Starting phenix.real_space_refine on Sun Aug 9 07:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.map" model { file = "/net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb5_54713/08_2026/9sb5_54713.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 53 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20227 2.51 5 N 5633 2.21 5 O 6234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32338 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10993 Classifications: {'peptide': 1396} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1331} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 223 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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 457 SG CYS A 67 56.802 70.347 85.606 1.00227.18 S ATOM 479 SG CYS A 70 55.911 73.661 83.951 1.00219.96 S ATOM 532 SG CYS A 77 59.563 72.528 84.100 1.00209.64 S ATOM 762 SG CYS A 107 74.991 79.923 128.691 1.00260.31 S ATOM 786 SG CYS A 110 72.942 83.058 128.005 1.00255.71 S ATOM 1091 SG CYS A 148 75.579 83.071 130.720 1.00277.74 S ATOM 1190 SG CYS A 167 72.259 80.978 131.056 1.00279.92 S ATOM 19767 SG CYS B1163 58.292 86.878 93.717 1.00197.62 S ATOM 19785 SG CYS B1166 60.803 84.597 95.146 1.00194.10 S ATOM 19910 SG CYS B1182 57.320 83.304 93.821 1.00200.66 S ATOM 19929 SG CYS B1185 57.674 85.121 97.154 1.00196.81 S ATOM 20917 SG CYS C 86 84.195 60.708 21.572 1.00188.03 S ATOM 20934 SG CYS C 88 81.997 58.370 23.607 1.00222.42 S ATOM 20967 SG CYS C 92 83.649 56.928 20.827 1.00170.47 S ATOM 20990 SG CYS C 95 85.560 58.086 24.088 1.00146.08 S ATOM 28575 SG CYS I 7 133.065 49.056 136.220 1.00357.74 S ATOM 28600 SG CYS I 10 129.374 48.483 135.838 1.00355.93 S ATOM 28766 SG CYS I 29 130.510 51.821 137.161 1.00364.42 S ATOM 28790 SG CYS I 32 130.937 48.707 139.323 1.00366.70 S ATOM 29117 SG CYS I 75 157.960 58.182 99.021 1.00380.29 S ATOM 29139 SG CYS I 78 159.573 54.860 98.822 1.00377.29 S ATOM 29355 SG CYS I 103 155.904 55.103 97.745 1.00351.38 S ATOM 29375 SG CYS I 106 156.934 55.621 101.441 1.00372.97 S ATOM 29494 SG CYS J 7 113.612 58.729 39.509 1.00 96.09 S ATOM 29517 SG CYS J 10 113.622 60.279 36.101 1.00 93.71 S ATOM 29797 SG CYS J 45 116.477 61.043 38.396 1.00 99.74 S ATOM 29803 SG CYS J 46 116.128 57.763 36.533 1.00102.31 S ATOM 30926 SG CYS L 31 89.130 27.853 56.445 1.00265.59 S ATOM 30946 SG CYS L 34 90.028 24.907 54.183 1.00277.64 S ATOM 31050 SG CYS L 48 86.509 25.282 55.715 1.00276.96 S ATOM 31073 SG CYS L 51 89.708 24.243 57.708 1.00289.51 S Time building chain proxies: 6.56, per 1000 atoms: 0.20 Number of scatterers: 32338 At special positions: 0 Unit cell: (171.084, 155.925, 159.173, 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 182 16.00 P 53 15.00 Mg 1 11.99 O 6234 8.00 N 5633 7.00 C 20227 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7386 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 45 sheets defined 38.0% alpha, 18.0% beta 26 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.58 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 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.594A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.649A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 4.168A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.459A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.583A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.511A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.652A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.742A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.788A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.526A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.972A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1175 Processing helix chain 'A' and resid 1178 through 1185 removed outlier: 3.710A pdb=" N GLU A1182 " --> pdb=" O ASP A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.784A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.874A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.738A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.003A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.489A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.683A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.807A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.758A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 4.103A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.596A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.093A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.648A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.758A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.694A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.680A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.105A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.851A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.360A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.952A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 4.075A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1209 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.516A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.817A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 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 removed outlier: 3.549A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.993A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.042A pdb=" N GLN D 132 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 156 through 169 removed outlier: 4.191A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.806A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.669A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.500A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.506A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.501A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 188 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: 3.663A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.732A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.501A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.659A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.728A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.612A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.522A pdb=" N ALA K 86 " --> pdb=" O ASP K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.635A pdb=" N GLU A 16 " --> pdb=" O TYR B1217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 10.141A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.648A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 184 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.636A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.621A pdb=" N ALA A 349 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.309A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.009A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.816A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1147 through 1153 removed outlier: 6.324A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 143 through 147 removed outlier: 3.530A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 removed outlier: 5.643A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 removed outlier: 5.643A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.259A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.824A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 242 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS B 257 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 280 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.930A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.334A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.538A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.538A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.876A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.869A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.516A pdb=" N GLU B1181 " --> pdb=" O ILE B1172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.941A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 229 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE C 178 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASN C 231 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 176 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU C 233 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.638A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.613A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.359A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 156 removed outlier: 3.786A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 13 removed outlier: 3.921A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR G 44 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 86 through 88 removed outlier: 4.286A pdb=" N VAL G 87 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.705A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.677A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.599A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 21 through 23 1265 hydrogen bonds defined for protein. 3489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 9.04 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 13897 1.44 - 1.67: 18823 1.67 - 1.90: 295 1.90 - 2.12: 1 2.12 - 2.35: 4 Bond restraints: 33020 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.528 2.090 -0.562 1.59e-02 3.96e+03 1.25e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.352 -0.970 3.00e-02 1.11e+03 1.05e+03 bond pdb=" CE1 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.342 -0.960 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.338 -0.956 3.00e-02 1.11e+03 1.01e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.324 -0.942 3.00e-02 1.11e+03 9.85e+02 ... (remaining 33015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 44781 4.94 - 9.88: 19 9.88 - 14.82: 2 14.82 - 19.76: 2 19.76 - 24.70: 1 Bond angle restraints: 44805 Sorted by residual: angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 135.20 -24.70 1.70e+00 3.46e-01 2.11e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 128.18 -18.58 1.50e+00 4.44e-01 1.53e+02 angle pdb=" OG1 THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 109.30 91.89 17.41 2.00e+00 2.50e-01 7.57e+01 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.36 102.18 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.85 124.11 -13.26 1.70e+00 3.46e-01 6.08e+01 ... (remaining 44800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 19499 26.30 - 52.60: 508 52.60 - 78.89: 83 78.89 - 105.19: 3 105.19 - 131.49: 1 Dihedral angle restraints: 20094 sinusoidal: 8690 harmonic: 11404 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -141.38 19.38 0 2.50e+00 1.60e-01 6.01e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 139.01 -15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" CA LEU A 997 " pdb=" C LEU A 997 " pdb=" N LEU A 998 " pdb=" CA LEU A 998 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 20091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 5041 0.184 - 0.367: 0 0.367 - 0.551: 0 0.551 - 0.735: 0 0.735 - 0.918: 1 Chirality restraints: 5042 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 1.63 0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 5039 not shown) Planarity restraints: 5621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " -0.000 2.00e-02 2.50e+03 5.24e-02 4.81e+01 pdb=" CG PHE D 70 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.079 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.086 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C THR D 133 " 0.040 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 134 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.039 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 245 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.032 5.00e-02 4.00e+02 ... (remaining 5618 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 207 2.52 - 3.11: 24093 3.11 - 3.71: 48955 3.71 - 4.30: 70050 4.30 - 4.90: 117682 Nonbonded interactions: 260987 Sorted by model distance: nonbonded pdb=" O3' A R 18 " pdb="MG MG A1801 " model vdw 1.920 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 1.938 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1801 " model vdw 1.963 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.047 3.340 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.076 3.040 ... (remaining 260982 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.012 0.970 33052 Z= 0.476 Angle : 0.599 24.697 44850 Z= 0.355 Chirality : 0.045 0.918 5042 Planarity : 0.004 0.058 5621 Dihedral : 11.992 131.491 12708 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3878 helix: 1.19 (0.15), residues: 1296 sheet: -0.47 (0.23), residues: 520 loop : -0.84 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.029 0.001 TYR B 797 PHE 0.086 0.002 PHE D 70 TRP 0.014 0.001 TRP A 954 HIS 0.007 0.001 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.48 (33020) covalent geometry : angle 0.58518 / 0.35 (44805) hydrogen bonds : bond 0.18088 / 11.41 ( 1310) hydrogen bonds : angle 6.96039 / 4.96 ( 3627) metal coordination : bond 0.00620 / 0.45 ( 32) metal coordination : angle 4.10557 / 2.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7245 (mtpt) cc_final: 0.6918 (tptp) REVERT: A 143 LYS cc_start: 0.5931 (pttt) cc_final: 0.5577 (ptmm) REVERT: A 146 MET cc_start: 0.4846 (mmm) cc_final: 0.4444 (mmt) REVERT: A 291 GLU cc_start: 0.6965 (tt0) cc_final: 0.6502 (mm-30) REVERT: A 316 GLN cc_start: 0.5692 (tp40) cc_final: 0.5146 (mt0) REVERT: A 340 LEU cc_start: 0.8657 (mt) cc_final: 0.8422 (mt) REVERT: A 393 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7572 (ttp80) REVERT: A 619 LYS cc_start: 0.8702 (tttt) cc_final: 0.8436 (tptm) REVERT: A 715 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7705 (pp20) REVERT: A 800 VAL cc_start: 0.9402 (t) cc_final: 0.9081 (p) REVERT: A 1013 ASP cc_start: 0.8610 (m-30) cc_final: 0.8347 (t0) REVERT: A 1134 ILE cc_start: 0.8961 (mm) cc_final: 0.8742 (mm) REVERT: A 1139 GLU cc_start: 0.7725 (tt0) cc_final: 0.7055 (tt0) REVERT: A 1211 GLN cc_start: 0.7023 (mt0) cc_final: 0.6802 (pp30) REVERT: A 1227 ILE cc_start: 0.7040 (mt) cc_final: 0.6767 (mt) REVERT: A 1276 VAL cc_start: 0.8163 (t) cc_final: 0.7569 (t) REVERT: A 1285 MET cc_start: 0.7882 (mmt) cc_final: 0.7677 (mmm) REVERT: A 1315 GLU cc_start: 0.8990 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 1420 ASP cc_start: 0.8446 (t0) cc_final: 0.8145 (t0) REVERT: A 1424 VAL cc_start: 0.8867 (m) cc_final: 0.8515 (p) REVERT: A 1445 ILE cc_start: 0.8346 (tp) cc_final: 0.8062 (tp) REVERT: A 1452 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7652 (tptp) REVERT: B 224 GLN cc_start: 0.8692 (mt0) cc_final: 0.8122 (mt0) REVERT: B 239 GLU cc_start: 0.8659 (pt0) cc_final: 0.7942 (pm20) REVERT: B 310 MET cc_start: 0.8667 (mtp) cc_final: 0.8253 (mmm) REVERT: B 313 MET cc_start: 0.7823 (tpp) cc_final: 0.7214 (tpt) REVERT: B 398 ARG cc_start: 0.7657 (mtt-85) cc_final: 0.7349 (ptt180) REVERT: B 412 LEU cc_start: 0.9080 (mt) cc_final: 0.8844 (mt) REVERT: B 542 MET cc_start: 0.8719 (mtm) cc_final: 0.8202 (mtp) REVERT: B 627 PHE cc_start: 0.8988 (m-80) cc_final: 0.8528 (m-80) REVERT: B 809 MET cc_start: 0.8912 (mtt) cc_final: 0.8681 (mtm) REVERT: B 860 MET cc_start: 0.7941 (ttt) cc_final: 0.7539 (tmm) REVERT: B 948 ILE cc_start: 0.8698 (mp) cc_final: 0.8271 (tt) REVERT: B 1004 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 1074 ASN cc_start: 0.8827 (t0) cc_final: 0.8582 (t0) REVERT: B 1152 MET cc_start: 0.8329 (mmm) cc_final: 0.7739 (mmm) REVERT: B 1162 ILE cc_start: 0.7744 (mm) cc_final: 0.7486 (tp) REVERT: B 1180 PHE cc_start: 0.8048 (m-80) cc_final: 0.7558 (m-10) REVERT: C 249 ASP cc_start: 0.8224 (t0) cc_final: 0.7941 (t0) REVERT: D 1 MET cc_start: 0.1218 (pmm) cc_final: 0.0735 (ttp) REVERT: E 74 ASP cc_start: 0.8680 (m-30) cc_final: 0.8119 (p0) REVERT: E 94 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7658 (ptmt) REVERT: E 150 VAL cc_start: 0.9636 (t) cc_final: 0.9404 (m) REVERT: G 16 SER cc_start: 0.4077 (p) cc_final: 0.3604 (t) REVERT: G 73 LYS cc_start: 0.6012 (mmtp) cc_final: 0.5779 (mmtm) REVERT: H 24 CYS cc_start: 0.8793 (m) cc_final: 0.8455 (m) REVERT: H 37 LYS cc_start: 0.8739 (ptpt) cc_final: 0.8368 (ptpt) REVERT: H 53 ASP cc_start: 0.7674 (m-30) cc_final: 0.7336 (m-30) REVERT: H 94 ASP cc_start: 0.8701 (m-30) cc_final: 0.8447 (t0) REVERT: H 109 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7925 (pttp) REVERT: I 1 MET cc_start: 0.3871 (tpp) cc_final: 0.2709 (mtm) REVERT: I 97 MET cc_start: 0.3334 (mtp) cc_final: 0.2670 (mtp) REVERT: J 24 LEU cc_start: 0.9177 (mt) cc_final: 0.8876 (mp) REVERT: J 42 LYS cc_start: 0.8960 (pttt) cc_final: 0.8742 (tppt) REVERT: J 49 MET cc_start: 0.8885 (tpp) cc_final: 0.8332 (tpp) REVERT: K 17 SER cc_start: 0.9156 (m) cc_final: 0.8922 (t) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.2282 time to fit residues: 207.1851 Evaluate side-chains 319 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 9.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 358 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 903 ASN A1130 GLN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 822 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN D 216 ASN E 104 ASN E 146 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097476 restraints weight = 83916.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100583 restraints weight = 42804.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100762 restraints weight = 24130.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100975 restraints weight = 19923.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101176 restraints weight = 19670.119| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.026 33052 Z= 0.469 Angle : 0.660 24.264 44850 Z= 0.342 Chirality : 0.046 0.778 5042 Planarity : 0.004 0.059 5621 Dihedral : 11.570 133.877 4863 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 1.04 % Allowed : 6.02 % Favored : 92.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3878 helix: 1.20 (0.14), residues: 1326 sheet: -0.33 (0.22), residues: 541 loop : -0.83 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 392 TYR 0.019 0.001 TYR B 797 PHE 0.085 0.002 PHE D 70 TRP 0.011 0.001 TRP B 308 HIS 0.005 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01229 / 0.47 (33020) covalent geometry : angle 0.63524 / 0.34 (44805) hydrogen bonds : bond 0.04833 / 3.22 ( 1310) hydrogen bonds : angle 5.44058 / 3.88 ( 3627) metal coordination : bond 0.01122 / 0.69 ( 32) metal coordination : angle 5.69370 / 3.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6865 (tptp) REVERT: A 143 LYS cc_start: 0.6422 (pttt) cc_final: 0.6203 (ptmm) REVERT: A 291 GLU cc_start: 0.7347 (tt0) cc_final: 0.6789 (mm-30) REVERT: A 393 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7659 (ttp80) REVERT: A 453 MET cc_start: 0.8680 (mpp) cc_final: 0.8361 (mtp) REVERT: A 715 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7948 (pp20) REVERT: A 939 ASP cc_start: 0.7587 (m-30) cc_final: 0.7192 (t0) REVERT: A 1139 GLU cc_start: 0.7792 (tt0) cc_final: 0.7467 (tt0) REVERT: A 1309 ASP cc_start: 0.8168 (m-30) cc_final: 0.7915 (m-30) REVERT: A 1420 ASP cc_start: 0.8190 (t0) cc_final: 0.7966 (t0) REVERT: A 1444 MET cc_start: 0.7710 (mpp) cc_final: 0.7279 (mtm) REVERT: A 1452 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7664 (tptp) REVERT: B 310 MET cc_start: 0.8470 (mtp) cc_final: 0.8133 (mmm) REVERT: B 563 MET cc_start: 0.7806 (tmm) cc_final: 0.7477 (tmm) REVERT: B 627 PHE cc_start: 0.8764 (m-80) cc_final: 0.8355 (m-80) REVERT: B 860 MET cc_start: 0.7565 (ttt) cc_final: 0.7318 (tmm) REVERT: B 862 GLN cc_start: 0.6717 (mt0) cc_final: 0.6473 (pm20) REVERT: B 948 ILE cc_start: 0.8984 (mp) cc_final: 0.8623 (tt) REVERT: B 1111 MET cc_start: 0.6530 (mmt) cc_final: 0.6142 (mmt) REVERT: B 1162 ILE cc_start: 0.8083 (mm) cc_final: 0.7715 (tt) REVERT: B 1180 PHE cc_start: 0.8006 (m-80) cc_final: 0.7711 (m-10) REVERT: B 1206 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 249 ASP cc_start: 0.7864 (t0) cc_final: 0.7639 (t0) REVERT: D 1 MET cc_start: 0.0898 (pmm) cc_final: 0.0318 (ttp) REVERT: E 22 MET cc_start: 0.8681 (ttm) cc_final: 0.8432 (ttp) REVERT: E 74 ASP cc_start: 0.8381 (m-30) cc_final: 0.7941 (p0) REVERT: E 150 VAL cc_start: 0.9557 (t) cc_final: 0.9346 (m) REVERT: E 187 TYR cc_start: 0.8853 (t80) cc_final: 0.8537 (t80) REVERT: F 103 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.6059 (tmm) REVERT: G 58 ARG cc_start: 0.5587 (mtm-85) cc_final: 0.5125 (mtm-85) REVERT: H 8 ASP cc_start: 0.6869 (t0) cc_final: 0.6451 (t0) REVERT: H 24 CYS cc_start: 0.7956 (m) cc_final: 0.7736 (m) REVERT: H 97 MET cc_start: 0.8164 (mtp) cc_final: 0.7783 (mtm) REVERT: H 103 LYS cc_start: 0.9270 (tppt) cc_final: 0.9049 (tppp) REVERT: H 105 GLU cc_start: 0.7780 (tt0) cc_final: 0.7101 (tm-30) REVERT: I 1 MET cc_start: 0.4013 (tpp) cc_final: 0.3315 (mtm) REVERT: I 97 MET cc_start: 0.3317 (mtp) cc_final: 0.2790 (mtp) REVERT: J 24 LEU cc_start: 0.9229 (mt) cc_final: 0.8954 (mp) REVERT: J 49 MET cc_start: 0.8584 (tpp) cc_final: 0.8139 (tpp) REVERT: K 64 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7869 (mt-10) outliers start: 36 outliers final: 21 residues processed: 360 average time/residue: 0.1987 time to fit residues: 115.8062 Evaluate side-chains 297 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 15 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 382 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 363 GLN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN G 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.127980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094144 restraints weight = 86283.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097137 restraints weight = 45291.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097135 restraints weight = 26353.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097523 restraints weight = 21842.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097615 restraints weight = 21417.544| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.037 33052 Z= 0.506 Angle : 0.690 24.106 44850 Z= 0.355 Chirality : 0.046 0.730 5042 Planarity : 0.005 0.092 5621 Dihedral : 11.680 134.978 4863 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 1.65 % Allowed : 8.24 % Favored : 90.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3878 helix: 1.09 (0.14), residues: 1316 sheet: -0.48 (0.22), residues: 538 loop : -0.94 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1239 TYR 0.016 0.002 TYR B1192 PHE 0.074 0.002 PHE D 70 TRP 0.011 0.002 TRP A 139 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01308 / 0.51 (33020) covalent geometry : angle 0.66621 / 0.35 (44805) hydrogen bonds : bond 0.04597 / 3.08 ( 1310) hydrogen bonds : angle 5.18979 / 3.69 ( 3627) metal coordination : bond 0.00989 / 0.72 ( 32) metal coordination : angle 5.73032 / 3.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7382 (mtpt) cc_final: 0.7010 (tptp) REVERT: A 146 MET cc_start: 0.6027 (mmt) cc_final: 0.5571 (mmm) REVERT: A 291 GLU cc_start: 0.7373 (tt0) cc_final: 0.6775 (mm-30) REVERT: A 341 MET cc_start: 0.8144 (mmt) cc_final: 0.7846 (mmt) REVERT: A 393 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7715 (ttp80) REVERT: A 470 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 715 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7721 (pp20) REVERT: A 849 MET cc_start: 0.8546 (ttm) cc_final: 0.8208 (ttm) REVERT: A 939 ASP cc_start: 0.7627 (m-30) cc_final: 0.7225 (t0) REVERT: A 1013 ASP cc_start: 0.8696 (t0) cc_final: 0.8231 (t0) REVERT: A 1063 MET cc_start: 0.8117 (mmm) cc_final: 0.7845 (tpt) REVERT: A 1139 GLU cc_start: 0.7839 (tt0) cc_final: 0.7574 (tt0) REVERT: A 1276 VAL cc_start: 0.8761 (t) cc_final: 0.8475 (t) REVERT: A 1420 ASP cc_start: 0.8235 (t0) cc_final: 0.8008 (t0) REVERT: A 1444 MET cc_start: 0.7766 (mpp) cc_final: 0.7347 (mtm) REVERT: A 1452 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7637 (tptp) REVERT: B 310 MET cc_start: 0.8689 (mtp) cc_final: 0.8224 (mtt) REVERT: B 313 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6447 (tpt) REVERT: B 563 MET cc_start: 0.7848 (tmm) cc_final: 0.7506 (tmm) REVERT: B 627 PHE cc_start: 0.8820 (m-80) cc_final: 0.8403 (m-80) REVERT: B 860 MET cc_start: 0.7705 (ttt) cc_final: 0.7498 (tmm) REVERT: B 948 ILE cc_start: 0.9038 (mp) cc_final: 0.8662 (tt) REVERT: B 1162 ILE cc_start: 0.8095 (mm) cc_final: 0.7889 (tt) REVERT: B 1169 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: B 1206 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 249 ASP cc_start: 0.7852 (t0) cc_final: 0.7550 (t0) REVERT: D 1 MET cc_start: 0.1055 (pmm) cc_final: 0.0598 (ttp) REVERT: E 74 ASP cc_start: 0.8346 (m-30) cc_final: 0.7864 (p0) REVERT: E 150 VAL cc_start: 0.9566 (t) cc_final: 0.9344 (m) REVERT: H 97 MET cc_start: 0.8085 (mtp) cc_final: 0.7682 (mtm) REVERT: H 105 GLU cc_start: 0.7808 (tt0) cc_final: 0.7170 (tm-30) REVERT: I 1 MET cc_start: 0.4445 (tpp) cc_final: 0.3523 (mtm) REVERT: J 24 LEU cc_start: 0.9268 (mt) cc_final: 0.9039 (mp) REVERT: J 49 MET cc_start: 0.8574 (tpp) cc_final: 0.8128 (tpp) REVERT: K 64 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7929 (mt-10) outliers start: 57 outliers final: 35 residues processed: 308 average time/residue: 0.2082 time to fit residues: 105.0666 Evaluate side-chains 291 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 388 optimal weight: 50.0000 chunk 361 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094158 restraints weight = 85785.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097069 restraints weight = 44569.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097195 restraints weight = 25647.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097542 restraints weight = 21632.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097663 restraints weight = 20796.613| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.039 33052 Z= 0.490 Angle : 0.650 24.095 44850 Z= 0.336 Chirality : 0.045 0.713 5042 Planarity : 0.004 0.077 5621 Dihedral : 11.696 134.058 4863 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 1.88 % Allowed : 9.49 % Favored : 88.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3878 helix: 1.11 (0.14), residues: 1316 sheet: -0.55 (0.22), residues: 540 loop : -0.95 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.012 0.001 TYR B1192 PHE 0.075 0.002 PHE D 70 TRP 0.010 0.001 TRP A 233 HIS 0.012 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01277 / 0.49 (33020) covalent geometry : angle 0.62752 / 0.33 (44805) hydrogen bonds : bond 0.04252 / 2.87 ( 1310) hydrogen bonds : angle 4.99039 / 3.56 ( 3627) metal coordination : bond 0.00836 / 0.61 ( 32) metal coordination : angle 5.36960 / 3.64 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7204 (tptp) REVERT: A 146 MET cc_start: 0.6192 (mmt) cc_final: 0.5722 (mmm) REVERT: A 291 GLU cc_start: 0.7375 (tt0) cc_final: 0.6781 (mm-30) REVERT: A 341 MET cc_start: 0.8148 (mmt) cc_final: 0.7922 (mmt) REVERT: A 393 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7768 (ttp80) REVERT: A 470 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8065 (pp) REVERT: A 715 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7731 (pp20) REVERT: A 939 ASP cc_start: 0.7571 (m-30) cc_final: 0.7212 (t0) REVERT: A 1013 ASP cc_start: 0.8678 (t0) cc_final: 0.8103 (t0) REVERT: A 1063 MET cc_start: 0.8082 (mmm) cc_final: 0.7816 (tpt) REVERT: A 1400 CYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 1420 ASP cc_start: 0.8252 (t0) cc_final: 0.8030 (t0) REVERT: A 1444 MET cc_start: 0.7770 (mpp) cc_final: 0.7399 (mtm) REVERT: B 310 MET cc_start: 0.8745 (mtp) cc_final: 0.8239 (mtt) REVERT: B 549 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8379 (m) REVERT: B 563 MET cc_start: 0.7971 (tmm) cc_final: 0.7654 (tmm) REVERT: B 627 PHE cc_start: 0.8799 (m-80) cc_final: 0.8376 (m-80) REVERT: B 860 MET cc_start: 0.7663 (ttt) cc_final: 0.7310 (tmm) REVERT: B 862 GLN cc_start: 0.6538 (mt0) cc_final: 0.6298 (pm20) REVERT: B 948 ILE cc_start: 0.9063 (mp) cc_final: 0.8703 (tt) REVERT: B 1162 ILE cc_start: 0.8106 (mm) cc_final: 0.7903 (tt) REVERT: B 1169 MET cc_start: 0.8428 (mtm) cc_final: 0.8140 (mmm) REVERT: C 249 ASP cc_start: 0.7874 (t0) cc_final: 0.7616 (t0) REVERT: D 1 MET cc_start: 0.0737 (pmm) cc_final: 0.0495 (ttp) REVERT: E 74 ASP cc_start: 0.8356 (m-30) cc_final: 0.7861 (p0) REVERT: E 150 VAL cc_start: 0.9570 (t) cc_final: 0.9349 (m) REVERT: H 97 MET cc_start: 0.8012 (mtp) cc_final: 0.7640 (mtm) REVERT: H 105 GLU cc_start: 0.7811 (tt0) cc_final: 0.7167 (tm-30) REVERT: I 1 MET cc_start: 0.4578 (tpp) cc_final: 0.3657 (mtm) REVERT: J 24 LEU cc_start: 0.9259 (mt) cc_final: 0.8952 (mp) REVERT: J 49 MET cc_start: 0.8528 (tpp) cc_final: 0.8042 (tpp) REVERT: K 64 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7944 (mt-10) outliers start: 65 outliers final: 34 residues processed: 320 average time/residue: 0.1902 time to fit residues: 101.0073 Evaluate side-chains 289 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 136 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 339 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN ** B1187 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 = 0.3994 r_free = 0.3994 target = 0.127601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094879 restraints weight = 84376.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097883 restraints weight = 44156.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098001 restraints weight = 25040.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098232 restraints weight = 20801.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098294 restraints weight = 21103.781| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.038 33052 Z= 0.478 Angle : 0.633 24.054 44850 Z= 0.327 Chirality : 0.045 0.711 5042 Planarity : 0.004 0.058 5621 Dihedral : 11.674 133.807 4863 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 1.82 % Allowed : 10.50 % Favored : 87.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3878 helix: 1.25 (0.14), residues: 1309 sheet: -0.59 (0.22), residues: 535 loop : -0.92 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 392 TYR 0.021 0.001 TYR E 187 PHE 0.074 0.002 PHE D 70 TRP 0.013 0.001 TRP B 308 HIS 0.007 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01252 / 0.48 (33020) covalent geometry : angle 0.61190 / 0.33 (44805) hydrogen bonds : bond 0.04092 / 2.78 ( 1310) hydrogen bonds : angle 4.84424 / 3.45 ( 3627) metal coordination : bond 0.00753 / 0.55 ( 32) metal coordination : angle 5.11718 / 3.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5739 (t80) REVERT: A 129 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7220 (tptp) REVERT: A 146 MET cc_start: 0.6376 (mmt) cc_final: 0.5917 (mmm) REVERT: A 291 GLU cc_start: 0.7332 (tt0) cc_final: 0.6777 (mm-30) REVERT: A 341 MET cc_start: 0.8210 (mmt) cc_final: 0.7997 (mmt) REVERT: A 393 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7746 (ttp80) REVERT: A 470 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8038 (pp) REVERT: A 487 MET cc_start: 0.8787 (mtm) cc_final: 0.8575 (mtp) REVERT: A 715 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8011 (pp20) REVERT: A 740 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 849 MET cc_start: 0.8519 (ttm) cc_final: 0.8257 (ttm) REVERT: A 939 ASP cc_start: 0.7565 (m-30) cc_final: 0.7201 (t0) REVERT: A 1013 ASP cc_start: 0.8680 (t0) cc_final: 0.8122 (t0) REVERT: A 1276 VAL cc_start: 0.8966 (t) cc_final: 0.8644 (t) REVERT: A 1400 CYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 1420 ASP cc_start: 0.8240 (t0) cc_final: 0.7963 (t0) REVERT: A 1444 MET cc_start: 0.7787 (mpp) cc_final: 0.7424 (mtm) REVERT: B 310 MET cc_start: 0.8709 (mtp) cc_final: 0.8179 (mtt) REVERT: B 380 TYR cc_start: 0.7918 (t80) cc_final: 0.7188 (t80) REVERT: B 549 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (m) REVERT: B 563 MET cc_start: 0.7997 (tmm) cc_final: 0.7664 (tmm) REVERT: B 627 PHE cc_start: 0.8816 (m-80) cc_final: 0.8401 (m-80) REVERT: B 637 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8644 (pp) REVERT: B 948 ILE cc_start: 0.9080 (mp) cc_final: 0.8670 (tt) REVERT: B 1162 ILE cc_start: 0.8085 (mm) cc_final: 0.7869 (tt) REVERT: B 1169 MET cc_start: 0.8427 (mtm) cc_final: 0.8132 (mmm) REVERT: C 61 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 249 ASP cc_start: 0.7892 (t0) cc_final: 0.7635 (t0) REVERT: D 1 MET cc_start: 0.0948 (pmm) cc_final: 0.0732 (ttp) REVERT: E 74 ASP cc_start: 0.8366 (m-30) cc_final: 0.7871 (p0) REVERT: E 150 VAL cc_start: 0.9575 (t) cc_final: 0.9353 (m) REVERT: H 97 MET cc_start: 0.8039 (mtp) cc_final: 0.7669 (mtm) REVERT: H 105 GLU cc_start: 0.7749 (tt0) cc_final: 0.7114 (tm-30) REVERT: I 1 MET cc_start: 0.4744 (tpp) cc_final: 0.3761 (mtm) REVERT: J 24 LEU cc_start: 0.9238 (mt) cc_final: 0.9006 (mp) REVERT: J 49 MET cc_start: 0.8585 (tpp) cc_final: 0.8020 (tpp) REVERT: K 24 ASP cc_start: 0.7169 (t0) cc_final: 0.6932 (t0) REVERT: K 64 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7927 (mt-10) outliers start: 63 outliers final: 42 residues processed: 306 average time/residue: 0.1953 time to fit residues: 99.7839 Evaluate side-chains 298 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 31 optimal weight: 7.9990 chunk 267 optimal weight: 0.0980 chunk 250 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 325 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 349 optimal weight: 0.0770 chunk 374 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095537 restraints weight = 83874.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098559 restraints weight = 43596.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098749 restraints weight = 24670.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098901 restraints weight = 20454.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099144 restraints weight = 20526.268| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.036 33052 Z= 0.462 Angle : 0.596 24.040 44850 Z= 0.310 Chirality : 0.044 0.708 5042 Planarity : 0.004 0.057 5621 Dihedral : 11.628 133.543 4863 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 1.76 % Allowed : 11.42 % Favored : 86.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 3878 helix: 1.35 (0.15), residues: 1310 sheet: -0.51 (0.22), residues: 543 loop : -0.87 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 961 TYR 0.015 0.001 TYR E 187 PHE 0.074 0.002 PHE D 70 TRP 0.009 0.001 TRP B 308 HIS 0.020 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01219 / 0.46 (33020) covalent geometry : angle 0.57779 / 0.31 (44805) hydrogen bonds : bond 0.03873 / 2.64 ( 1310) hydrogen bonds : angle 4.69290 / 3.35 ( 3627) metal coordination : bond 0.00671 / 0.48 ( 32) metal coordination : angle 4.70115 / 3.19 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.5776 (t80) REVERT: A 129 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7207 (tptp) REVERT: A 146 MET cc_start: 0.6483 (mmt) cc_final: 0.5954 (mmm) REVERT: A 291 GLU cc_start: 0.7384 (tt0) cc_final: 0.6795 (mm-30) REVERT: A 393 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7762 (ttp80) REVERT: A 470 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 474 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9204 (p) REVERT: A 715 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7996 (pp20) REVERT: A 740 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8363 (pp) REVERT: A 939 ASP cc_start: 0.7521 (m-30) cc_final: 0.7158 (t0) REVERT: A 1013 ASP cc_start: 0.8656 (t0) cc_final: 0.8076 (t0) REVERT: A 1063 MET cc_start: 0.7789 (tpp) cc_final: 0.7570 (mmm) REVERT: A 1239 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7147 (mtm180) REVERT: A 1400 CYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 1420 ASP cc_start: 0.8200 (t0) cc_final: 0.7941 (t0) REVERT: A 1444 MET cc_start: 0.7749 (mpp) cc_final: 0.7386 (mtm) REVERT: B 310 MET cc_start: 0.8678 (mtp) cc_final: 0.8243 (mtt) REVERT: B 563 MET cc_start: 0.8031 (tmm) cc_final: 0.7716 (tmm) REVERT: B 627 PHE cc_start: 0.8777 (m-80) cc_final: 0.8363 (m-80) REVERT: B 637 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8606 (pp) REVERT: B 891 ASP cc_start: 0.6297 (m-30) cc_final: 0.5423 (t0) REVERT: B 948 ILE cc_start: 0.9086 (mp) cc_final: 0.8740 (tt) REVERT: B 1162 ILE cc_start: 0.8082 (mm) cc_final: 0.7873 (tt) REVERT: B 1169 MET cc_start: 0.8328 (mtm) cc_final: 0.8044 (mmm) REVERT: C 61 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 249 ASP cc_start: 0.7832 (t0) cc_final: 0.7577 (t0) REVERT: E 74 ASP cc_start: 0.8315 (m-30) cc_final: 0.7913 (p0) REVERT: E 150 VAL cc_start: 0.9544 (t) cc_final: 0.9312 (m) REVERT: G 18 PHE cc_start: 0.8659 (m-80) cc_final: 0.8305 (m-80) REVERT: H 97 MET cc_start: 0.7979 (mtp) cc_final: 0.7600 (mtm) REVERT: H 105 GLU cc_start: 0.7713 (tt0) cc_final: 0.7114 (tm-30) REVERT: I 1 MET cc_start: 0.4713 (tpp) cc_final: 0.3738 (mtm) REVERT: J 24 LEU cc_start: 0.9225 (mt) cc_final: 0.8916 (mp) REVERT: J 49 MET cc_start: 0.8548 (tpp) cc_final: 0.8088 (tpp) REVERT: K 24 ASP cc_start: 0.7048 (t0) cc_final: 0.6815 (t0) REVERT: K 64 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7830 (mt-10) REVERT: L 53 HIS cc_start: 0.5879 (OUTLIER) cc_final: 0.5663 (m-70) outliers start: 61 outliers final: 38 residues processed: 311 average time/residue: 0.1893 time to fit residues: 98.1014 Evaluate side-chains 298 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 241 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096506 restraints weight = 83796.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099531 restraints weight = 43307.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099719 restraints weight = 24685.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099823 restraints weight = 20040.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100025 restraints weight = 19837.392| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.036 33052 Z= 0.455 Angle : 0.576 24.037 44850 Z= 0.301 Chirality : 0.043 0.706 5042 Planarity : 0.004 0.055 5621 Dihedral : 11.568 133.575 4863 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 1.71 % Allowed : 11.68 % Favored : 86.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3878 helix: 1.45 (0.15), residues: 1311 sheet: -0.35 (0.22), residues: 542 loop : -0.82 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 896 TYR 0.014 0.001 TYR E 187 PHE 0.074 0.001 PHE D 70 TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01203 / 0.45 (33020) covalent geometry : angle 0.56086 / 0.30 (44805) hydrogen bonds : bond 0.03674 / 2.51 ( 1310) hydrogen bonds : angle 4.54746 / 3.25 ( 3627) metal coordination : bond 0.00593 / 0.42 ( 32) metal coordination : angle 4.16972 / 2.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7528 (mtpt) cc_final: 0.7221 (tptp) REVERT: A 146 MET cc_start: 0.6562 (mmt) cc_final: 0.6026 (mmm) REVERT: A 262 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5997 (tt) REVERT: A 291 GLU cc_start: 0.7390 (tt0) cc_final: 0.6781 (mm-30) REVERT: A 341 MET cc_start: 0.8196 (mmt) cc_final: 0.7959 (mmt) REVERT: A 393 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7790 (ttp80) REVERT: A 470 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.7981 (pp) REVERT: A 474 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9192 (p) REVERT: A 715 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7976 (pp20) REVERT: A 939 ASP cc_start: 0.7503 (m-30) cc_final: 0.7135 (t0) REVERT: A 1013 ASP cc_start: 0.8664 (t0) cc_final: 0.7988 (t0) REVERT: A 1239 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7196 (mtm180) REVERT: A 1351 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 1444 MET cc_start: 0.7595 (mpp) cc_final: 0.7349 (mtm) REVERT: B 310 MET cc_start: 0.8630 (mtp) cc_final: 0.8225 (mtt) REVERT: B 563 MET cc_start: 0.8043 (tmm) cc_final: 0.7732 (tmm) REVERT: B 603 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8745 (tp) REVERT: B 627 PHE cc_start: 0.8732 (m-80) cc_final: 0.8334 (m-80) REVERT: B 637 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 891 ASP cc_start: 0.6229 (m-30) cc_final: 0.5361 (t0) REVERT: B 948 ILE cc_start: 0.9086 (mp) cc_final: 0.8742 (tt) REVERT: B 956 THR cc_start: 0.8515 (p) cc_final: 0.8302 (t) REVERT: B 1162 ILE cc_start: 0.8022 (mm) cc_final: 0.7813 (tt) REVERT: B 1169 MET cc_start: 0.8322 (mtm) cc_final: 0.8050 (mmm) REVERT: C 61 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 249 ASP cc_start: 0.7816 (t0) cc_final: 0.7567 (t0) REVERT: E 74 ASP cc_start: 0.8262 (m-30) cc_final: 0.7914 (p0) REVERT: E 150 VAL cc_start: 0.9521 (t) cc_final: 0.9288 (m) REVERT: G 18 PHE cc_start: 0.8609 (m-80) cc_final: 0.8259 (m-80) REVERT: H 97 MET cc_start: 0.7919 (mtp) cc_final: 0.7609 (mtm) REVERT: H 105 GLU cc_start: 0.7656 (tt0) cc_final: 0.7074 (tm-30) REVERT: I 1 MET cc_start: 0.4712 (tpp) cc_final: 0.3737 (mtm) REVERT: J 24 LEU cc_start: 0.9221 (mt) cc_final: 0.8906 (mp) REVERT: J 49 MET cc_start: 0.8521 (tpp) cc_final: 0.8089 (tpp) REVERT: K 24 ASP cc_start: 0.7033 (t0) cc_final: 0.6817 (t0) REVERT: L 53 HIS cc_start: 0.5732 (OUTLIER) cc_final: 0.5485 (m-70) outliers start: 59 outliers final: 40 residues processed: 316 average time/residue: 0.1838 time to fit residues: 97.2874 Evaluate side-chains 304 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 313 optimal weight: 3.9990 chunk 377 optimal weight: 7.9990 chunk 267 optimal weight: 0.4980 chunk 286 optimal weight: 10.0000 chunk 357 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN C 188 HIS I 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.126902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094590 restraints weight = 83739.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097563 restraints weight = 43901.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097623 restraints weight = 24824.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097907 restraints weight = 20932.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098041 restraints weight = 20585.127| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.035 33052 Z= 0.494 Angle : 0.655 24.072 44850 Z= 0.337 Chirality : 0.045 0.726 5042 Planarity : 0.004 0.055 5621 Dihedral : 11.648 135.105 4863 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.00 % Allowed : 12.09 % Favored : 85.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 3878 helix: 1.33 (0.15), residues: 1305 sheet: -0.45 (0.22), residues: 536 loop : -0.89 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1422 TYR 0.011 0.001 TYR J 44 PHE 0.074 0.002 PHE D 70 TRP 0.008 0.001 TRP B 31 HIS 0.042 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01286 / 0.49 (33020) covalent geometry : angle 0.63747 / 0.34 (44805) hydrogen bonds : bond 0.04027 / 2.74 ( 1310) hydrogen bonds : angle 4.69609 / 3.35 ( 3627) metal coordination : bond 0.00788 / 0.55 ( 32) metal coordination : angle 4.73430 / 3.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7253 (tptp) REVERT: A 146 MET cc_start: 0.6741 (mmt) cc_final: 0.6174 (mmm) REVERT: A 262 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5895 (tt) REVERT: A 291 GLU cc_start: 0.7456 (tt0) cc_final: 0.6832 (mm-30) REVERT: A 341 MET cc_start: 0.8221 (mmt) cc_final: 0.7976 (mmt) REVERT: A 393 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7765 (ttp80) REVERT: A 470 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8013 (pp) REVERT: A 474 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9262 (p) REVERT: A 715 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8035 (pp20) REVERT: A 740 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8374 (pp) REVERT: A 939 ASP cc_start: 0.7474 (m-30) cc_final: 0.7153 (t0) REVERT: A 1013 ASP cc_start: 0.8663 (t0) cc_final: 0.8068 (t0) REVERT: A 1220 PHE cc_start: 0.7632 (m-10) cc_final: 0.7138 (t80) REVERT: A 1239 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7104 (mtm180) REVERT: A 1400 CYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 1444 MET cc_start: 0.7637 (mpp) cc_final: 0.7429 (mtm) REVERT: B 310 MET cc_start: 0.8694 (mtp) cc_final: 0.8308 (mtt) REVERT: B 563 MET cc_start: 0.8033 (tmm) cc_final: 0.7718 (tmm) REVERT: B 603 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8733 (tp) REVERT: B 637 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8650 (pp) REVERT: B 891 ASP cc_start: 0.6077 (m-30) cc_final: 0.5071 (t0) REVERT: B 948 ILE cc_start: 0.9109 (mp) cc_final: 0.8756 (tt) REVERT: B 956 THR cc_start: 0.8534 (p) cc_final: 0.8316 (t) REVERT: B 1162 ILE cc_start: 0.8085 (mm) cc_final: 0.7838 (tt) REVERT: B 1169 MET cc_start: 0.8347 (mtm) cc_final: 0.8048 (mmm) REVERT: C 61 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 249 ASP cc_start: 0.7859 (t0) cc_final: 0.7583 (t0) REVERT: D 117 GLU cc_start: 0.5789 (mt-10) cc_final: 0.5567 (mp0) REVERT: E 150 VAL cc_start: 0.9550 (t) cc_final: 0.9316 (m) REVERT: F 85 MET cc_start: 0.8647 (tmm) cc_final: 0.8362 (ttt) REVERT: G 18 PHE cc_start: 0.8641 (m-80) cc_final: 0.8255 (m-80) REVERT: H 97 MET cc_start: 0.8016 (mtp) cc_final: 0.7647 (mtm) REVERT: H 105 GLU cc_start: 0.7697 (tt0) cc_final: 0.7111 (tm-30) REVERT: I 1 MET cc_start: 0.4746 (tpp) cc_final: 0.3720 (mtm) REVERT: J 49 MET cc_start: 0.8566 (tpp) cc_final: 0.8114 (tpp) REVERT: K 24 ASP cc_start: 0.7159 (t0) cc_final: 0.6931 (t0) outliers start: 69 outliers final: 49 residues processed: 303 average time/residue: 0.1886 time to fit residues: 96.1089 Evaluate side-chains 308 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 747 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 47 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 325 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 295 optimal weight: 0.1980 chunk 365 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS C 188 HIS ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096488 restraints weight = 83293.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099490 restraints weight = 43385.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099534 restraints weight = 24732.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099837 restraints weight = 20943.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099966 restraints weight = 20041.057| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.035 33052 Z= 0.454 Angle : 0.582 24.015 44850 Z= 0.304 Chirality : 0.043 0.709 5042 Planarity : 0.004 0.055 5621 Dihedral : 11.576 133.423 4863 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 1.36 % Allowed : 12.67 % Favored : 85.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3878 helix: 1.51 (0.15), residues: 1305 sheet: -0.30 (0.22), residues: 537 loop : -0.80 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1422 TYR 0.012 0.001 TYR B 830 PHE 0.074 0.002 PHE D 70 TRP 0.009 0.001 TRP A 556 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01202 / 0.45 (33020) covalent geometry : angle 0.56832 / 0.30 (44805) hydrogen bonds : bond 0.03598 / 2.46 ( 1310) hydrogen bonds : angle 4.49781 / 3.22 ( 3627) metal coordination : bond 0.00572 / 0.41 ( 32) metal coordination : angle 4.02015 / 2.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7235 (tptp) REVERT: A 146 MET cc_start: 0.6748 (mmt) cc_final: 0.6232 (mmm) REVERT: A 291 GLU cc_start: 0.7415 (tt0) cc_final: 0.6832 (mm-30) REVERT: A 341 MET cc_start: 0.8153 (mmt) cc_final: 0.7876 (mmt) REVERT: A 393 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7804 (ttp80) REVERT: A 470 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8119 (pp) REVERT: A 474 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9206 (p) REVERT: A 715 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7979 (pp20) REVERT: A 740 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 873 MET cc_start: 0.8484 (mmt) cc_final: 0.8200 (mmp) REVERT: A 939 ASP cc_start: 0.7519 (m-30) cc_final: 0.7146 (t0) REVERT: A 1013 ASP cc_start: 0.8652 (t0) cc_final: 0.7997 (t0) REVERT: A 1063 MET cc_start: 0.7878 (tpp) cc_final: 0.7560 (mmm) REVERT: A 1111 MET cc_start: 0.7892 (pmm) cc_final: 0.7638 (pmm) REVERT: A 1139 GLU cc_start: 0.7347 (tt0) cc_final: 0.6875 (mt-10) REVERT: A 1351 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 1400 CYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 1444 MET cc_start: 0.7615 (mpp) cc_final: 0.7184 (mtm) REVERT: A 1454 MET cc_start: 0.6040 (tmm) cc_final: 0.5801 (tmm) REVERT: B 310 MET cc_start: 0.8630 (mtp) cc_final: 0.8178 (mtt) REVERT: B 563 MET cc_start: 0.8047 (tmm) cc_final: 0.7726 (tmm) REVERT: B 603 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 891 ASP cc_start: 0.6147 (m-30) cc_final: 0.5145 (t0) REVERT: B 948 ILE cc_start: 0.9085 (mp) cc_final: 0.8739 (tt) REVERT: B 956 THR cc_start: 0.8507 (p) cc_final: 0.8282 (t) REVERT: B 1162 ILE cc_start: 0.8014 (mm) cc_final: 0.7630 (tt) REVERT: C 61 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 249 ASP cc_start: 0.7857 (t0) cc_final: 0.7580 (t0) REVERT: E 150 VAL cc_start: 0.9539 (t) cc_final: 0.9299 (m) REVERT: F 85 MET cc_start: 0.8676 (tmm) cc_final: 0.8441 (ttt) REVERT: G 18 PHE cc_start: 0.8562 (m-80) cc_final: 0.8093 (m-80) REVERT: G 22 MET cc_start: 0.6020 (ppp) cc_final: 0.5307 (ppp) REVERT: H 97 MET cc_start: 0.7917 (mtp) cc_final: 0.7585 (mtm) REVERT: H 105 GLU cc_start: 0.7691 (tt0) cc_final: 0.7036 (tm-30) REVERT: I 1 MET cc_start: 0.4783 (tpp) cc_final: 0.3764 (mtm) REVERT: J 24 LEU cc_start: 0.9249 (mt) cc_final: 0.8900 (mp) REVERT: L 53 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5343 (m-70) outliers start: 47 outliers final: 35 residues processed: 307 average time/residue: 0.2008 time to fit residues: 102.6389 Evaluate side-chains 302 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 83 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 369 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.128728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095238 restraints weight = 85424.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098225 restraints weight = 44307.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098526 restraints weight = 25732.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098536 restraints weight = 20090.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098830 restraints weight = 21257.919| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.035 33052 Z= 0.460 Angle : 0.596 24.033 44850 Z= 0.309 Chirality : 0.044 0.715 5042 Planarity : 0.004 0.053 5621 Dihedral : 11.564 134.437 4863 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 1.33 % Allowed : 13.13 % Favored : 85.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3878 helix: 1.48 (0.15), residues: 1312 sheet: -0.33 (0.22), residues: 551 loop : -0.80 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 48 TYR 0.011 0.001 TYR E 187 PHE 0.074 0.001 PHE D 70 TRP 0.011 0.001 TRP A 185 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.46 (33020) covalent geometry : angle 0.58367 / 0.31 (44805) hydrogen bonds : bond 0.03617 / 2.46 ( 1310) hydrogen bonds : angle 4.47413 / 3.20 ( 3627) metal coordination : bond 0.00611 / 0.43 ( 32) metal coordination : angle 3.88373 / 2.59 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7626 (mtpt) cc_final: 0.7218 (tptp) REVERT: A 146 MET cc_start: 0.6697 (mmt) cc_final: 0.6197 (mmm) REVERT: A 262 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5991 (tt) REVERT: A 291 GLU cc_start: 0.7413 (tt0) cc_final: 0.6815 (mm-30) REVERT: A 341 MET cc_start: 0.8161 (mmt) cc_final: 0.7866 (mmt) REVERT: A 393 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7766 (ttp80) REVERT: A 470 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8149 (pp) REVERT: A 474 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9231 (p) REVERT: A 715 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7984 (pp20) REVERT: A 740 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8386 (pp) REVERT: A 939 ASP cc_start: 0.7517 (m-30) cc_final: 0.7168 (t0) REVERT: A 1013 ASP cc_start: 0.8637 (t0) cc_final: 0.7974 (t0) REVERT: A 1139 GLU cc_start: 0.7341 (tt0) cc_final: 0.6869 (mt-10) REVERT: A 1220 PHE cc_start: 0.7654 (m-10) cc_final: 0.7120 (t80) REVERT: A 1280 GLU cc_start: 0.8240 (pm20) cc_final: 0.8007 (pm20) REVERT: A 1351 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8330 (mm-30) REVERT: A 1400 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 1444 MET cc_start: 0.7604 (mpp) cc_final: 0.7375 (mtm) REVERT: A 1454 MET cc_start: 0.6075 (tmm) cc_final: 0.5829 (tmm) REVERT: B 310 MET cc_start: 0.8639 (mtp) cc_final: 0.8191 (mtt) REVERT: B 563 MET cc_start: 0.8036 (tmm) cc_final: 0.7713 (tmm) REVERT: B 603 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8734 (tp) REVERT: B 891 ASP cc_start: 0.6092 (m-30) cc_final: 0.5066 (t0) REVERT: B 948 ILE cc_start: 0.9099 (mp) cc_final: 0.8753 (tt) REVERT: B 956 THR cc_start: 0.8505 (p) cc_final: 0.8274 (t) REVERT: B 1162 ILE cc_start: 0.7980 (mm) cc_final: 0.7553 (tt) REVERT: C 61 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 249 ASP cc_start: 0.7848 (t0) cc_final: 0.7575 (t0) REVERT: D 117 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5778 (mp0) REVERT: E 150 VAL cc_start: 0.9541 (t) cc_final: 0.9299 (m) REVERT: F 85 MET cc_start: 0.8722 (tmm) cc_final: 0.8504 (ttt) REVERT: G 18 PHE cc_start: 0.8494 (m-80) cc_final: 0.8043 (m-80) REVERT: G 22 MET cc_start: 0.5829 (ppp) cc_final: 0.5142 (ppp) REVERT: H 97 MET cc_start: 0.7984 (mtp) cc_final: 0.7662 (mtm) REVERT: H 105 GLU cc_start: 0.7752 (tt0) cc_final: 0.7126 (tm-30) REVERT: I 1 MET cc_start: 0.4675 (tpp) cc_final: 0.3634 (mtm) REVERT: J 24 LEU cc_start: 0.9306 (mt) cc_final: 0.8960 (mp) REVERT: L 56 LEU cc_start: 0.8288 (mm) cc_final: 0.7848 (pp) outliers start: 46 outliers final: 38 residues processed: 293 average time/residue: 0.1778 time to fit residues: 87.6303 Evaluate side-chains 302 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 115 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 199 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 328 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096316 restraints weight = 83617.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099222 restraints weight = 43653.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099386 restraints weight = 24955.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099616 restraints weight = 20754.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099751 restraints weight = 20606.002| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.035 33052 Z= 0.456 Angle : 0.588 24.028 44850 Z= 0.305 Chirality : 0.043 0.713 5042 Planarity : 0.004 0.053 5621 Dihedral : 11.544 134.423 4863 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.24 % Allowed : 13.33 % Favored : 85.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3878 helix: 1.54 (0.15), residues: 1307 sheet: -0.32 (0.22), residues: 547 loop : -0.74 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1422 TYR 0.011 0.001 TYR F 84 PHE 0.074 0.001 PHE D 70 TRP 0.009 0.001 TRP B 31 HIS 0.009 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01206 / 0.46 (33020) covalent geometry : angle 0.57672 / 0.30 (44805) hydrogen bonds : bond 0.03572 / 2.44 ( 1310) hydrogen bonds : angle 4.43624 / 3.18 ( 3627) metal coordination : bond 0.00561 / 0.40 ( 32) metal coordination : angle 3.70568 / 2.41 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.04 seconds wall clock time: 88 minutes 39.05 seconds (5319.05 seconds total)