Starting phenix.real_space_refine on Tue Aug 26 21:28:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfq_39226/08_2025/8yfq_39226.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 88 5.49 5 Mg 1 5.21 5 S 225 5.16 5 C 26388 2.51 5 N 7324 2.21 5 O 8133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42167 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 11027 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 3, 'PTRANS': 62, 'TRANS': 1332} Chain breaks: 5 Chain: "B" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9139 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 50, 'TRANS': 1095} Chain breaks: 6 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1302 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 2 Chain: "E" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1732 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 568 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} 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: "P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 471 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 17} Chain: "R" Number of atoms: 6135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6135 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 47, 'TRANS': 698} Chain breaks: 1 Chain: "S" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3093 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 16, 'TRANS': 360} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 85.501 115.488 83.146 1.00 89.46 S ATOM 549 SG CYS A 70 83.837 112.892 80.884 1.00 84.84 S ATOM 594 SG CYS A 77 85.421 111.785 84.164 1.00 69.24 S ATOM 829 SG CYS A 107 133.281 108.458 85.092 1.00107.10 S ATOM 851 SG CYS A 110 133.330 108.806 81.383 1.00110.06 S ATOM 1157 SG CYS A 148 136.149 106.826 83.174 1.00117.01 S ATOM 1210 SG CYS A 168 135.896 110.641 83.502 1.00120.09 S ATOM 19698 SG CYS B1163 96.894 106.077 71.753 1.00 61.59 S ATOM 19716 SG CYS B1166 98.305 106.548 74.550 1.00 63.99 S ATOM 19839 SG CYS B1182 96.266 109.580 73.531 1.00 78.39 S ATOM 19862 SG CYS B1185 99.889 108.603 71.961 1.00 80.26 S ATOM 20807 SG CYS C 85 29.706 85.509 110.932 1.00 71.19 S ATOM 20820 SG CYS C 87 30.960 89.027 111.340 1.00 97.25 S ATOM 20855 SG CYS C 91 28.329 87.756 113.698 1.00 70.74 S ATOM 20878 SG CYS C 94 31.807 86.373 114.029 1.00 58.59 S ATOM 28945 SG CYS I 75 121.231 55.762 160.664 1.00122.68 S ATOM 28967 SG CYS I 78 120.254 56.034 164.199 1.00123.12 S ATOM 29183 SG CYS I 103 118.441 58.213 161.603 1.00100.25 S ATOM 29205 SG CYS I 106 122.038 58.996 162.471 1.00106.71 S ATOM 28397 SG CYS I 7 150.404 89.024 147.990 1.00117.36 S ATOM 28420 SG CYS I 10 148.892 91.991 146.338 1.00119.73 S ATOM 28583 SG CYS I 29 150.307 89.300 144.067 1.00118.09 S ATOM 28608 SG CYS I 32 152.670 91.359 146.356 1.00119.28 S ATOM 29324 SG CYS J 7 53.469 70.310 131.926 1.00 15.68 S ATOM 29347 SG CYS J 10 50.663 67.986 130.946 1.00 17.53 S ATOM 29623 SG CYS J 44 53.960 66.575 132.344 1.00 20.12 S ATOM 29629 SG CYS J 45 51.477 68.340 134.593 1.00 18.63 S ATOM 30791 SG CYS L 33 59.728 113.585 137.706 1.00 73.64 S ATOM 30806 SG CYS L 36 57.220 114.465 140.404 1.00 82.60 S ATOM 30916 SG CYS L 50 58.128 117.036 137.765 1.00 87.41 S ATOM 30940 SG CYS L 53 60.696 116.144 140.338 1.00 90.76 S Time building chain proxies: 7.84, per 1000 atoms: 0.19 Number of scatterers: 42167 At special positions: 0 Unit cell: (175.13, 185.92, 184.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 225 16.00 P 88 15.00 Mg 1 11.99 O 8133 8.00 N 7324 7.00 C 26388 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 45 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9476 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 56 sheets defined 40.0% alpha, 17.7% beta 36 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.522A pdb=" N LYS A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.578A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 261 through 282 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.667A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.915A pdb=" N ASP A 424 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 425' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.770A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 846 removed outlier: 3.917A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 5.171A pdb=" N LEU A1019 " --> pdb=" O ASN A1015 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1081 Proline residue: A1077 - end of helix removed outlier: 3.939A pdb=" N GLN A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.635A pdb=" N LYS A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.721A pdb=" N PHE A1222 " --> pdb=" O ILE A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.863A pdb=" N ILE A1274 " --> pdb=" O MET A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.641A pdb=" N VAL A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.923A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 removed outlier: 3.519A pdb=" N ASN A1393 " --> pdb=" O ARG A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1427 through 1433 Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1449 through 1456 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 53 removed outlier: 5.363A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.650A pdb=" N GLY B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.501A pdb=" N LEU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 336 through 351 removed outlier: 4.141A pdb=" N LYS B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.207A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 431 removed outlier: 3.571A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 457 removed outlier: 4.422A pdb=" N ILE B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 585 through 599 Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.629A pdb=" N GLU B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 806 through 812 removed outlier: 3.617A pdb=" N GLU B 810 " --> pdb=" O GLN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.547A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.893A 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 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.582A pdb=" N TRP C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.545A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.954A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 removed outlier: 4.031A pdb=" N THR D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 146 removed outlier: 3.552A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.685A pdb=" N ILE D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.701A pdb=" N MET E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 58' Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.758A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.801A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.978A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.709A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.866A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.203A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.000A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'R' and resid 7 through 14 Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 73 through 92 Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.140A pdb=" N ASN R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN R 112 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 151 Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 164 through 185 Processing helix chain 'R' and resid 186 through 189 removed outlier: 3.699A pdb=" N SER R 189 " --> pdb=" O PRO R 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 186 through 189' Processing helix chain 'R' and resid 204 through 217 Processing helix chain 'R' and resid 235 through 241 removed outlier: 4.089A pdb=" N LEU R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 270 removed outlier: 3.751A pdb=" N ARG R 270 " --> pdb=" O GLN R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 281 Processing helix chain 'R' and resid 291 through 302 removed outlier: 3.621A pdb=" N ILE R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 328 Processing helix chain 'R' and resid 342 through 356 removed outlier: 3.524A pdb=" N VAL R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR R 350 " --> pdb=" O THR R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 407 removed outlier: 4.095A pdb=" N ASP R 386 " --> pdb=" O ALA R 382 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 552 removed outlier: 3.987A pdb=" N ARG R 545 " --> pdb=" O GLY R 541 " (cutoff:3.500A) Processing helix chain 'R' and resid 555 through 581 removed outlier: 3.505A pdb=" N TYR R 581 " --> pdb=" O VAL R 577 " (cutoff:3.500A) Processing helix chain 'R' and resid 599 through 603 Processing helix chain 'R' and resid 605 through 609 Processing helix chain 'R' and resid 620 through 629 Processing helix chain 'R' and resid 630 through 634 removed outlier: 3.618A pdb=" N SER R 633 " --> pdb=" O PRO R 630 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER R 634 " --> pdb=" O ALA R 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 630 through 634' Processing helix chain 'R' and resid 642 through 647 Processing helix chain 'R' and resid 652 through 656 removed outlier: 3.670A pdb=" N PHE R 655 " --> pdb=" O ILE R 652 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR R 656 " --> pdb=" O ILE R 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 652 through 656' Processing helix chain 'R' and resid 681 through 691 Processing helix chain 'R' and resid 697 through 703 Processing helix chain 'R' and resid 719 through 728 Processing helix chain 'R' and resid 812 through 817 Processing helix chain 'R' and resid 831 through 835 removed outlier: 3.767A pdb=" N GLU R 834 " --> pdb=" O SER R 831 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN R 835 " --> pdb=" O PRO R 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 831 through 835' Processing helix chain 'R' and resid 856 through 870 Processing helix chain 'S' and resid 48 through 54 removed outlier: 4.039A pdb=" N ILE S 52 " --> pdb=" O PRO S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 3.556A pdb=" N HIS S 64 " --> pdb=" O GLY S 61 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 61 through 65' Processing helix chain 'S' and resid 69 through 75 Processing helix chain 'S' and resid 76 through 89 Processing helix chain 'S' and resid 102 through 111 Processing helix chain 'S' and resid 135 through 147 Processing helix chain 'S' and resid 151 through 167 Processing helix chain 'S' and resid 172 through 176 Processing helix chain 'S' and resid 178 through 183 Processing helix chain 'S' and resid 184 through 187 Processing helix chain 'S' and resid 225 through 228 Processing helix chain 'S' and resid 241 through 261 removed outlier: 3.898A pdb=" N LEU S 261 " --> pdb=" O ALA S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 288 through 295 Processing helix chain 'S' and resid 306 through 324 removed outlier: 3.681A pdb=" N SER S 310 " --> pdb=" O ASN S 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 363 Processing helix chain 'S' and resid 364 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 10.184A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 254 removed outlier: 3.635A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A 253 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.639A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 8.144A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.807A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.778A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.576A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL H 12 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.758A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB4, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.810A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1285 through 1295 Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB8, first strand: chain 'A' and resid 1193 through 1199 removed outlier: 3.583A pdb=" N ILE A1154 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR I 44 " --> pdb=" O ILE A1154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1226 through 1230 Processing sheet with id=AC1, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AC2, first strand: chain 'B' and resid 77 through 84 removed outlier: 5.572A pdb=" N PHE B 79 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU B 120 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS B 81 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'B' and resid 397 through 400 removed outlier: 6.104A pdb=" N ALA B 205 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 214 through 218 removed outlier: 4.036A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC9, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.531A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.656A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.656A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.366A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.049A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.654A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 6 through 13 removed outlier: 6.666A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 122 removed outlier: 5.669A pdb=" N LYS C 120 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU C 99 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 122 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.716A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE5, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.992A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL G 77 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AE7, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE8, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.461A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.102A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 86 through 95 removed outlier: 3.551A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.609A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.518A pdb=" N CYS K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 18 through 20 removed outlier: 6.419A pdb=" N HIS R 227 " --> pdb=" O LYS R 249 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU R 251 " --> pdb=" O HIS R 227 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE R 229 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU R 253 " --> pdb=" O ILE R 229 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP R 48 " --> pdb=" O ARG R 94 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 97 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 364 through 365 Processing sheet with id=AF8, first strand: chain 'R' and resid 759 through 760 Processing sheet with id=AF9, first strand: chain 'S' and resid 5 through 8 removed outlier: 4.951A pdb=" N TRP S 101 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N PHE S 134 " --> pdb=" O TRP S 101 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG S 200 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN S 23 " --> pdb=" O ARG S 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 44 through 45 Processing sheet with id=AG2, first strand: chain 'S' and resid 216 through 217 removed outlier: 3.775A pdb=" N CYS S 216 " --> pdb=" O ILE S 231 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR S 230 " --> pdb=" O LYS S 266 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE S 268 " --> pdb=" O TYR S 230 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU S 232 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY S 270 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS S 234 " --> pdb=" O GLY S 270 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG S 272 " --> pdb=" O LYS S 234 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR S 236 " --> pdb=" O ARG S 272 " (cutoff:3.500A) 1791 hydrogen bonds defined for protein. 4983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 9.78 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10715 1.33 - 1.45: 8110 1.45 - 1.57: 23809 1.57 - 1.69: 172 1.69 - 1.82: 367 Bond restraints: 43173 Sorted by residual: bond pdb=" C ASN R 828 " pdb=" N ARG R 829 " ideal model delta sigma weight residual 1.332 1.245 0.086 1.29e-02 6.01e+03 4.48e+01 bond pdb=" C ARG R 827 " pdb=" N ASN R 828 " ideal model delta sigma weight residual 1.331 1.368 -0.036 1.78e-02 3.16e+03 4.20e+00 bond pdb=" C TYR S 269 " pdb=" O TYR S 269 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.12e-02 7.97e+03 4.02e+00 bond pdb=" CA ASN B1187 " pdb=" C ASN B1187 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.24e-02 6.50e+03 3.46e+00 bond pdb=" CA CYS B1166 " pdb=" C CYS B1166 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.35e-02 5.49e+03 2.65e+00 ... (remaining 43168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 57756 1.84 - 3.67: 790 3.67 - 5.51: 111 5.51 - 7.35: 24 7.35 - 9.19: 4 Bond angle restraints: 58685 Sorted by residual: angle pdb=" O ARG R 827 " pdb=" C ARG R 827 " pdb=" N ASN R 828 " ideal model delta sigma weight residual 122.63 116.49 6.14 1.22e+00 6.72e-01 2.54e+01 angle pdb=" N ILE B 495 " pdb=" CA ILE B 495 " pdb=" C ILE B 495 " ideal model delta sigma weight residual 113.53 108.87 4.66 9.80e-01 1.04e+00 2.26e+01 angle pdb=" N SER R 62 " pdb=" CA SER R 62 " pdb=" C SER R 62 " ideal model delta sigma weight residual 113.18 107.03 6.15 1.33e+00 5.65e-01 2.14e+01 angle pdb=" N ASP D 125 " pdb=" CA ASP D 125 " pdb=" C ASP D 125 " ideal model delta sigma weight residual 111.02 105.62 5.40 1.22e+00 6.72e-01 1.96e+01 angle pdb=" N LYS K 112 " pdb=" CA LYS K 112 " pdb=" C LYS K 112 " ideal model delta sigma weight residual 107.37 115.81 -8.44 2.07e+00 2.33e-01 1.66e+01 ... (remaining 58680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 25443 35.30 - 70.61: 760 70.61 - 105.91: 54 105.91 - 141.21: 0 141.21 - 176.52: 2 Dihedral angle restraints: 26259 sinusoidal: 11601 harmonic: 14658 Sorted by residual: dihedral pdb=" O4' U P 4 " pdb=" C1' U P 4 " pdb=" N1 U P 4 " pdb=" C2 U P 4 " ideal model delta sinusoidal sigma weight residual 200.00 44.56 155.44 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" CA GLN R 203 " pdb=" C GLN R 203 " pdb=" N GLY R 204 " pdb=" CA GLY R 204 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' A P 9 " pdb=" C3' A P 9 " pdb=" O3' A P 9 " pdb=" P U P 10 " ideal model delta sinusoidal sigma weight residual -110.00 66.52 -176.52 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 26256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5273 0.051 - 0.102: 997 0.102 - 0.153: 216 0.153 - 0.204: 6 0.204 - 0.255: 1 Chirality restraints: 6493 Sorted by residual: chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU B 175 " pdb=" CB LEU B 175 " pdb=" CD1 LEU B 175 " pdb=" CD2 LEU B 175 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB ILE G 163 " pdb=" CA ILE G 163 " pdb=" CG1 ILE G 163 " pdb=" CG2 ILE G 163 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 6490 not shown) Planarity restraints: 7291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 127 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO E 128 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B1164 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C GLY B1164 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B1164 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B1165 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 828 " -0.011 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C ASN R 828 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN R 828 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 829 " -0.015 2.00e-02 2.50e+03 ... (remaining 7288 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 481 2.65 - 3.21: 36823 3.21 - 3.77: 65310 3.77 - 4.34: 90052 4.34 - 4.90: 147591 Nonbonded interactions: 340257 Sorted by model distance: nonbonded pdb=" OD1 ASP A 482 " pdb="MG MG A1803 " model vdw 2.087 2.170 nonbonded pdb=" O PRO G 96 " pdb=" OG1 THR G 112 " model vdw 2.228 3.040 nonbonded pdb=" O THR R 347 " pdb=" OG1 THR R 350 " model vdw 2.244 3.040 nonbonded pdb=" O GLY A1343 " pdb=" OG1 THR A1347 " model vdw 2.246 3.040 nonbonded pdb=" OG SER R 120 " pdb=" OG SER R 157 " model vdw 2.251 3.040 ... (remaining 340252 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 41.720 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.086 43205 Z= 0.120 Angle : 0.544 23.938 58730 Z= 0.283 Chirality : 0.042 0.255 6493 Planarity : 0.004 0.077 7291 Dihedral : 15.914 176.515 16783 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 0.13 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.12), residues: 4974 helix: 1.43 (0.13), residues: 1795 sheet: 0.43 (0.18), residues: 791 loop : -0.05 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 151 TYR 0.029 0.001 TYR B 797 PHE 0.028 0.001 PHE R 860 TRP 0.031 0.001 TRP C 170 HIS 0.008 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00240 (43173) covalent geometry : angle 0.52770 (58685) hydrogen bonds : bond 0.14261 ( 1841) hydrogen bonds : angle 5.55951 ( 5149) metal coordination : bond 0.00486 ( 32) metal coordination : angle 4.78082 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 450 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8717 (mmt) cc_final: 0.8422 (mmm) REVERT: G 55 ASP cc_start: 0.8009 (t0) cc_final: 0.7773 (t0) REVERT: H 45 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7388 (mt-10) REVERT: R 770 TYR cc_start: 0.2544 (OUTLIER) cc_final: 0.1632 (m-80) REVERT: R 834 GLU cc_start: 0.5576 (pm20) cc_final: 0.4771 (pm20) REVERT: S 366 TRP cc_start: 0.4587 (p90) cc_final: 0.4211 (p-90) outliers start: 6 outliers final: 2 residues processed: 456 average time/residue: 0.2379 time to fit residues: 175.4430 Evaluate side-chains 310 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain R residue 770 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 472 ASN A 649 ASN A 651 GLN A 743 ASN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 129 HIS E 94 ASN E 113 ASN I 51 ASN R 151 ASN R 206 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.098053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055098 restraints weight = 140226.780| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.99 r_work: 0.2587 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 43205 Z= 0.228 Angle : 0.567 9.580 58730 Z= 0.298 Chirality : 0.043 0.201 6493 Planarity : 0.004 0.062 7291 Dihedral : 13.161 169.366 6576 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 0.87 % Allowed : 5.32 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.12), residues: 4974 helix: 1.66 (0.13), residues: 1821 sheet: 0.29 (0.18), residues: 778 loop : 0.09 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 151 TYR 0.022 0.001 TYR B 797 PHE 0.019 0.001 PHE B 217 TRP 0.019 0.001 TRP C 170 HIS 0.008 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00515 (43173) covalent geometry : angle 0.55989 (58685) hydrogen bonds : bond 0.04641 ( 1841) hydrogen bonds : angle 4.65194 ( 5149) metal coordination : bond 0.00922 ( 32) metal coordination : angle 3.20220 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 328 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9132 (mmt) cc_final: 0.8549 (mmm) REVERT: A 308 ASP cc_start: 0.8857 (t0) cc_final: 0.8466 (t0) REVERT: A 770 MET cc_start: 0.9389 (mmm) cc_final: 0.9102 (mmm) REVERT: B 1136 ASP cc_start: 0.9209 (m-30) cc_final: 0.8970 (m-30) REVERT: D 34 PHE cc_start: 0.8213 (m-80) cc_final: 0.8008 (m-10) REVERT: F 78 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8833 (mm-30) REVERT: G 50 ASP cc_start: 0.9110 (t0) cc_final: 0.8507 (t0) REVERT: G 55 ASP cc_start: 0.8810 (t0) cc_final: 0.8357 (t0) REVERT: G 75 ARG cc_start: 0.8023 (ttm170) cc_final: 0.7772 (tpp80) REVERT: I 5 ARG cc_start: 0.8231 (mmp80) cc_final: 0.7981 (mmp80) REVERT: I 45 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8220 (tpp80) REVERT: I 65 ASP cc_start: 0.8907 (t0) cc_final: 0.8696 (t0) REVERT: R 770 TYR cc_start: 0.5536 (OUTLIER) cc_final: 0.4257 (m-80) REVERT: R 834 GLU cc_start: 0.7363 (pm20) cc_final: 0.7159 (pm20) REVERT: S 292 MET cc_start: 0.7830 (ppp) cc_final: 0.7614 (ppp) REVERT: S 366 TRP cc_start: 0.5512 (p90) cc_final: 0.4755 (p-90) outliers start: 39 outliers final: 22 residues processed: 349 average time/residue: 0.2508 time to fit residues: 141.5946 Evaluate side-chains 317 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain R residue 819 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 466 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 302 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 488 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 552 HIS S 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.098536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.055592 restraints weight = 138632.804| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.03 r_work: 0.2607 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43205 Z= 0.126 Angle : 0.498 8.274 58730 Z= 0.261 Chirality : 0.041 0.187 6493 Planarity : 0.003 0.053 7291 Dihedral : 13.173 169.618 6574 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 0.67 % Allowed : 7.09 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.12), residues: 4974 helix: 1.71 (0.13), residues: 1822 sheet: 0.29 (0.18), residues: 768 loop : 0.08 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 119 TYR 0.016 0.001 TYR B 797 PHE 0.016 0.001 PHE K 71 TRP 0.025 0.001 TRP R 320 HIS 0.010 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00282 (43173) covalent geometry : angle 0.49250 (58685) hydrogen bonds : bond 0.03852 ( 1841) hydrogen bonds : angle 4.37115 ( 5149) metal coordination : bond 0.00593 ( 32) metal coordination : angle 2.62373 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 311 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8877 (ptt180) cc_final: 0.8563 (ptt180) REVERT: A 305 MET cc_start: 0.9148 (mmt) cc_final: 0.8599 (mmm) REVERT: A 308 ASP cc_start: 0.8927 (t0) cc_final: 0.8456 (t0) REVERT: A 470 ARG cc_start: 0.8838 (mmt-90) cc_final: 0.8522 (mpt180) REVERT: A 770 MET cc_start: 0.9405 (mmm) cc_final: 0.8734 (mmm) REVERT: A 1229 MET cc_start: 0.8926 (tmm) cc_final: 0.8567 (tmm) REVERT: B 1136 ASP cc_start: 0.9234 (m-30) cc_final: 0.8968 (m-30) REVERT: D 39 TYR cc_start: 0.7526 (m-80) cc_final: 0.7314 (m-80) REVERT: G 44 TYR cc_start: 0.7778 (m-10) cc_final: 0.7552 (m-10) REVERT: G 50 ASP cc_start: 0.8649 (t0) cc_final: 0.8445 (t0) REVERT: G 55 ASP cc_start: 0.8819 (t0) cc_final: 0.8394 (t0) REVERT: G 83 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8385 (tptp) REVERT: G 158 TYR cc_start: 0.7578 (m-80) cc_final: 0.6940 (m-80) REVERT: I 5 ARG cc_start: 0.8138 (mmp80) cc_final: 0.7860 (mmp80) REVERT: I 33 ASP cc_start: 0.8935 (m-30) cc_final: 0.8603 (t70) REVERT: I 45 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8276 (tpp80) REVERT: I 65 ASP cc_start: 0.8949 (t0) cc_final: 0.8634 (t0) REVERT: I 81 ARG cc_start: 0.8065 (mmp-170) cc_final: 0.7786 (mmp80) REVERT: R 566 MET cc_start: 0.2011 (ttm) cc_final: 0.1518 (mtp) REVERT: R 770 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: R 833 GLU cc_start: 0.8277 (mp0) cc_final: 0.8061 (mp0) REVERT: S 292 MET cc_start: 0.7636 (ppp) cc_final: 0.7315 (ppp) REVERT: S 366 TRP cc_start: 0.5444 (p90) cc_final: 0.4688 (p-90) outliers start: 30 outliers final: 21 residues processed: 328 average time/residue: 0.2398 time to fit residues: 127.9842 Evaluate side-chains 311 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 15 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 206 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 452 optimal weight: 50.0000 chunk 295 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN R 59 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.097470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.054517 restraints weight = 138499.478| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.99 r_work: 0.2571 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43205 Z= 0.172 Angle : 0.513 9.008 58730 Z= 0.267 Chirality : 0.042 0.163 6493 Planarity : 0.003 0.049 7291 Dihedral : 13.202 169.282 6574 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 1.01 % Allowed : 8.66 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 4974 helix: 1.78 (0.13), residues: 1819 sheet: 0.25 (0.18), residues: 762 loop : 0.11 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.028 0.001 TYR G 158 PHE 0.016 0.001 PHE K 71 TRP 0.010 0.001 TRP S 366 HIS 0.010 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00395 (43173) covalent geometry : angle 0.50491 (58685) hydrogen bonds : bond 0.03994 ( 1841) hydrogen bonds : angle 4.32096 ( 5149) metal coordination : bond 0.00844 ( 32) metal coordination : angle 3.35436 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9170 (mmt) cc_final: 0.8637 (mmm) REVERT: A 308 ASP cc_start: 0.8996 (t0) cc_final: 0.8524 (t0) REVERT: A 438 MET cc_start: 0.9297 (mmm) cc_final: 0.9038 (mmt) REVERT: A 770 MET cc_start: 0.9381 (mmm) cc_final: 0.8851 (mmm) REVERT: A 1229 MET cc_start: 0.9002 (tmm) cc_final: 0.8554 (tmm) REVERT: A 1425 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8339 (mtm110) REVERT: B 1136 ASP cc_start: 0.9240 (m-30) cc_final: 0.8971 (m-30) REVERT: D 39 TYR cc_start: 0.7473 (m-80) cc_final: 0.7266 (m-80) REVERT: G 55 ASP cc_start: 0.8909 (t0) cc_final: 0.8494 (t0) REVERT: G 83 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8612 (tptp) REVERT: G 146 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8861 (ptmt) REVERT: I 5 ARG cc_start: 0.8092 (mmp80) cc_final: 0.7845 (mmp80) REVERT: I 25 LEU cc_start: 0.7914 (pt) cc_final: 0.7325 (tp) REVERT: I 33 ASP cc_start: 0.8970 (m-30) cc_final: 0.8640 (t70) REVERT: I 45 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8267 (tpp80) REVERT: I 65 ASP cc_start: 0.8987 (t0) cc_final: 0.8647 (t0) REVERT: I 81 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7742 (mmp80) REVERT: R 770 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.4335 (m-80) REVERT: S 292 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7278 (ppp) REVERT: S 366 TRP cc_start: 0.5534 (p90) cc_final: 0.4754 (p-90) outliers start: 45 outliers final: 32 residues processed: 327 average time/residue: 0.2457 time to fit residues: 130.7538 Evaluate side-chains 315 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 331 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 484 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 300 HIS ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053910 restraints weight = 138220.167| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.97 r_work: 0.2557 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43205 Z= 0.190 Angle : 0.526 10.035 58730 Z= 0.273 Chirality : 0.042 0.216 6493 Planarity : 0.003 0.047 7291 Dihedral : 13.229 169.348 6574 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Rotamer: Outliers : 1.23 % Allowed : 9.56 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 4974 helix: 1.79 (0.13), residues: 1811 sheet: 0.22 (0.18), residues: 778 loop : 0.14 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 111 TYR 0.015 0.001 TYR R 594 PHE 0.029 0.001 PHE G 2 TRP 0.020 0.001 TRP R 320 HIS 0.006 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00440 (43173) covalent geometry : angle 0.51729 (58685) hydrogen bonds : bond 0.04080 ( 1841) hydrogen bonds : angle 4.31466 ( 5149) metal coordination : bond 0.00874 ( 32) metal coordination : angle 3.43852 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8917 (ptt180) cc_final: 0.8632 (ptt90) REVERT: A 295 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: A 305 MET cc_start: 0.9180 (mmt) cc_final: 0.8647 (mmm) REVERT: A 308 ASP cc_start: 0.9031 (t0) cc_final: 0.8577 (t0) REVERT: A 438 MET cc_start: 0.9314 (mmm) cc_final: 0.9046 (mmt) REVERT: A 709 MET cc_start: 0.8890 (mtm) cc_final: 0.8671 (ptp) REVERT: A 770 MET cc_start: 0.9351 (mmm) cc_final: 0.8707 (mmm) REVERT: A 1229 MET cc_start: 0.9012 (tmm) cc_final: 0.8500 (tmm) REVERT: B 1136 ASP cc_start: 0.9238 (m-30) cc_final: 0.8993 (m-30) REVERT: D 37 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7781 (mmmm) REVERT: G 55 ASP cc_start: 0.8929 (t0) cc_final: 0.8531 (t0) REVERT: I 25 LEU cc_start: 0.7928 (pt) cc_final: 0.7367 (tp) REVERT: I 33 ASP cc_start: 0.8999 (m-30) cc_final: 0.8703 (t70) REVERT: I 45 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8284 (tpp80) REVERT: I 65 ASP cc_start: 0.9013 (t0) cc_final: 0.8672 (t0) REVERT: I 81 ARG cc_start: 0.7954 (mmp-170) cc_final: 0.7558 (mmp80) REVERT: R 97 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7746 (tp) REVERT: R 566 MET cc_start: 0.0522 (tpp) cc_final: -0.0721 (mtp) REVERT: R 645 MET cc_start: 0.5530 (mtt) cc_final: 0.5180 (mtt) REVERT: R 770 TYR cc_start: 0.5577 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: S 366 TRP cc_start: 0.5576 (p90) cc_final: 0.4732 (p-90) outliers start: 55 outliers final: 37 residues processed: 329 average time/residue: 0.2322 time to fit residues: 123.9491 Evaluate side-chains 326 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 85 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 103 optimal weight: 5.9990 chunk 444 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 478 optimal weight: 40.0000 chunk 344 optimal weight: 3.9990 chunk 432 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 441 optimal weight: 50.0000 chunk 222 optimal weight: 9.9990 chunk 291 optimal weight: 50.0000 chunk 54 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.096773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.053914 restraints weight = 139219.290| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.97 r_work: 0.2562 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43205 Z= 0.170 Angle : 0.514 10.655 58730 Z= 0.267 Chirality : 0.041 0.160 6493 Planarity : 0.003 0.047 7291 Dihedral : 13.229 169.243 6574 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 1.10 % Allowed : 10.54 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4974 helix: 1.85 (0.13), residues: 1804 sheet: 0.27 (0.18), residues: 777 loop : 0.13 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 111 TYR 0.013 0.001 TYR J 43 PHE 0.017 0.001 PHE K 71 TRP 0.012 0.001 TRP S 332 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00392 (43173) covalent geometry : angle 0.50680 (58685) hydrogen bonds : bond 0.03953 ( 1841) hydrogen bonds : angle 4.28085 ( 5149) metal coordination : bond 0.00759 ( 32) metal coordination : angle 3.22185 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8971 (ptt180) cc_final: 0.8713 (ptt90) REVERT: A 305 MET cc_start: 0.9155 (mmt) cc_final: 0.8640 (mmm) REVERT: A 308 ASP cc_start: 0.9045 (t0) cc_final: 0.8583 (t0) REVERT: A 438 MET cc_start: 0.9311 (mmm) cc_final: 0.9039 (mmt) REVERT: A 709 MET cc_start: 0.8858 (mtm) cc_final: 0.8394 (ptp) REVERT: A 770 MET cc_start: 0.9346 (mmm) cc_final: 0.8691 (mmm) REVERT: A 1229 MET cc_start: 0.8989 (tmm) cc_final: 0.8489 (tmm) REVERT: B 1136 ASP cc_start: 0.9231 (m-30) cc_final: 0.8975 (m-30) REVERT: D 37 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7796 (mmmm) REVERT: D 39 TYR cc_start: 0.7344 (m-80) cc_final: 0.7090 (m-80) REVERT: G 35 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8138 (mm-30) REVERT: G 55 ASP cc_start: 0.8939 (t0) cc_final: 0.8539 (t0) REVERT: G 60 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8653 (tmm-80) REVERT: I 25 LEU cc_start: 0.7942 (pt) cc_final: 0.7386 (tp) REVERT: I 33 ASP cc_start: 0.8977 (m-30) cc_final: 0.8692 (t70) REVERT: I 45 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8339 (tpp80) REVERT: I 65 ASP cc_start: 0.9007 (t0) cc_final: 0.8685 (t0) REVERT: I 81 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7585 (mmp-170) REVERT: I 111 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8221 (mmm-85) REVERT: R 97 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7770 (tp) REVERT: R 566 MET cc_start: 0.0405 (tpp) cc_final: -0.0855 (mtp) REVERT: R 645 MET cc_start: 0.5583 (mtt) cc_final: 0.5068 (mtp) REVERT: R 770 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: S 366 TRP cc_start: 0.5598 (p90) cc_final: 0.4724 (p-90) outliers start: 49 outliers final: 36 residues processed: 333 average time/residue: 0.2877 time to fit residues: 155.2766 Evaluate side-chains 329 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 85 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 403 optimal weight: 50.0000 chunk 290 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 700 HIS ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.053181 restraints weight = 138426.590| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.97 r_work: 0.2539 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 43205 Z= 0.209 Angle : 0.544 9.658 58730 Z= 0.282 Chirality : 0.042 0.157 6493 Planarity : 0.003 0.046 7291 Dihedral : 13.264 168.547 6574 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 1.19 % Allowed : 10.90 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 4974 helix: 1.79 (0.13), residues: 1809 sheet: 0.18 (0.18), residues: 765 loop : 0.10 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 111 TYR 0.015 0.001 TYR S 308 PHE 0.023 0.001 PHE G 2 TRP 0.011 0.001 TRP S 101 HIS 0.007 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00485 (43173) covalent geometry : angle 0.53556 (58685) hydrogen bonds : bond 0.04231 ( 1841) hydrogen bonds : angle 4.33281 ( 5149) metal coordination : bond 0.00935 ( 32) metal coordination : angle 3.47018 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9039 (ptt180) cc_final: 0.8788 (ptt90) REVERT: A 295 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: A 305 MET cc_start: 0.9214 (mmt) cc_final: 0.8660 (mmm) REVERT: A 308 ASP cc_start: 0.9070 (t0) cc_final: 0.8635 (t0) REVERT: A 438 MET cc_start: 0.9330 (mmm) cc_final: 0.9056 (mmt) REVERT: A 709 MET cc_start: 0.8888 (mtm) cc_final: 0.8516 (ptp) REVERT: A 770 MET cc_start: 0.9328 (mmm) cc_final: 0.8677 (mmm) REVERT: A 1229 MET cc_start: 0.9014 (tmm) cc_final: 0.8523 (tmm) REVERT: B 123 MET cc_start: 0.5657 (tpt) cc_final: 0.4919 (tpp) REVERT: B 1136 ASP cc_start: 0.9239 (m-30) cc_final: 0.8990 (m-30) REVERT: D 37 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7732 (mmmm) REVERT: D 39 TYR cc_start: 0.7430 (m-80) cc_final: 0.7183 (m-80) REVERT: G 35 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8244 (mm-30) REVERT: G 44 TYR cc_start: 0.8297 (m-80) cc_final: 0.8034 (m-10) REVERT: G 55 ASP cc_start: 0.8968 (t0) cc_final: 0.8641 (t0) REVERT: G 60 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8639 (tmm-80) REVERT: G 146 LYS cc_start: 0.9054 (ptpt) cc_final: 0.8833 (ptpt) REVERT: I 25 LEU cc_start: 0.7965 (pt) cc_final: 0.7385 (tp) REVERT: I 45 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8373 (tpp80) REVERT: I 65 ASP cc_start: 0.9081 (t0) cc_final: 0.8802 (t0) REVERT: I 111 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8244 (mmm-85) REVERT: R 97 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7774 (tp) REVERT: R 566 MET cc_start: 0.0632 (tpp) cc_final: -0.0118 (tpp) REVERT: R 645 MET cc_start: 0.5622 (mtt) cc_final: 0.5336 (mtt) REVERT: R 770 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4322 (m-80) REVERT: S 339 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5139 (ptt-90) REVERT: S 366 TRP cc_start: 0.5547 (p90) cc_final: 0.4658 (p-90) outliers start: 53 outliers final: 37 residues processed: 336 average time/residue: 0.2660 time to fit residues: 142.4979 Evaluate side-chains 327 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 324 GLU Chi-restraints excluded: chain S residue 339 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 226 optimal weight: 4.9990 chunk 453 optimal weight: 40.0000 chunk 492 optimal weight: 6.9990 chunk 458 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 499 optimal weight: 0.0030 chunk 450 optimal weight: 0.0370 chunk 244 optimal weight: 1.9990 overall best weight: 2.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A1213 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054064 restraints weight = 137897.841| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.97 r_work: 0.2566 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43205 Z= 0.132 Angle : 0.510 9.172 58730 Z= 0.264 Chirality : 0.041 0.158 6493 Planarity : 0.003 0.045 7291 Dihedral : 13.230 168.554 6574 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 0.94 % Allowed : 11.51 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4974 helix: 1.87 (0.13), residues: 1806 sheet: 0.22 (0.18), residues: 760 loop : 0.12 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 111 TYR 0.012 0.001 TYR J 43 PHE 0.017 0.001 PHE K 71 TRP 0.009 0.001 TRP C 192 HIS 0.006 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00302 (43173) covalent geometry : angle 0.50388 (58685) hydrogen bonds : bond 0.03790 ( 1841) hydrogen bonds : angle 4.20967 ( 5149) metal coordination : bond 0.00622 ( 32) metal coordination : angle 2.91302 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9069 (ptt180) cc_final: 0.8826 (ptt90) REVERT: A 305 MET cc_start: 0.9209 (mmt) cc_final: 0.8677 (mmm) REVERT: A 308 ASP cc_start: 0.9058 (t0) cc_final: 0.8617 (t0) REVERT: A 438 MET cc_start: 0.9304 (mmm) cc_final: 0.9070 (mmm) REVERT: A 709 MET cc_start: 0.8872 (mtm) cc_final: 0.8383 (ptp) REVERT: A 770 MET cc_start: 0.9329 (mmm) cc_final: 0.8713 (mmm) REVERT: A 1229 MET cc_start: 0.8983 (tmm) cc_final: 0.8494 (tmm) REVERT: B 123 MET cc_start: 0.5559 (tpt) cc_final: 0.4855 (tpp) REVERT: B 245 MET cc_start: 0.8720 (tmm) cc_final: 0.8246 (tmm) REVERT: B 1136 ASP cc_start: 0.9236 (m-30) cc_final: 0.8967 (m-30) REVERT: D 37 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7805 (mmmm) REVERT: D 39 TYR cc_start: 0.7430 (m-80) cc_final: 0.7189 (m-80) REVERT: F 77 GLU cc_start: 0.8707 (pm20) cc_final: 0.8479 (pm20) REVERT: G 44 TYR cc_start: 0.8296 (m-80) cc_final: 0.8033 (m-10) REVERT: G 50 ASP cc_start: 0.8208 (t0) cc_final: 0.8002 (t0) REVERT: G 55 ASP cc_start: 0.8976 (t0) cc_final: 0.8653 (t0) REVERT: G 60 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8610 (tmm-80) REVERT: G 83 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8099 (tppp) REVERT: I 5 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7718 (mmp80) REVERT: I 25 LEU cc_start: 0.7962 (pt) cc_final: 0.7383 (tp) REVERT: I 45 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8367 (tpp80) REVERT: I 65 ASP cc_start: 0.9030 (t0) cc_final: 0.8732 (t0) REVERT: I 111 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8218 (mmm-85) REVERT: R 97 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7766 (tp) REVERT: R 566 MET cc_start: 0.0633 (tpp) cc_final: -0.0118 (tpp) REVERT: R 645 MET cc_start: 0.5629 (mtt) cc_final: 0.5338 (mtt) REVERT: R 770 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: S 366 TRP cc_start: 0.5540 (p90) cc_final: 0.4651 (p-90) outliers start: 42 outliers final: 34 residues processed: 323 average time/residue: 0.2494 time to fit residues: 131.1888 Evaluate side-chains 325 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 324 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 386 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 421 optimal weight: 30.0000 chunk 323 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 433 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 405 optimal weight: 30.0000 chunk 444 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.095144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052260 restraints weight = 139183.247| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.95 r_work: 0.2519 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 43205 Z= 0.278 Angle : 0.602 11.951 58730 Z= 0.309 Chirality : 0.044 0.155 6493 Planarity : 0.004 0.045 7291 Dihedral : 13.298 168.035 6574 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 1.05 % Allowed : 11.64 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.12), residues: 4974 helix: 1.75 (0.13), residues: 1801 sheet: 0.09 (0.18), residues: 758 loop : 0.04 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 227 TYR 0.016 0.001 TYR J 43 PHE 0.017 0.001 PHE K 71 TRP 0.012 0.001 TRP R 538 HIS 0.008 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00645 (43173) covalent geometry : angle 0.59284 (58685) hydrogen bonds : bond 0.04667 ( 1841) hydrogen bonds : angle 4.45143 ( 5149) metal coordination : bond 0.01240 ( 32) metal coordination : angle 3.85311 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: A 305 MET cc_start: 0.9226 (mmt) cc_final: 0.8662 (mmm) REVERT: A 308 ASP cc_start: 0.9072 (t0) cc_final: 0.8644 (t0) REVERT: A 770 MET cc_start: 0.9327 (mmm) cc_final: 0.8665 (mmm) REVERT: A 1229 MET cc_start: 0.8994 (tmm) cc_final: 0.8381 (tmm) REVERT: B 123 MET cc_start: 0.5871 (tpt) cc_final: 0.5219 (tpp) REVERT: B 245 MET cc_start: 0.8735 (tmm) cc_final: 0.8260 (tmm) REVERT: D 37 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7775 (mmmm) REVERT: D 39 TYR cc_start: 0.7547 (m-80) cc_final: 0.7322 (m-80) REVERT: G 44 TYR cc_start: 0.8425 (m-80) cc_final: 0.8178 (m-10) REVERT: G 55 ASP cc_start: 0.8978 (t0) cc_final: 0.8663 (t0) REVERT: G 60 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8672 (tmm-80) REVERT: G 83 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8150 (tppp) REVERT: G 146 LYS cc_start: 0.8997 (ptpt) cc_final: 0.8504 (ptpt) REVERT: I 25 LEU cc_start: 0.7972 (pt) cc_final: 0.7377 (tp) REVERT: I 45 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8440 (tpp80) REVERT: I 65 ASP cc_start: 0.9111 (t0) cc_final: 0.8848 (t0) REVERT: I 81 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7662 (mmm160) REVERT: I 111 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8241 (mmm-85) REVERT: R 97 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7788 (tp) REVERT: R 566 MET cc_start: 0.0923 (tpp) cc_final: 0.0191 (tpp) REVERT: R 770 TYR cc_start: 0.5550 (OUTLIER) cc_final: 0.4228 (m-80) REVERT: R 797 MET cc_start: 0.1558 (ptt) cc_final: 0.1295 (ttp) REVERT: S 339 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.5147 (ptt-90) REVERT: S 366 TRP cc_start: 0.5506 (p90) cc_final: 0.4581 (p-90) outliers start: 47 outliers final: 36 residues processed: 321 average time/residue: 0.2719 time to fit residues: 141.9606 Evaluate side-chains 321 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1242 CYS Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 324 GLU Chi-restraints excluded: chain S residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 187 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 439 optimal weight: 0.2980 chunk 319 optimal weight: 30.0000 chunk 269 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 470 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 315 optimal weight: 0.9980 chunk 487 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN G 122 ASN ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.054149 restraints weight = 138674.939| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.97 r_work: 0.2572 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43205 Z= 0.113 Angle : 0.522 10.436 58730 Z= 0.271 Chirality : 0.041 0.162 6493 Planarity : 0.003 0.045 7291 Dihedral : 13.224 168.020 6574 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 0.90 % Allowed : 11.96 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 4974 helix: 1.86 (0.13), residues: 1803 sheet: 0.16 (0.18), residues: 747 loop : 0.09 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 321 TYR 0.017 0.001 TYR G 130 PHE 0.018 0.001 PHE K 71 TRP 0.012 0.001 TRP C 192 HIS 0.006 0.001 HIS R 864 Details of bonding type rmsd covalent geometry : bond 0.00256 (43173) covalent geometry : angle 0.51674 (58685) hydrogen bonds : bond 0.03757 ( 1841) hydrogen bonds : angle 4.23358 ( 5149) metal coordination : bond 0.00570 ( 32) metal coordination : angle 2.81381 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9948 Ramachandran restraints generated. 4974 Oldfield, 0 Emsley, 4974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 1.538 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: A 63 ARG cc_start: 0.9103 (ptt180) cc_final: 0.8856 (ptt90) REVERT: A 122 MET cc_start: 0.8855 (ttm) cc_final: 0.8547 (ttm) REVERT: A 305 MET cc_start: 0.9209 (mmt) cc_final: 0.8682 (mmm) REVERT: A 308 ASP cc_start: 0.9052 (t0) cc_final: 0.8616 (t0) REVERT: A 438 MET cc_start: 0.9298 (mmm) cc_final: 0.9079 (mmm) REVERT: A 470 ARG cc_start: 0.8821 (mmt-90) cc_final: 0.8450 (mpt180) REVERT: A 770 MET cc_start: 0.9320 (mmm) cc_final: 0.8735 (mmm) REVERT: A 1229 MET cc_start: 0.8904 (tmm) cc_final: 0.8337 (tmm) REVERT: B 123 MET cc_start: 0.5529 (tpt) cc_final: 0.4860 (tpp) REVERT: B 245 MET cc_start: 0.8689 (tmm) cc_final: 0.8242 (tmm) REVERT: B 1136 ASP cc_start: 0.9214 (m-30) cc_final: 0.8944 (m-30) REVERT: D 37 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7777 (mmmm) REVERT: D 39 TYR cc_start: 0.7509 (m-80) cc_final: 0.7292 (m-80) REVERT: G 44 TYR cc_start: 0.8397 (m-80) cc_final: 0.8132 (m-10) REVERT: G 55 ASP cc_start: 0.8958 (t0) cc_final: 0.8653 (t0) REVERT: G 60 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (tmm-80) REVERT: G 83 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8151 (tppp) REVERT: I 5 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7688 (mmp80) REVERT: I 25 LEU cc_start: 0.7939 (pt) cc_final: 0.7363 (tp) REVERT: I 45 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8440 (tpp80) REVERT: I 65 ASP cc_start: 0.9034 (t0) cc_final: 0.8748 (t0) REVERT: I 81 ARG cc_start: 0.7852 (mmp-170) cc_final: 0.7593 (mmm160) REVERT: I 111 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: L 44 LYS cc_start: 0.9164 (tmtt) cc_final: 0.8644 (ptpp) REVERT: R 97 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7824 (tp) REVERT: R 167 MET cc_start: 0.6264 (tmm) cc_final: 0.6054 (ttp) REVERT: R 566 MET cc_start: 0.0858 (tpp) cc_final: 0.0150 (tpp) REVERT: R 645 MET cc_start: 0.5914 (mtt) cc_final: 0.5464 (ttm) REVERT: R 770 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4288 (m-80) REVERT: S 339 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.5047 (ptt-90) REVERT: S 366 TRP cc_start: 0.5548 (p90) cc_final: 0.4665 (p-90) outliers start: 40 outliers final: 29 residues processed: 317 average time/residue: 0.2767 time to fit residues: 142.5883 Evaluate side-chains 315 residues out of total 4458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 712 VAL Chi-restraints excluded: chain R residue 770 TYR Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 324 GLU Chi-restraints excluded: chain S residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 383 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 chunk 462 optimal weight: 50.0000 chunk 372 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.096035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.053426 restraints weight = 139806.089| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.95 r_work: 0.2554 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43205 Z= 0.168 Angle : 0.537 10.027 58730 Z= 0.278 Chirality : 0.041 0.156 6493 Planarity : 0.003 0.045 7291 Dihedral : 13.180 167.837 6574 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 0.81 % Allowed : 12.27 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.12), residues: 4974 helix: 1.90 (0.13), residues: 1798 sheet: 0.16 (0.18), residues: 750 loop : 0.08 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 111 TYR 0.015 0.001 TYR S 46 PHE 0.017 0.001 PHE K 71 TRP 0.010 0.001 TRP S 101 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00388 (43173) covalent geometry : angle 0.53048 (58685) hydrogen bonds : bond 0.03992 ( 1841) hydrogen bonds : angle 4.27452 ( 5149) metal coordination : bond 0.00766 ( 32) metal coordination : angle 3.04844 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12909.17 seconds wall clock time: 220 minutes 56.78 seconds (13256.78 seconds total)