O MET Z 140 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS Z 198 " --> pdb=" O ARG Z 194 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 621 through 626 removed outlier: 3.701A pdb=" N ARG Z 621 " --> pdb=" O SER Z 616 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N MET Z 615 " --> pdb=" O VAL Z 604 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL Z 604 " --> pdb=" O MET Z 615 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 676 through 680 removed outlier: 6.858A pdb=" N LYS Z 668 " --> pdb=" O ILE Z 660 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE Z 648 " --> pdb=" O ILE Z 688 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 697 through 698 Processing sheet with id=AG8, first strand: chain 'Z' and resid 744 through 747 removed outlier: 7.044A pdb=" N PHE Z 732 " --> pdb=" O LEU Z 724 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 837 through 840 removed outlier: 3.793A pdb=" N ASP Z 821 " --> pdb=" O THR Z 828 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU Z 830 " --> pdb=" O VAL Z 819 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL Z 819 " --> pdb=" O GLU Z 830 " (cutoff:3.500A) 1722 hydrogen bonds defined for protein. 4758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 15.02 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13776 1.34 - 1.46: 5940 1.46 - 1.57: 23646 1.57 - 1.69: 183 1.69 - 1.81: 371 Bond restraints: 43916 Sorted by residual: bond pdb=" C3' DC T 34 " pdb=" C2' DC T 34 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 bond pdb=" C1' DT T 8 " pdb=" N1 DT T 8 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.74e+00 bond pdb=" C1' DT N 49 " pdb=" N1 DT N 49 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.63e+00 bond pdb=" C3' DC N 43 " pdb=" C2' DC N 43 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 bond pdb=" C1' DC N 44 " pdb=" N1 DC N 44 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.36e+00 ... (remaining 43911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 57700 0.93 - 1.86: 1492 1.86 - 2.78: 221 2.78 - 3.71: 219 3.71 - 4.64: 44 Bond angle restraints: 59676 Sorted by residual: angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" O4 DT T 12 " pdb=" C4 DT T 12 " pdb=" C5 DT T 12 " ideal model delta sigma weight residual 124.90 121.95 2.95 7.00e-01 2.04e+00 1.77e+01 ... (remaining 59671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 26267 30.69 - 61.38: 446 61.38 - 92.06: 33 92.06 - 122.75: 2 122.75 - 153.44: 2 Dihedral angle restraints: 26750 sinusoidal: 11774 harmonic: 14976 Sorted by residual: dihedral pdb=" C4' DC T 34 " pdb=" C3' DC T 34 " pdb=" O3' DC T 34 " pdb=" P DA T 35 " ideal model delta sinusoidal sigma weight residual 220.00 66.56 153.44 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG T 14 " pdb=" C3' DG T 14 " pdb=" O3' DG T 14 " pdb=" P DA T 15 " ideal model delta sinusoidal sigma weight residual 220.00 71.95 148.05 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" O4' U P 12 " pdb=" C1' U P 12 " pdb=" N1 U P 12 " pdb=" C2 U P 12 " ideal model delta sinusoidal sigma weight residual -128.00 -78.50 -49.50 1 1.70e+01 3.46e-03 1.16e+01 ... (remaining 26747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4751 0.032 - 0.063: 1166 0.063 - 0.095: 371 0.095 - 0.127: 369 0.127 - 0.159: 67 Chirality restraints: 6724 Sorted by residual: chirality pdb=" C3' DC N 44 " pdb=" C4' DC N 44 " pdb=" O3' DC N 44 " pdb=" C2' DC N 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" C3' DG T 17 " pdb=" C4' DG T 17 " pdb=" O3' DG T 17 " pdb=" C2' DG T 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" C3' DA T 25 " pdb=" C4' DA T 25 " pdb=" O3' DA T 25 " pdb=" C2' DA T 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 6721 not shown) Planarity restraints: 7379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1301 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1302 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1302 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1302 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 417 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C PHE B 417 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE B 417 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS B 418 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 124 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO E 125 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " -0.016 5.00e-02 4.00e+02 ... (remaining 7376 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 374 2.53 - 3.12: 35205 3.12 - 3.72: 66818 3.72 - 4.31: 94560 4.31 - 4.90: 158904 Nonbonded interactions: 355861 Sorted by model distance: nonbonded pdb=" O3' U P 35 " pdb="MG MG A1803 " model vdw 1.940 2.170 nonbonded pdb=" OD1 ASP A 853 " pdb=" OG1 THR A 855 " model vdw 1.948 3.040 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 1.974 2.170 nonbonded pdb=" OH TYR J 21 " pdb=" OE1 GLU J 32 " model vdw 1.994 3.040 nonbonded pdb=" O THR B 98 " pdb=" OG SER B 126 " model vdw 1.995 3.040 ... (remaining 355856 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 53.410 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 43947 Z= 0.150 Angle : 0.417 5.612 59712 Z= 0.275 Chirality : 0.041 0.159 6724 Planarity : 0.002 0.040 7379 Dihedral : 10.326 153.441 17060 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.13), residues: 5091 helix: 3.38 (0.13), residues: 1750 sheet: 0.48 (0.17), residues: 901 loop : 0.53 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 336 TYR 0.006 0.001 TYR A 836 PHE 0.009 0.001 PHE A 219 TRP 0.007 0.000 TRP O1688 HIS 0.002 0.000 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.15 (43916) covalent geometry : angle 0.41456 / 0.28 (59676) hydrogen bonds : bond 0.13929 / 9.55 ( 1800) hydrogen bonds : angle 5.22373 / 3.77 ( 4924) metal coordination : bond 0.00177 / 0.09 ( 31) metal coordination : angle 1.75545 / 1.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1040 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8791 (mm) cc_final: 0.8496 (tp) REVERT: A 279 LEU cc_start: 0.8457 (mt) cc_final: 0.8201 (tt) REVERT: A 818 MET cc_start: 0.8951 (mtp) cc_final: 0.8697 (mtp) REVERT: A 1281 ARG cc_start: 0.7581 (ptt90) cc_final: 0.6886 (ppt170) REVERT: A 1411 GLU cc_start: 0.8168 (tp30) cc_final: 0.7926 (tp30) REVERT: B 789 MET cc_start: 0.8826 (mmm) cc_final: 0.8494 (mmt) REVERT: B 961 LEU cc_start: 0.8034 (pt) cc_final: 0.7594 (pp) REVERT: B 1098 MET cc_start: 0.8575 (mtm) cc_final: 0.8205 (mtt) REVERT: C 123 ASN cc_start: 0.8337 (t0) cc_final: 0.8081 (t0) REVERT: D 118 THR cc_start: 0.5665 (p) cc_final: 0.4961 (p) REVERT: E 8 ASN cc_start: 0.7759 (m110) cc_final: 0.7509 (m110) REVERT: F 110 ASP cc_start: 0.7862 (p0) cc_final: 0.7619 (p0) REVERT: G 10 ASN cc_start: 0.8868 (m-40) cc_final: 0.8497 (m110) REVERT: G 28 THR cc_start: 0.8667 (p) cc_final: 0.8431 (p) REVERT: G 38 CYS cc_start: 0.7824 (t) cc_final: 0.7410 (t) REVERT: G 41 LYS cc_start: 0.8409 (tptp) cc_final: 0.7873 (mttt) REVERT: G 53 ASN cc_start: 0.8231 (t0) cc_final: 0.7241 (t0) REVERT: H 107 VAL cc_start: 0.7493 (t) cc_final: 0.7182 (m) REVERT: H 112 ILE cc_start: 0.9048 (tt) cc_final: 0.8477 (tp) REVERT: H 126 GLU cc_start: 0.7522 (tt0) cc_final: 0.7151 (tt0) REVERT: I 4 PHE cc_start: 0.6811 (t80) cc_final: 0.6571 (t80) REVERT: I 90 GLN cc_start: 0.8441 (pt0) cc_final: 0.8098 (pt0) REVERT: K 97 LYS cc_start: 0.9098 (mttt) cc_final: 0.8845 (mttt) REVERT: O 1633 LYS cc_start: 0.9361 (mttt) cc_final: 0.9111 (mtpm) REVERT: O 1783 PHE cc_start: 0.8887 (t80) cc_final: 0.8498 (t80) REVERT: O 1814 MET cc_start: 0.7562 (mtp) cc_final: 0.7215 (mmp) REVERT: O 1830 HIS cc_start: 0.8858 (t-90) cc_final: 0.8655 (t70) REVERT: Y 50 MET cc_start: 0.4969 (tpp) cc_final: 0.4464 (tmm) REVERT: Z 182 MET cc_start: 0.3023 (mtm) cc_final: 0.2784 (pp-130) REVERT: Z 615 MET cc_start: -0.4921 (tpp) cc_final: -0.6017 (mtt) outliers start: 2 outliers final: 2 residues processed: 1042 average time/residue: 0.8567 time to fit residues: 1081.1505 Evaluate side-chains 517 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 515 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain H residue 92 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 488 ASN A 493 GLN A 503 GLN A 517 ASN A 742 ASN A 881 GLN A1070 GLN A1270 ASN B 115 GLN B 178 ASN B 383 ASN B 515 HIS B 538 ASN B 648 HIS C 31 ASN C 135 GLN C 188 HIS C 203 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 143 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN F 78 GLN K 44 ASN ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1241 HIS Z 629 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.130827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078695 restraints weight = 94265.249| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.92 r_work: 0.2993 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 43947 Z= 0.241 Angle : 0.697 14.680 59712 Z= 0.360 Chirality : 0.047 0.337 6724 Planarity : 0.006 0.071 7379 Dihedral : 12.582 165.137 6770 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.97 % Allowed : 12.78 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 5091 helix: 2.18 (0.12), residues: 1771 sheet: 0.37 (0.17), residues: 922 loop : 0.25 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1096 TYR 0.032 0.002 TYR G 167 PHE 0.027 0.002 PHE O1807 TRP 0.027 0.002 TRP O1840 HIS 0.017 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (43916) covalent geometry : angle 0.69040 / 0.36 (59676) hydrogen bonds : bond 0.04254 / 2.85 ( 1800) hydrogen bonds : angle 4.64672 / 3.34 ( 4924) metal coordination : bond 0.00718 / 0.39 ( 31) metal coordination : angle 4.06634 / 2.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 546 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8995 (mm) cc_final: 0.8602 (tp) REVERT: A 250 ILE cc_start: 0.8750 (pp) cc_final: 0.8479 (tt) REVERT: A 416 ARG cc_start: 0.8717 (ptt-90) cc_final: 0.8253 (ptt90) REVERT: A 618 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 712 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8588 (pt0) REVERT: A 745 GLN cc_start: 0.8916 (mt0) cc_final: 0.8701 (mt0) REVERT: A 838 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7939 (tp40) REVERT: A 1070 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9024 (mt0) REVERT: A 1196 GLU cc_start: 0.8497 (tt0) cc_final: 0.7855 (tm-30) REVERT: A 1214 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8511 (mm-30) REVERT: A 1215 ARG cc_start: 0.9091 (tpp-160) cc_final: 0.8595 (mmm160) REVERT: A 1281 ARG cc_start: 0.7927 (ptt90) cc_final: 0.7590 (ppt170) REVERT: A 1284 MET cc_start: 0.8377 (mtm) cc_final: 0.8177 (mtt) REVERT: A 1411 GLU cc_start: 0.8913 (tp30) cc_final: 0.8643 (tp30) REVERT: B 349 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 350 GLN cc_start: 0.7884 (pm20) cc_final: 0.7668 (pm20) REVERT: B 401 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: B 789 MET cc_start: 0.9264 (mmm) cc_final: 0.9015 (mmt) REVERT: B 836 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8109 (mm-30) REVERT: B 899 ILE cc_start: 0.9018 (pt) cc_final: 0.8814 (pp) REVERT: B 1152 MET cc_start: 0.8740 (mmm) cc_final: 0.8345 (mmm) REVERT: B 1168 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9033 (mp) REVERT: D 70 PHE cc_start: 0.8941 (m-80) cc_final: 0.8731 (m-80) REVERT: D 140 ASP cc_start: 0.8365 (t0) cc_final: 0.8110 (t0) REVERT: E 8 ASN cc_start: 0.8511 (m110) cc_final: 0.7981 (m110) REVERT: E 112 TYR cc_start: 0.8151 (p90) cc_final: 0.7727 (p90) REVERT: E 113 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: F 110 ASP cc_start: 0.8791 (p0) cc_final: 0.8409 (p0) REVERT: G 6 ASP cc_start: 0.7320 (p0) cc_final: 0.7091 (OUTLIER) REVERT: G 10 ASN cc_start: 0.8844 (m-40) cc_final: 0.8593 (m110) REVERT: G 21 ARG cc_start: 0.8576 (ptp-110) cc_final: 0.7940 (ptp-110) REVERT: G 38 CYS cc_start: 0.8424 (t) cc_final: 0.8037 (t) REVERT: G 44 TYR cc_start: 0.7785 (t80) cc_final: 0.7339 (t80) REVERT: G 50 ASP cc_start: 0.9077 (t0) cc_final: 0.8352 (t0) REVERT: G 58 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7170 (mtt180) REVERT: G 75 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8252 (ttm-80) REVERT: H 21 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8608 (p0) REVERT: H 126 GLU cc_start: 0.8634 (tt0) cc_final: 0.8252 (tt0) REVERT: I 72 ASP cc_start: 0.8413 (p0) cc_final: 0.8050 (p0) REVERT: K 24 ASP cc_start: 0.7864 (t0) cc_final: 0.7528 (t0) REVERT: K 82 ASP cc_start: 0.8488 (t0) cc_final: 0.8149 (t0) REVERT: M 70 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4496 (t80) REVERT: O 1104 HIS cc_start: 0.9062 (m-70) cc_final: 0.8861 (m-70) REVERT: O 1118 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (pp20) REVERT: O 1633 LYS cc_start: 0.9655 (mttt) cc_final: 0.9418 (ttmm) REVERT: O 1719 MET cc_start: 0.9430 (tpp) cc_final: 0.9229 (tpp) REVERT: O 1783 PHE cc_start: 0.9310 (t80) cc_final: 0.8705 (t80) REVERT: O 1830 HIS cc_start: 0.9319 (t-90) cc_final: 0.9032 (t70) REVERT: Z 82 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6617 (pt) REVERT: Z 99 LEU cc_start: 0.8834 (mt) cc_final: 0.8557 (pp) REVERT: Z 615 MET cc_start: -0.6259 (tpp) cc_final: -0.6679 (mtt) outliers start: 135 outliers final: 31 residues processed: 633 average time/residue: 0.8394 time to fit residues: 646.7390 Evaluate side-chains 485 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 443 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1070 GLN Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1118 GLU Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain Z residue 82 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 474 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 363 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 525 GLN A1270 ASN B 178 ASN B 278 GLN B 484 ASN B 648 HIS C 151 GLN C 203 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN K 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.131174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.078877 restraints weight = 93890.399| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.89 r_work: 0.2999 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 43947 Z= 0.143 Angle : 0.592 13.355 59712 Z= 0.303 Chirality : 0.043 0.197 6724 Planarity : 0.004 0.065 7379 Dihedral : 12.597 159.235 6767 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.88 % Allowed : 13.92 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 5091 helix: 2.08 (0.13), residues: 1776 sheet: 0.33 (0.17), residues: 907 loop : 0.16 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 434 TYR 0.023 0.001 TYR G 25 PHE 0.026 0.001 PHE B 963 TRP 0.028 0.001 TRP O1688 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (43916) covalent geometry : angle 0.58711 / 0.30 (59676) hydrogen bonds : bond 0.03630 / 2.46 ( 1800) hydrogen bonds : angle 4.47198 / 3.21 ( 4924) metal coordination : bond 0.00432 / 0.23 ( 31) metal coordination : angle 3.12923 / 1.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 472 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8946 (mm) cc_final: 0.8547 (tp) REVERT: A 181 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 311 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: A 497 THR cc_start: 0.9453 (m) cc_final: 0.9209 (p) REVERT: A 618 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: A 712 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8653 (pt0) REVERT: A 736 ASN cc_start: 0.9037 (t0) cc_final: 0.8747 (t160) REVERT: A 827 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 838 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7897 (tp-100) REVERT: A 1196 GLU cc_start: 0.8444 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 1281 ARG cc_start: 0.7863 (ptt90) cc_final: 0.7577 (ppt170) REVERT: A 1284 MET cc_start: 0.8374 (mtm) cc_final: 0.8146 (mtm) REVERT: A 1311 VAL cc_start: 0.8524 (t) cc_final: 0.8272 (t) REVERT: A 1411 GLU cc_start: 0.8910 (tp30) cc_final: 0.8597 (tp30) REVERT: B 401 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: B 789 MET cc_start: 0.9245 (mmm) cc_final: 0.8908 (mmt) REVERT: B 811 TYR cc_start: 0.8967 (m-80) cc_final: 0.8654 (m-80) REVERT: B 836 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 1152 MET cc_start: 0.8767 (mmm) cc_final: 0.8475 (mmm) REVERT: B 1168 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9062 (mp) REVERT: D 70 PHE cc_start: 0.8972 (m-80) cc_final: 0.8648 (m-10) REVERT: E 8 ASN cc_start: 0.8445 (m110) cc_final: 0.8029 (m110) REVERT: E 32 GLN cc_start: 0.8917 (tp40) cc_final: 0.8683 (tp40) REVERT: F 110 ASP cc_start: 0.8763 (p0) cc_final: 0.8463 (p0) REVERT: G 6 ASP cc_start: 0.7550 (p0) cc_final: 0.7339 (OUTLIER) REVERT: G 21 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.8087 (ptp90) REVERT: G 38 CYS cc_start: 0.8494 (t) cc_final: 0.8275 (t) REVERT: G 41 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7866 (mptt) REVERT: G 44 TYR cc_start: 0.7527 (t80) cc_final: 0.7312 (t80) REVERT: G 50 ASP cc_start: 0.9025 (t0) cc_final: 0.8662 (t0) REVERT: G 75 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8282 (ttm-80) REVERT: G 115 MET cc_start: 0.1035 (mmt) cc_final: 0.0687 (mmt) REVERT: G 163 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.7919 (mm) REVERT: H 21 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8604 (p0) REVERT: H 126 GLU cc_start: 0.8645 (tt0) cc_final: 0.8323 (tt0) REVERT: I 72 ASP cc_start: 0.8522 (p0) cc_final: 0.8204 (p0) REVERT: J 26 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8226 (OUTLIER) REVERT: J 55 ASP cc_start: 0.8705 (t0) cc_final: 0.8469 (t0) REVERT: K 24 ASP cc_start: 0.7916 (t0) cc_final: 0.7577 (t0) REVERT: K 82 ASP cc_start: 0.8642 (t0) cc_final: 0.8391 (t0) REVERT: M 70 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.4577 (t80) REVERT: O 1633 LYS cc_start: 0.9658 (mttt) cc_final: 0.9400 (ttmm) REVERT: O 1638 LEU cc_start: 0.9317 (pt) cc_final: 0.9017 (tm) REVERT: O 1719 MET cc_start: 0.9455 (tpp) cc_final: 0.9240 (tpp) REVERT: O 1759 MET cc_start: 0.8748 (ttp) cc_final: 0.8239 (pp-130) REVERT: O 1830 HIS cc_start: 0.9277 (t-90) cc_final: 0.8999 (t70) REVERT: Y 50 MET cc_start: 0.4589 (tmm) cc_final: 0.4251 (tmm) REVERT: Z 31 LEU cc_start: 0.7689 (mm) cc_final: 0.7205 (pp) REVERT: Z 99 LEU cc_start: 0.8875 (mt) cc_final: 0.8600 (pp) REVERT: Z 615 MET cc_start: -0.6180 (tpp) cc_final: -0.6604 (mtt) REVERT: Z 812 TYR cc_start: 0.8299 (m-80) cc_final: 0.5676 (m-80) outliers start: 131 outliers final: 45 residues processed: 551 average time/residue: 0.8033 time to fit residues: 541.2634 Evaluate side-chains 487 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 432 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 40 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 380 optimal weight: 0.5980 chunk 272 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 chunk 486 optimal weight: 50.0000 chunk 512 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN B 178 ASN B 648 HIS B 887 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 53 ASN G 71 ASN K 112 GLN O1689 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078501 restraints weight = 93792.667| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.93 r_work: 0.2989 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43947 Z= 0.136 Angle : 0.581 13.067 59712 Z= 0.295 Chirality : 0.043 0.365 6724 Planarity : 0.004 0.059 7379 Dihedral : 12.580 158.763 6765 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 14.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 5091 helix: 2.00 (0.13), residues: 1783 sheet: 0.22 (0.17), residues: 906 loop : 0.12 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 119 TYR 0.035 0.001 TYR G 25 PHE 0.023 0.001 PHE B 963 TRP 0.030 0.001 TRP O1688 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (43916) covalent geometry : angle 0.57689 / 0.29 (59676) hydrogen bonds : bond 0.03385 / 2.29 ( 1800) hydrogen bonds : angle 4.38873 / 3.15 ( 4924) metal coordination : bond 0.00374 / 0.21 ( 31) metal coordination : angle 2.80075 / 1.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 457 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8940 (mm) cc_final: 0.8545 (tp) REVERT: A 181 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 250 ILE cc_start: 0.8796 (pp) cc_final: 0.8462 (tt) REVERT: A 311 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: A 497 THR cc_start: 0.9440 (m) cc_final: 0.9178 (p) REVERT: A 618 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: A 712 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8571 (pt0) REVERT: A 818 MET cc_start: 0.9274 (mtp) cc_final: 0.8937 (mtm) REVERT: A 827 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 838 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7965 (tp40) REVERT: A 1196 GLU cc_start: 0.8465 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 1209 MET cc_start: 0.9335 (mmm) cc_final: 0.9085 (tpp) REVERT: A 1281 ARG cc_start: 0.7851 (ptt90) cc_final: 0.7562 (ppt170) REVERT: A 1311 VAL cc_start: 0.8626 (t) cc_final: 0.8394 (t) REVERT: A 1411 GLU cc_start: 0.8929 (tp30) cc_final: 0.8606 (tp30) REVERT: B 401 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: B 789 MET cc_start: 0.9244 (mmm) cc_final: 0.8947 (mmt) REVERT: B 811 TYR cc_start: 0.8956 (m-80) cc_final: 0.8685 (m-80) REVERT: B 836 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 1152 MET cc_start: 0.8980 (mmm) cc_final: 0.8688 (mmm) REVERT: B 1168 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9079 (mp) REVERT: D 70 PHE cc_start: 0.9012 (m-80) cc_final: 0.8752 (m-10) REVERT: E 5 ASN cc_start: 0.9360 (t0) cc_final: 0.9021 (t0) REVERT: E 7 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8517 (ppp80) REVERT: E 8 ASN cc_start: 0.8745 (m110) cc_final: 0.8216 (m110) REVERT: E 32 GLN cc_start: 0.8977 (tp40) cc_final: 0.8721 (tp40) REVERT: F 110 ASP cc_start: 0.8757 (p0) cc_final: 0.8442 (p0) REVERT: G 6 ASP cc_start: 0.7591 (p0) cc_final: 0.7176 (OUTLIER) REVERT: G 21 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.8193 (ptp-110) REVERT: G 53 ASN cc_start: 0.8716 (m-40) cc_final: 0.8276 (t0) REVERT: G 58 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7465 (mtt180) REVERT: G 75 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8027 (mmt90) REVERT: H 8 ASP cc_start: 0.7952 (t70) cc_final: 0.7584 (t0) REVERT: H 21 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (p0) REVERT: H 126 GLU cc_start: 0.8682 (tt0) cc_final: 0.8364 (tt0) REVERT: I 36 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: I 72 ASP cc_start: 0.8568 (p0) cc_final: 0.8231 (p0) REVERT: J 26 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: J 49 MET cc_start: 0.9214 (tpp) cc_final: 0.8839 (mmm) REVERT: K 22 ASP cc_start: 0.8480 (p0) cc_final: 0.8023 (p0) REVERT: K 24 ASP cc_start: 0.7952 (t0) cc_final: 0.7589 (t0) REVERT: K 82 ASP cc_start: 0.8701 (t0) cc_final: 0.8493 (t0) REVERT: M 65 GLN cc_start: 0.6977 (mp10) cc_final: 0.6621 (mm-40) REVERT: M 70 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.4604 (t80) REVERT: O 1104 HIS cc_start: 0.9029 (m-70) cc_final: 0.8787 (m-70) REVERT: O 1118 GLU cc_start: 0.8537 (pp20) cc_final: 0.8291 (pp20) REVERT: O 1633 LYS cc_start: 0.9656 (mttt) cc_final: 0.9396 (ttmm) REVERT: O 1719 MET cc_start: 0.9487 (tpp) cc_final: 0.9269 (tpp) REVERT: O 1756 MET cc_start: 0.8214 (mpp) cc_final: 0.7527 (mpt) REVERT: O 1759 MET cc_start: 0.8625 (ttp) cc_final: 0.8272 (pp-130) REVERT: O 1830 HIS cc_start: 0.9252 (t-90) cc_final: 0.8961 (t70) REVERT: Y 50 MET cc_start: 0.4147 (tmm) cc_final: 0.2256 (tmm) REVERT: Y 71 MET cc_start: 0.6841 (ppp) cc_final: 0.5961 (tpp) REVERT: Z 99 LEU cc_start: 0.8844 (mt) cc_final: 0.8587 (pp) REVERT: Z 615 MET cc_start: -0.6318 (tpp) cc_final: -0.6699 (mtt) outliers start: 117 outliers final: 52 residues processed: 533 average time/residue: 0.8000 time to fit residues: 523.1678 Evaluate side-chains 484 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 420 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 171 optimal weight: 0.6980 chunk 416 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 417 optimal weight: 0.0050 chunk 372 optimal weight: 4.9990 chunk 426 optimal weight: 20.0000 chunk 446 optimal weight: 30.0000 chunk 323 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 525 GLN A1270 ASN B 103 ASN B 178 ASN B 587 HIS B 648 HIS ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B1025 HIS B1117 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 104 ASN G 10 ASN H 52 GLN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN Z 646 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073976 restraints weight = 93068.145| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.82 r_work: 0.2877 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 43947 Z= 0.235 Angle : 0.635 13.288 59712 Z= 0.326 Chirality : 0.045 0.217 6724 Planarity : 0.005 0.084 7379 Dihedral : 12.730 158.755 6765 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.95 % Allowed : 15.02 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 5091 helix: 1.81 (0.12), residues: 1784 sheet: 0.05 (0.16), residues: 938 loop : 0.11 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 68 TYR 0.042 0.002 TYR G 25 PHE 0.026 0.002 PHE A 219 TRP 0.038 0.002 TRP O1688 HIS 0.017 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (43916) covalent geometry : angle 0.62728 / 0.33 (59676) hydrogen bonds : bond 0.03856 / 2.60 ( 1800) hydrogen bonds : angle 4.47089 / 3.22 ( 4924) metal coordination : bond 0.00821 / 0.47 ( 31) metal coordination : angle 4.15405 / 2.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 435 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.9071 (mm) cc_final: 0.8679 (tp) REVERT: A 311 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 618 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: A 712 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8573 (pt0) REVERT: A 827 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 838 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8112 (tp40) REVERT: A 1196 GLU cc_start: 0.8435 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 1199 ARG cc_start: 0.9059 (ttm110) cc_final: 0.8619 (mtt90) REVERT: A 1281 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7593 (ppt170) REVERT: A 1411 GLU cc_start: 0.9053 (tp30) cc_final: 0.8631 (tp30) REVERT: B 401 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: B 727 LYS cc_start: 0.9053 (mppt) cc_final: 0.8829 (mppt) REVERT: B 789 MET cc_start: 0.9307 (mmm) cc_final: 0.9099 (mmm) REVERT: B 1152 MET cc_start: 0.9047 (mmm) cc_final: 0.8804 (mmm) REVERT: B 1168 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9106 (mp) REVERT: D 39 ASN cc_start: 0.8656 (t0) cc_final: 0.8455 (t0) REVERT: D 70 PHE cc_start: 0.9034 (m-80) cc_final: 0.8827 (m-80) REVERT: E 5 ASN cc_start: 0.9379 (t0) cc_final: 0.9132 (t0) REVERT: E 8 ASN cc_start: 0.8741 (m110) cc_final: 0.8227 (m110) REVERT: E 32 GLN cc_start: 0.8993 (tp40) cc_final: 0.8723 (tp40) REVERT: E 50 MET cc_start: 0.7816 (pp-130) cc_final: 0.6937 (pp-130) REVERT: E 91 LYS cc_start: 0.9240 (mmpt) cc_final: 0.9018 (tppt) REVERT: E 203 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: F 77 ASP cc_start: 0.8533 (t0) cc_final: 0.8263 (p0) REVERT: F 78 GLN cc_start: 0.9349 (pt0) cc_final: 0.8863 (pm20) REVERT: F 110 ASP cc_start: 0.8889 (p0) cc_final: 0.8511 (p0) REVERT: G 21 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8149 (ptp90) REVERT: G 25 TYR cc_start: 0.8600 (m-80) cc_final: 0.8342 (m-80) REVERT: G 53 ASN cc_start: 0.8867 (m-40) cc_final: 0.8463 (t0) REVERT: H 8 ASP cc_start: 0.7966 (t70) cc_final: 0.7671 (t0) REVERT: H 21 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8670 (p0) REVERT: H 126 GLU cc_start: 0.8654 (tt0) cc_final: 0.8335 (tt0) REVERT: I 36 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: I 72 ASP cc_start: 0.8735 (p0) cc_final: 0.8434 (p0) REVERT: J 26 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: K 24 ASP cc_start: 0.8047 (t0) cc_final: 0.7728 (t0) REVERT: K 82 ASP cc_start: 0.8784 (t0) cc_final: 0.8579 (t0) REVERT: L 41 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8323 (p) REVERT: M 70 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.4833 (t80) REVERT: O 1104 HIS cc_start: 0.9076 (m-70) cc_final: 0.8820 (m-70) REVERT: O 1118 GLU cc_start: 0.8641 (pp20) cc_final: 0.8440 (pp20) REVERT: O 1175 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8317 (ptp90) REVERT: O 1633 LYS cc_start: 0.9689 (mttt) cc_final: 0.9430 (ttmm) REVERT: O 1719 MET cc_start: 0.9510 (tpp) cc_final: 0.9280 (tpp) REVERT: O 1756 MET cc_start: 0.8426 (mpp) cc_final: 0.7680 (mpt) REVERT: O 1759 MET cc_start: 0.8652 (ttp) cc_final: 0.8322 (pp-130) REVERT: O 1830 HIS cc_start: 0.9235 (t-90) cc_final: 0.8942 (t70) REVERT: Y 50 MET cc_start: 0.4580 (tmm) cc_final: 0.3024 (tmm) REVERT: Y 71 MET cc_start: 0.6996 (ppp) cc_final: 0.6138 (tpp) REVERT: Z 99 LEU cc_start: 0.8967 (mt) cc_final: 0.8705 (pp) REVERT: Z 615 MET cc_start: -0.6256 (tpp) cc_final: -0.6638 (mtt) outliers start: 134 outliers final: 58 residues processed: 524 average time/residue: 0.7882 time to fit residues: 507.4205 Evaluate side-chains 477 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 407 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1105 MET Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 377 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 503 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 439 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS A1270 ASN B 648 HIS ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074115 restraints weight = 93010.144| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.81 r_work: 0.2881 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43947 Z= 0.188 Angle : 0.615 12.729 59712 Z= 0.310 Chirality : 0.044 0.198 6724 Planarity : 0.004 0.058 7379 Dihedral : 12.756 158.416 6765 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.84 % Allowed : 16.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 5091 helix: 1.79 (0.13), residues: 1784 sheet: 0.00 (0.17), residues: 927 loop : 0.09 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 52 TYR 0.030 0.001 TYR G 25 PHE 0.022 0.001 PHE A 219 TRP 0.040 0.001 TRP O1688 HIS 0.010 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (43916) covalent geometry : angle 0.60721 / 0.31 (59676) hydrogen bonds : bond 0.03547 / 2.40 ( 1800) hydrogen bonds : angle 4.40495 / 3.17 ( 4924) metal coordination : bond 0.00633 / 0.37 ( 31) metal coordination : angle 3.92065 / 2.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 423 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8508 (mp0) REVERT: A 311 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: A 450 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8927 (mp) REVERT: A 618 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: A 712 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8714 (mt-10) REVERT: A 827 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 838 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8081 (tp40) REVERT: A 1196 GLU cc_start: 0.8479 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 1199 ARG cc_start: 0.9052 (ttm110) cc_final: 0.8708 (mtt90) REVERT: A 1236 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7548 (pp) REVERT: A 1281 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7470 (ppt170) REVERT: A 1411 GLU cc_start: 0.9063 (tp30) cc_final: 0.8631 (tp30) REVERT: B 178 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8605 (t0) REVERT: B 401 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: B 662 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8101 (mpp) REVERT: B 727 LYS cc_start: 0.9055 (mppt) cc_final: 0.8827 (mppt) REVERT: B 789 MET cc_start: 0.9296 (mmm) cc_final: 0.8963 (mmt) REVERT: B 883 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7491 (mm) REVERT: B 997 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: B 1152 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8839 (mmm) REVERT: D 39 ASN cc_start: 0.8743 (t0) cc_final: 0.8508 (t0) REVERT: D 66 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8409 (mtt-85) REVERT: D 70 PHE cc_start: 0.9048 (m-80) cc_final: 0.8820 (m-80) REVERT: E 8 ASN cc_start: 0.8775 (m110) cc_final: 0.8260 (m-40) REVERT: E 32 GLN cc_start: 0.8988 (tp40) cc_final: 0.8764 (tp40) REVERT: E 50 MET cc_start: 0.8140 (pp-130) cc_final: 0.7919 (pp-130) REVERT: F 77 ASP cc_start: 0.8572 (t0) cc_final: 0.8257 (p0) REVERT: F 78 GLN cc_start: 0.9325 (pt0) cc_final: 0.8851 (pm20) REVERT: F 110 ASP cc_start: 0.8886 (p0) cc_final: 0.8516 (p0) REVERT: G 21 ARG cc_start: 0.8477 (ptp-110) cc_final: 0.8127 (ptp90) REVERT: G 25 TYR cc_start: 0.8681 (m-80) cc_final: 0.8397 (m-80) REVERT: G 53 ASN cc_start: 0.8869 (m-40) cc_final: 0.8493 (t0) REVERT: H 8 ASP cc_start: 0.8029 (t70) cc_final: 0.7700 (t0) REVERT: H 126 GLU cc_start: 0.8661 (tt0) cc_final: 0.8323 (tt0) REVERT: I 36 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: I 72 ASP cc_start: 0.8741 (p0) cc_final: 0.8518 (p0) REVERT: J 26 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: K 24 ASP cc_start: 0.8050 (t0) cc_final: 0.7601 (t0) REVERT: L 41 SER cc_start: 0.8733 (m) cc_final: 0.8378 (p) REVERT: L 47 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8365 (ptm160) REVERT: M 70 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.4809 (t80) REVERT: O 1104 HIS cc_start: 0.9100 (m-70) cc_final: 0.8843 (m-70) REVERT: O 1118 GLU cc_start: 0.8681 (pp20) cc_final: 0.8413 (pp20) REVERT: O 1175 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8389 (ptp90) REVERT: O 1633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9428 (ttmm) REVERT: O 1719 MET cc_start: 0.9523 (tpp) cc_final: 0.9287 (tpp) REVERT: O 1756 MET cc_start: 0.8438 (mpp) cc_final: 0.7662 (mpt) REVERT: O 1759 MET cc_start: 0.8654 (ttp) cc_final: 0.8335 (pp-130) REVERT: O 1830 HIS cc_start: 0.9212 (t-90) cc_final: 0.8929 (t70) REVERT: Y 50 MET cc_start: 0.4895 (tmm) cc_final: 0.3357 (tmm) REVERT: Y 71 MET cc_start: 0.6938 (ppp) cc_final: 0.6129 (tpp) REVERT: Z 99 LEU cc_start: 0.8944 (mt) cc_final: 0.8648 (pp) REVERT: Z 615 MET cc_start: -0.6288 (tpp) cc_final: -0.6625 (mtt) REVERT: Z 812 TYR cc_start: 0.8635 (m-80) cc_final: 0.7789 (m-80) outliers start: 129 outliers final: 51 residues processed: 507 average time/residue: 0.8284 time to fit residues: 513.4121 Evaluate side-chains 471 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain Z residue 746 VAL Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 158 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 428 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 423 optimal weight: 9.9990 chunk 507 optimal weight: 50.0000 chunk 419 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 654 ASN A 700 ASN A1011 GLN A1270 ASN B 103 ASN B 115 GLN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN G 10 ASN H 83 GLN J 53 HIS K 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069286 restraints weight = 92559.119| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.78 r_work: 0.2767 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 43947 Z= 0.377 Angle : 0.757 18.035 59712 Z= 0.382 Chirality : 0.048 0.255 6724 Planarity : 0.005 0.076 7379 Dihedral : 12.985 160.389 6765 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.30 % Allowed : 15.83 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 5091 helix: 1.46 (0.12), residues: 1782 sheet: -0.18 (0.17), residues: 890 loop : -0.05 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 52 TYR 0.027 0.002 TYR G 25 PHE 0.034 0.002 PHE A 219 TRP 0.047 0.002 TRP O1688 HIS 0.024 0.002 HIS B 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.38 (43916) covalent geometry : angle 0.74268 / 0.38 (59676) hydrogen bonds : bond 0.04521 / 3.05 ( 1800) hydrogen bonds : angle 4.69562 / 3.39 ( 4924) metal coordination : bond 0.01438 / 0.87 ( 31) metal coordination : angle 5.99571 / 3.35 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 430 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 HIS cc_start: 0.9334 (t70) cc_final: 0.8865 (t-90) REVERT: A 311 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: A 433 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8760 (mp0) REVERT: A 450 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9012 (mp) REVERT: A 618 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: A 712 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8770 (mt-10) REVERT: A 1196 GLU cc_start: 0.8457 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 1281 ARG cc_start: 0.7847 (ptt90) cc_final: 0.7575 (ppt170) REVERT: A 1411 GLU cc_start: 0.9107 (tp30) cc_final: 0.8526 (tp30) REVERT: B 178 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 312 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 354 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8614 (p0) REVERT: B 598 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8715 (tm-30) REVERT: B 710 LEU cc_start: 0.8024 (mm) cc_final: 0.7738 (mp) REVERT: B 727 LYS cc_start: 0.9084 (mppt) cc_final: 0.8851 (mppt) REVERT: B 778 MET cc_start: 0.9133 (ptp) cc_final: 0.8811 (ptp) REVERT: B 883 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 1152 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8889 (mmm) REVERT: D 39 ASN cc_start: 0.8713 (t0) cc_final: 0.8486 (t0) REVERT: D 66 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.8375 (mtt-85) REVERT: D 70 PHE cc_start: 0.9072 (m-80) cc_final: 0.8815 (m-80) REVERT: E 8 ASN cc_start: 0.8807 (m-40) cc_final: 0.8161 (m110) REVERT: E 25 ASP cc_start: 0.8579 (m-30) cc_final: 0.8272 (m-30) REVERT: E 32 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8735 (tp40) REVERT: E 91 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9037 (tppt) REVERT: F 77 ASP cc_start: 0.8680 (t0) cc_final: 0.8452 (t0) REVERT: F 78 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9061 (pm20) REVERT: F 110 ASP cc_start: 0.8949 (p0) cc_final: 0.8340 (p0) REVERT: G 21 ARG cc_start: 0.8548 (ptp-110) cc_final: 0.8207 (ptp90) REVERT: G 25 TYR cc_start: 0.8882 (m-80) cc_final: 0.8631 (m-80) REVERT: G 53 ASN cc_start: 0.9016 (m-40) cc_final: 0.8583 (t0) REVERT: H 126 GLU cc_start: 0.8736 (tt0) cc_final: 0.8449 (tt0) REVERT: I 36 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: I 47 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8239 (mm-30) REVERT: I 72 ASP cc_start: 0.8810 (p0) cc_final: 0.8383 (p0) REVERT: J 26 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: K 24 ASP cc_start: 0.8058 (t0) cc_final: 0.7599 (t0) REVERT: K 112 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (pp30) REVERT: L 41 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8008 (p) REVERT: M 70 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.4526 (t80) REVERT: O 1104 HIS cc_start: 0.9124 (m-70) cc_final: 0.8879 (m-70) REVERT: O 1118 GLU cc_start: 0.8810 (pp20) cc_final: 0.8508 (pp20) REVERT: O 1175 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8322 (ptp90) REVERT: O 1633 LYS cc_start: 0.9719 (mttt) cc_final: 0.9472 (ttmm) REVERT: O 1719 MET cc_start: 0.9566 (tpp) cc_final: 0.9339 (tpp) REVERT: O 1830 HIS cc_start: 0.9222 (t-90) cc_final: 0.8940 (t70) REVERT: Y 50 MET cc_start: 0.5090 (tmm) cc_final: 0.3502 (tmm) REVERT: Y 71 MET cc_start: 0.7099 (ppp) cc_final: 0.6276 (tpp) REVERT: Z 99 LEU cc_start: 0.9027 (mt) cc_final: 0.8741 (pp) REVERT: Z 615 MET cc_start: -0.6244 (tpp) cc_final: -0.6535 (ttm) outliers start: 150 outliers final: 64 residues processed: 529 average time/residue: 0.8064 time to fit residues: 522.5983 Evaluate side-chains 480 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 401 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1105 MET Chi-restraints excluded: chain O residue 1106 ARG Chi-restraints excluded: chain O residue 1407 LEU Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain O residue 1577 LEU Chi-restraints excluded: chain O residue 1688 TRP Chi-restraints excluded: chain Z residue 746 VAL Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 471 optimal weight: 7.9990 chunk 456 optimal weight: 30.0000 chunk 199 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 450 optimal weight: 7.9990 chunk 383 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 103 ASN B 648 HIS C 231 ASN E 5 ASN K 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.125971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071878 restraints weight = 92256.896| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.83 r_work: 0.2829 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43947 Z= 0.171 Angle : 0.662 14.839 59712 Z= 0.330 Chirality : 0.044 0.215 6724 Planarity : 0.004 0.060 7379 Dihedral : 12.939 159.829 6765 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.31 % Allowed : 17.42 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 5091 helix: 1.59 (0.12), residues: 1783 sheet: -0.19 (0.17), residues: 902 loop : -0.07 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 241 TYR 0.030 0.001 TYR E 112 PHE 0.022 0.001 PHE A 219 TRP 0.046 0.001 TRP O1688 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (43916) covalent geometry : angle 0.65210 / 0.33 (59676) hydrogen bonds : bond 0.03679 / 2.48 ( 1800) hydrogen bonds : angle 4.49500 / 3.24 ( 4924) metal coordination : bond 0.00703 / 0.41 ( 31) metal coordination : angle 4.77058 / 2.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 423 time to evaluate : 1.699 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 181 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 281 HIS cc_start: 0.9338 (t70) cc_final: 0.8867 (t-90) REVERT: A 311 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 450 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9009 (mp) REVERT: A 712 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 827 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 1196 GLU cc_start: 0.8457 (tt0) cc_final: 0.7817 (tm-30) REVERT: A 1281 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7483 (ppt170) REVERT: A 1411 GLU cc_start: 0.9073 (tp30) cc_final: 0.8612 (tp30) REVERT: B 178 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8590 (t0) REVERT: B 312 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 471 LYS cc_start: 0.8628 (mppt) cc_final: 0.7992 (mtmm) REVERT: B 563 MET cc_start: 0.8893 (tmt) cc_final: 0.8437 (tmt) REVERT: B 727 LYS cc_start: 0.9040 (mppt) cc_final: 0.8801 (mptt) REVERT: B 883 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 885 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.5900 (mpt) REVERT: B 1152 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8751 (mmm) REVERT: D 39 ASN cc_start: 0.8752 (t0) cc_final: 0.8499 (t0) REVERT: D 66 ARG cc_start: 0.8902 (mtt-85) cc_final: 0.8600 (mpt-90) REVERT: D 70 PHE cc_start: 0.9086 (m-80) cc_final: 0.8826 (m-80) REVERT: E 8 ASN cc_start: 0.8887 (m-40) cc_final: 0.8253 (m110) REVERT: E 25 ASP cc_start: 0.8499 (m-30) cc_final: 0.8170 (m-30) REVERT: E 32 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8760 (tp40) REVERT: E 116 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8094 (tp) REVERT: E 172 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8224 (mm-30) REVERT: F 78 GLN cc_start: 0.9338 (pt0) cc_final: 0.9018 (pm20) REVERT: F 110 ASP cc_start: 0.8781 (p0) cc_final: 0.8355 (p0) REVERT: F 112 GLU cc_start: 0.8061 (mp0) cc_final: 0.7740 (mp0) REVERT: G 21 ARG cc_start: 0.8531 (ptp-110) cc_final: 0.8188 (ptp90) REVERT: G 25 TYR cc_start: 0.8872 (m-80) cc_final: 0.8625 (m-80) REVERT: G 53 ASN cc_start: 0.9016 (m-40) cc_final: 0.8604 (t0) REVERT: H 8 ASP cc_start: 0.8054 (t0) cc_final: 0.7680 (t0) REVERT: H 126 GLU cc_start: 0.8717 (tt0) cc_final: 0.8414 (tt0) REVERT: I 37 GLU cc_start: 0.8600 (pm20) cc_final: 0.8384 (pp20) REVERT: I 47 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7987 (mm-30) REVERT: I 72 ASP cc_start: 0.8843 (p0) cc_final: 0.8459 (p0) REVERT: J 26 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: K 24 ASP cc_start: 0.8068 (t0) cc_final: 0.7638 (t0) REVERT: L 41 SER cc_start: 0.8636 (m) cc_final: 0.8263 (p) REVERT: L 47 ARG cc_start: 0.8693 (ptp-110) cc_final: 0.8341 (ptm160) REVERT: M 70 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.4528 (t80) REVERT: O 1104 HIS cc_start: 0.9111 (m-70) cc_final: 0.8861 (m-70) REVERT: O 1118 GLU cc_start: 0.8743 (pp20) cc_final: 0.8410 (pp20) REVERT: O 1175 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8342 (ptp90) REVERT: O 1633 LYS cc_start: 0.9705 (mttt) cc_final: 0.9478 (ttmm) REVERT: O 1719 MET cc_start: 0.9566 (tpp) cc_final: 0.9330 (tpp) REVERT: O 1756 MET cc_start: 0.8338 (mpp) cc_final: 0.7572 (mpt) REVERT: O 1759 MET cc_start: 0.8622 (ttp) cc_final: 0.8340 (pp-130) REVERT: O 1830 HIS cc_start: 0.9198 (t-90) cc_final: 0.8929 (t70) REVERT: Y 50 MET cc_start: 0.5337 (tmm) cc_final: 0.3751 (tmm) REVERT: Y 71 MET cc_start: 0.7068 (ppp) cc_final: 0.6321 (tpp) REVERT: Z 99 LEU cc_start: 0.9000 (mt) cc_final: 0.8718 (pp) REVERT: Z 615 MET cc_start: -0.6171 (tpp) cc_final: -0.6453 (ttm) outliers start: 105 outliers final: 57 residues processed: 487 average time/residue: 0.7851 time to fit residues: 466.2865 Evaluate side-chains 464 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 396 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1162 LEU Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain O residue 1613 MET Chi-restraints excluded: chain Z residue 606 MET Chi-restraints excluded: chain Z residue 746 VAL Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 69 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 494 optimal weight: 8.9990 chunk 444 optimal weight: 30.0000 chunk 93 optimal weight: 0.5980 chunk 307 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 380 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 648 HIS E 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.126180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072401 restraints weight = 92064.501| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.79 r_work: 0.2841 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 43947 Z= 0.167 Angle : 0.656 13.581 59712 Z= 0.327 Chirality : 0.044 0.205 6724 Planarity : 0.004 0.065 7379 Dihedral : 12.889 159.651 6765 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 17.73 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5091 helix: 1.67 (0.13), residues: 1770 sheet: -0.11 (0.17), residues: 892 loop : -0.09 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 75 TYR 0.060 0.001 TYR O1304 PHE 0.032 0.001 PHE D 151 TRP 0.060 0.001 TRP O1688 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (43916) covalent geometry : angle 0.64850 / 0.33 (59676) hydrogen bonds : bond 0.03556 / 2.39 ( 1800) hydrogen bonds : angle 4.45393 / 3.21 ( 4924) metal coordination : bond 0.00651 / 0.39 ( 31) metal coordination : angle 4.07304 / 2.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 415 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9069 (tpp) cc_final: 0.8789 (tpp) REVERT: A 181 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 281 HIS cc_start: 0.9334 (t70) cc_final: 0.8881 (t-90) REVERT: A 311 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: A 712 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8927 (mt-10) REVERT: A 827 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 1196 GLU cc_start: 0.8632 (tt0) cc_final: 0.7995 (tm-30) REVERT: A 1281 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7763 (ppt170) REVERT: A 1411 GLU cc_start: 0.9248 (tp30) cc_final: 0.8801 (tp30) REVERT: B 178 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8523 (t0) REVERT: B 259 TYR cc_start: 0.8975 (m-80) cc_final: 0.8484 (m-80) REVERT: B 312 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8337 (mm-30) REVERT: B 471 LYS cc_start: 0.8688 (mppt) cc_final: 0.8279 (mttt) REVERT: B 563 MET cc_start: 0.8916 (tmt) cc_final: 0.8434 (tmt) REVERT: B 727 LYS cc_start: 0.9011 (mppt) cc_final: 0.8756 (mptt) REVERT: B 883 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 885 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.5911 (mpt) REVERT: B 1152 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8734 (mmm) REVERT: D 39 ASN cc_start: 0.8731 (t0) cc_final: 0.8495 (t0) REVERT: D 66 ARG cc_start: 0.8901 (mtt-85) cc_final: 0.8437 (mtt-85) REVERT: D 70 PHE cc_start: 0.9058 (m-80) cc_final: 0.8803 (m-80) REVERT: D 140 ASP cc_start: 0.8510 (t0) cc_final: 0.8228 (t0) REVERT: E 8 ASN cc_start: 0.8972 (m-40) cc_final: 0.8328 (m110) REVERT: E 25 ASP cc_start: 0.8706 (m-30) cc_final: 0.8408 (m-30) REVERT: E 32 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8775 (tp40) REVERT: E 116 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8006 (tp) REVERT: E 172 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8444 (mm-30) REVERT: F 110 ASP cc_start: 0.8914 (p0) cc_final: 0.8449 (p0) REVERT: F 112 GLU cc_start: 0.8285 (mp0) cc_final: 0.8015 (mp0) REVERT: F 119 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8918 (mmm160) REVERT: G 21 ARG cc_start: 0.8674 (ptp-110) cc_final: 0.8321 (ptp90) REVERT: G 25 TYR cc_start: 0.8992 (m-80) cc_final: 0.8770 (m-80) REVERT: G 50 ASP cc_start: 0.8926 (t0) cc_final: 0.8502 (t0) REVERT: G 53 ASN cc_start: 0.9052 (m-40) cc_final: 0.8592 (t0) REVERT: H 126 GLU cc_start: 0.8969 (tt0) cc_final: 0.8682 (tt0) REVERT: I 36 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: I 47 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7998 (mm-30) REVERT: I 72 ASP cc_start: 0.8960 (p0) cc_final: 0.8562 (p0) REVERT: J 26 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: K 24 ASP cc_start: 0.8211 (t0) cc_final: 0.7736 (t0) REVERT: L 41 SER cc_start: 0.8385 (m) cc_final: 0.7936 (p) REVERT: L 47 ARG cc_start: 0.8762 (ptp-110) cc_final: 0.8446 (ptm160) REVERT: M 70 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.4842 (t80) REVERT: O 1104 HIS cc_start: 0.9123 (m-70) cc_final: 0.8851 (m-70) REVERT: O 1118 GLU cc_start: 0.8951 (pp20) cc_final: 0.8640 (pp20) REVERT: O 1175 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8428 (ptp90) REVERT: O 1304 TYR cc_start: 0.8477 (m-80) cc_final: 0.7948 (m-80) REVERT: O 1633 LYS cc_start: 0.9697 (mttt) cc_final: 0.9204 (mtmm) REVERT: O 1719 MET cc_start: 0.9569 (tpp) cc_final: 0.9332 (tpp) REVERT: O 1756 MET cc_start: 0.8375 (mpp) cc_final: 0.7956 (mpt) REVERT: O 1830 HIS cc_start: 0.9203 (t-90) cc_final: 0.8926 (t70) REVERT: Y 50 MET cc_start: 0.5385 (tmm) cc_final: 0.3854 (tmm) REVERT: Y 71 MET cc_start: 0.7127 (ppp) cc_final: 0.6379 (tpp) REVERT: Z 99 LEU cc_start: 0.8978 (mt) cc_final: 0.8714 (pp) REVERT: Z 615 MET cc_start: -0.6149 (tpp) cc_final: -0.6430 (ttm) REVERT: Z 812 TYR cc_start: 0.8743 (m-80) cc_final: 0.7897 (m-80) outliers start: 89 outliers final: 52 residues processed: 474 average time/residue: 0.8154 time to fit residues: 473.3426 Evaluate side-chains 461 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 398 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1106 ARG Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain O residue 1613 MET Chi-restraints excluded: chain O residue 1657 MET Chi-restraints excluded: chain Z residue 746 VAL Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 352 optimal weight: 9.9990 chunk 474 optimal weight: 30.0000 chunk 255 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 367 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 273 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS E 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072984 restraints weight = 92453.457| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.90 r_work: 0.2813 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 43947 Z= 0.197 Angle : 0.674 13.728 59712 Z= 0.337 Chirality : 0.045 0.252 6724 Planarity : 0.004 0.069 7379 Dihedral : 12.887 159.778 6765 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.69 % Allowed : 18.21 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 5091 helix: 1.60 (0.13), residues: 1789 sheet: -0.12 (0.17), residues: 892 loop : -0.09 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 320 TYR 0.046 0.001 TYR O1304 PHE 0.024 0.001 PHE A 219 TRP 0.060 0.002 TRP O1688 HIS 0.015 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (43916) covalent geometry : angle 0.66664 / 0.34 (59676) hydrogen bonds : bond 0.03611 / 2.43 ( 1800) hydrogen bonds : angle 4.46418 / 3.21 ( 4924) metal coordination : bond 0.00696 / 0.42 ( 31) metal coordination : angle 4.03077 / 2.20 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10182 Ramachandran restraints generated. 5091 Oldfield, 0 Emsley, 5091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 409 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8936 (pp) REVERT: A 281 HIS cc_start: 0.9292 (t70) cc_final: 0.8847 (t-90) REVERT: A 311 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: A 712 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8699 (mp0) REVERT: A 827 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 1196 GLU cc_start: 0.8479 (tt0) cc_final: 0.7744 (tm-30) REVERT: A 1281 ARG cc_start: 0.7787 (ptt90) cc_final: 0.7478 (ppt170) REVERT: A 1411 GLU cc_start: 0.9088 (tp30) cc_final: 0.8627 (tp30) REVERT: B 178 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8607 (t0) REVERT: B 259 TYR cc_start: 0.8921 (m-80) cc_final: 0.8428 (m-80) REVERT: B 471 LYS cc_start: 0.8571 (mppt) cc_final: 0.8199 (mttt) REVERT: B 563 MET cc_start: 0.8849 (tmt) cc_final: 0.8387 (tmt) REVERT: B 883 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8065 (mm) REVERT: B 885 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.5967 (mpt) REVERT: B 1152 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: D 39 ASN cc_start: 0.8766 (t0) cc_final: 0.8518 (t0) REVERT: D 66 ARG cc_start: 0.8925 (mtt-85) cc_final: 0.8510 (mtt180) REVERT: D 70 PHE cc_start: 0.9058 (m-80) cc_final: 0.8828 (m-80) REVERT: E 8 ASN cc_start: 0.8906 (m-40) cc_final: 0.8253 (m110) REVERT: E 25 ASP cc_start: 0.8514 (m-30) cc_final: 0.8187 (m-30) REVERT: E 32 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8721 (tp40) REVERT: E 122 LYS cc_start: 0.9432 (mtmt) cc_final: 0.9209 (ptpp) REVERT: E 172 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8216 (mm-30) REVERT: F 110 ASP cc_start: 0.8779 (p0) cc_final: 0.8314 (p0) REVERT: F 112 GLU cc_start: 0.8195 (mp0) cc_final: 0.7950 (mp0) REVERT: G 21 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8254 (ptp90) REVERT: G 25 TYR cc_start: 0.8923 (m-80) cc_final: 0.8717 (m-80) REVERT: G 50 ASP cc_start: 0.8919 (t0) cc_final: 0.8460 (t0) REVERT: G 53 ASN cc_start: 0.9021 (m-40) cc_final: 0.8585 (t0) REVERT: H 8 ASP cc_start: 0.7956 (t70) cc_final: 0.7724 (t0) REVERT: H 126 GLU cc_start: 0.8745 (tt0) cc_final: 0.8455 (tt0) REVERT: I 47 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7927 (mm-30) REVERT: I 72 ASP cc_start: 0.8863 (p0) cc_final: 0.8451 (p0) REVERT: J 26 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: K 24 ASP cc_start: 0.8045 (t0) cc_final: 0.7687 (t0) REVERT: L 41 SER cc_start: 0.8425 (m) cc_final: 0.7999 (p) REVERT: L 42 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7831 (tpp80) REVERT: L 47 ARG cc_start: 0.8706 (ptp-110) cc_final: 0.8394 (ptm160) REVERT: M 70 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.4922 (t80) REVERT: O 1104 HIS cc_start: 0.9139 (m-70) cc_final: 0.8863 (m-70) REVERT: O 1118 GLU cc_start: 0.8779 (pp20) cc_final: 0.8439 (pp20) REVERT: O 1175 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8360 (ptp90) REVERT: O 1304 TYR cc_start: 0.8395 (m-80) cc_final: 0.7652 (m-80) REVERT: O 1633 LYS cc_start: 0.9697 (mttt) cc_final: 0.9214 (mtmm) REVERT: O 1719 MET cc_start: 0.9576 (tpp) cc_final: 0.9345 (tpp) REVERT: O 1756 MET cc_start: 0.8353 (mpp) cc_final: 0.7894 (mpt) REVERT: O 1830 HIS cc_start: 0.9191 (t-90) cc_final: 0.8931 (t70) REVERT: Y 50 MET cc_start: 0.5350 (tmm) cc_final: 0.3868 (tmm) REVERT: Y 71 MET cc_start: 0.7230 (ppp) cc_final: 0.6426 (tpp) REVERT: Z 99 LEU cc_start: 0.9011 (mt) cc_final: 0.8752 (pp) REVERT: Z 615 MET cc_start: -0.6111 (tpp) cc_final: -0.6415 (ttm) outliers start: 77 outliers final: 55 residues processed: 459 average time/residue: 0.7329 time to fit residues: 411.7615 Evaluate side-chains 461 residues out of total 4547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 397 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain O residue 1106 ARG Chi-restraints excluded: chain O residue 1409 CYS Chi-restraints excluded: chain O residue 1613 MET Chi-restraints excluded: chain O residue 1657 MET Chi-restraints excluded: chain Z residue 746 VAL Chi-restraints excluded: chain Z residue 825 ASP Chi-restraints excluded: chain Z residue 846 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 408 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 498 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS E 5 ASN O1154 GLN ** O1707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.126292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072744 restraints weight = 92597.961| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.84 r_work: 0.2853 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43947 Z= 0.153 Angle : 0.658 13.294 59712 Z= 0.328 Chirality : 0.044 0.198 6724 Planarity : 0.004 0.060 7379 Dihedral : 12.870 159.595 6765 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.63 % Allowed : 18.43 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 5091 helix: 1.65 (0.13), residues: 1777 sheet: -0.09 (0.17), residues: 887 loop : -0.11 (0.13), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 320 TYR 0.039 0.001 TYR O1304 PHE 0.031 0.001 PHE D 151 TRP 0.063 0.001 TRP O1688 HIS 0.013 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (43916) covalent geometry : angle 0.65237 / 0.33 (59676) hydrogen bonds : bond 0.03427 / 2.32 ( 1800) hydrogen bonds : angle 4.42569 / 3.18 ( 4924) metal coordination : bond 0.00501 / 0.29 ( 31) metal coordination : angle 3.64822 / 2.01 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20076.77 seconds wall clock time: 341 minutes 49.47 seconds (20509.47 seconds total)