Starting phenix.real_space_refine on Thu May 29 19:33:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.map" model { file = "/net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xso_38624/05_2025/8xso_38624.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 73 5.49 5 Mg 1 5.21 5 S 197 5.16 5 C 20300 2.51 5 N 5701 2.21 5 O 6241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32521 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11254 Classifications: {'peptide': 1420} Link IDs: {'PTRANS': 69, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1337 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 511 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 758 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} 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 464 SG CYS A 71 106.623 38.887 71.598 1.00 96.97 S ATOM 486 SG CYS A 74 108.203 41.248 69.586 1.00 97.05 S ATOM 533 SG CYS A 81 105.488 42.377 71.676 1.00 83.39 S ATOM 768 SG CYS A 111 71.690 43.848 36.449 1.00137.47 S ATOM 796 SG CYS A 114 73.977 41.963 34.673 1.00139.32 S ATOM 1142 SG CYS A 184 70.269 41.309 34.432 1.00155.92 S ATOM 19886 SG CYS B1119 106.284 47.226 54.403 1.00 95.65 S ATOM 19908 SG CYS B1122 102.567 46.696 55.184 1.00 96.78 S ATOM 20023 SG CYS B1137 105.148 44.014 55.858 1.00109.34 S ATOM 20044 SG CYS B1140 104.008 44.805 52.308 1.00113.68 S ATOM 21011 SG CYS C 88 123.004 73.833 129.126 1.00106.80 S ATOM 21024 SG CYS C 90 122.820 70.492 129.223 1.00114.65 S ATOM 21059 SG CYS C 94 122.050 71.606 132.345 1.00 97.53 S ATOM 21081 SG CYS C 97 119.833 72.918 129.831 1.00 94.53 S ATOM 28301 SG CYS I 17 13.588 58.159 67.822 1.00152.65 S ATOM 28325 SG CYS I 20 16.345 55.153 68.587 1.00151.45 S ATOM 28486 SG CYS I 39 17.641 57.551 65.951 1.00160.78 S ATOM 28511 SG CYS I 42 14.667 55.861 65.163 1.00160.04 S ATOM 28863 SG CYS I 86 21.356 92.828 95.294 1.00135.44 S ATOM 28887 SG CYS I 89 19.984 92.421 98.304 1.00138.44 S ATOM 29091 SG CYS I 114 23.549 91.060 97.767 1.00124.29 S ATOM 29126 SG CYS I 119 20.293 89.605 96.667 1.00135.05 S ATOM 29236 SG CYS J 7 91.028 86.959 125.512 1.00 42.62 S ATOM 29260 SG CYS J 10 93.358 89.445 126.951 1.00 46.04 S ATOM 29524 SG CYS J 44 90.129 90.586 125.289 1.00 48.64 S ATOM 29530 SG CYS J 45 90.276 89.133 128.465 1.00 49.38 S ATOM 30676 SG CYS L 19 85.537 42.549 127.085 1.00119.56 S ATOM 30695 SG CYS L 22 84.852 42.464 130.516 1.00125.07 S ATOM 30812 SG CYS L 36 86.654 39.436 128.539 1.00125.45 S ATOM 30838 SG CYS L 39 83.275 40.137 128.636 1.00131.23 S Time building chain proxies: 17.48, per 1000 atoms: 0.54 Number of scatterers: 32521 At special positions: 0 Unit cell: (161.12, 155.82, 156.88, 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 197 16.00 P 73 15.00 Mg 1 11.99 O 6241 8.00 N 5701 7.00 C 20300 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: 8.70 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 39 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7314 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 48 sheets defined 39.2% alpha, 19.2% beta 32 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 11.28 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.833A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.635A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.520A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.752A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.576A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.853A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.154A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 611 through 616' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.631A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.737A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.511A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.511A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.802A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.251A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 3.595A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.296A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.062A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.939A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.594A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.133A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.644A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.025A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.550A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.967A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.623A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.656A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.626A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1470 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.674A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1483' Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.703A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.739A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.797A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.008A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.579A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.501A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.839A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.536A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.687A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.055A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.680A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.897A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 124 through 128 removed outlier: 4.132A pdb=" N VAL C 127 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE C 128 " --> pdb=" O PRO C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 128' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.715A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.947A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.111A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.978A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.029A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.670A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.021A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.666A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.648A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.977A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.784A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.888A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.748A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.580A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.158A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.158A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.495A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.185A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.541A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.684A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.274A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.654A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.654A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS L 46 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.000A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD7, first strand: chain 'B' and resid 865 through 867 removed outlier: 4.056A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 894 " --> pdb=" O ILE B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.712A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.759A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.759A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.677A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.556A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE6, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE7, first strand: chain 'G' and resid 84 through 93 removed outlier: 5.577A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.805A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.572A pdb=" N TYR I 25 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.840A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 17.54 Time building geometry restraints manager: 10.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8450 1.33 - 1.46: 6755 1.46 - 1.58: 17620 1.58 - 1.70: 142 1.70 - 1.83: 312 Bond restraints: 33279 Sorted by residual: bond pdb=" CA GLN A 461 " pdb=" C GLN A 461 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.26e-02 6.30e+03 2.05e+01 bond pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.58e-02 4.01e+03 1.98e+01 bond pdb=" CB THR A 511 " pdb=" OG1 THR A 511 " ideal model delta sigma weight residual 1.433 1.372 0.061 1.60e-02 3.91e+03 1.43e+01 bond pdb=" N PRO J 64 " pdb=" CD PRO J 64 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" CZ ARG B 591 " pdb=" NH2 ARG B 591 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 ... (remaining 33274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 39941 1.99 - 3.97: 4569 3.97 - 5.96: 691 5.96 - 7.94: 62 7.94 - 9.93: 5 Bond angle restraints: 45268 Sorted by residual: angle pdb=" C ALA A 75 " pdb=" N GLY A 76 " pdb=" CA GLY A 76 " ideal model delta sigma weight residual 119.92 127.01 -7.09 9.60e-01 1.09e+00 5.45e+01 angle pdb=" C MET A 520 " pdb=" N VAL A 521 " pdb=" CA VAL A 521 " ideal model delta sigma weight residual 120.33 125.52 -5.19 8.00e-01 1.56e+00 4.22e+01 angle pdb=" C GLY B1065 " pdb=" N PRO B1066 " pdb=" CA PRO B1066 " ideal model delta sigma weight residual 119.78 126.25 -6.47 1.03e+00 9.43e-01 3.94e+01 angle pdb=" N GLN A 461 " pdb=" CA GLN A 461 " pdb=" C GLN A 461 " ideal model delta sigma weight residual 113.16 121.67 -8.51 1.42e+00 4.96e-01 3.59e+01 angle pdb=" N PRO E 53 " pdb=" CA PRO E 53 " pdb=" CB PRO E 53 " ideal model delta sigma weight residual 102.65 106.65 -4.00 6.80e-01 2.16e+00 3.46e+01 ... (remaining 45263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 19714 35.19 - 70.38: 502 70.38 - 105.56: 29 105.56 - 140.75: 1 140.75 - 175.94: 2 Dihedral angle restraints: 20248 sinusoidal: 8940 harmonic: 11308 Sorted by residual: dihedral pdb=" CA ASP H 80 " pdb=" C ASP H 80 " pdb=" N ARG H 81 " pdb=" CA ARG H 81 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PRO E 53 " pdb=" C PRO E 53 " pdb=" N ARG E 54 " pdb=" CA ARG E 54 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 20245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4492 0.114 - 0.227: 508 0.227 - 0.341: 55 0.341 - 0.454: 10 0.454 - 0.568: 3 Chirality restraints: 5068 Sorted by residual: chirality pdb=" P A P 1 " pdb=" OP1 A P 1 " pdb=" OP2 A P 1 " pdb=" O5' A P 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" CA GLN A 461 " pdb=" N GLN A 461 " pdb=" C GLN A 461 " pdb=" CB GLN A 461 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" P DA T 7 " pdb=" OP1 DA T 7 " pdb=" OP2 DA T 7 " pdb=" O5' DA T 7 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 5065 not shown) Planarity restraints: 5617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 49 " 0.133 2.00e-02 2.50e+03 6.69e-02 1.12e+02 pdb=" CG TRP C 49 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 49 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 49 " -0.077 2.00e-02 2.50e+03 pdb=" NE1 TRP C 49 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP C 49 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP C 49 " -0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 49 " 0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 49 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 49 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 81 " 0.115 2.00e-02 2.50e+03 6.90e-02 9.51e+01 pdb=" CG TYR K 81 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR K 81 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR K 81 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR K 81 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR K 81 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR K 81 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR K 81 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 25 " 0.120 2.00e-02 2.50e+03 6.38e-02 8.14e+01 pdb=" CG TYR I 25 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR I 25 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR I 25 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR I 25 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR I 25 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR I 25 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 25 " 0.094 2.00e-02 2.50e+03 ... (remaining 5614 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 14 2.40 - 3.03: 17213 3.03 - 3.65: 46839 3.65 - 4.28: 73599 4.28 - 4.90: 121989 Nonbonded interactions: 259654 Sorted by model distance: nonbonded pdb=" OP1 U P 11 " pdb="MG MG A2003 " model vdw 1.775 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.182 2.170 nonbonded pdb=" OG SER B 31 " pdb=" OH TYR B 766 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.269 3.040 ... (remaining 259649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.040 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 87.640 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.010 0.511 33310 Z= 0.536 Angle : 1.304 19.921 45307 Z= 0.837 Chirality : 0.074 0.568 5068 Planarity : 0.011 0.133 5617 Dihedral : 14.525 175.938 12934 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3848 helix: 0.75 (0.14), residues: 1352 sheet: 0.13 (0.21), residues: 542 loop : -0.42 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.013 TRP C 49 HIS 0.032 0.002 HIS H 133 PHE 0.100 0.007 PHE C 229 TYR 0.120 0.007 TYR I 25 ARG 0.013 0.001 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.15352 ( 1407) hydrogen bonds : angle 6.59255 ( 3932) metal coordination : bond 0.15878 ( 31) metal coordination : angle 9.30664 ( 39) covalent geometry : bond 0.00838 (33279) covalent geometry : angle 1.27538 (45268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.1149 (mmm) cc_final: 0.0895 (tpt) REVERT: A 535 MET cc_start: 0.8763 (mtm) cc_final: 0.8519 (mtt) REVERT: A 660 MET cc_start: 0.9254 (mmm) cc_final: 0.8933 (mmp) REVERT: A 1244 ASN cc_start: 0.8852 (t0) cc_final: 0.8363 (m-40) REVERT: A 1247 PHE cc_start: 0.8605 (p90) cc_final: 0.7914 (p90) REVERT: A 1262 MET cc_start: 0.7373 (ttt) cc_final: 0.7144 (ttm) REVERT: B 98 HIS cc_start: 0.6679 (m90) cc_final: 0.6305 (m170) REVERT: B 108 MET cc_start: 0.8924 (ttp) cc_final: 0.8522 (ttm) REVERT: B 239 MET cc_start: 0.8678 (ttm) cc_final: 0.8464 (ttm) REVERT: B 300 MET cc_start: 0.8746 (mtp) cc_final: 0.8466 (mtp) REVERT: B 494 LYS cc_start: 0.7658 (mptt) cc_final: 0.7364 (mttp) REVERT: B 1163 MET cc_start: 0.8885 (mtp) cc_final: 0.8558 (mtp) REVERT: C 83 GLN cc_start: 0.8021 (mt0) cc_final: 0.7708 (mt0) REVERT: E 49 SER cc_start: 0.8504 (t) cc_final: 0.8005 (p) REVERT: E 110 MET cc_start: 0.8641 (mtp) cc_final: 0.8396 (ttm) REVERT: F 80 MET cc_start: 0.8584 (mmm) cc_final: 0.8293 (mmm) REVERT: F 83 LEU cc_start: 0.8916 (pt) cc_final: 0.8492 (pp) REVERT: F 86 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7448 (mm-30) REVERT: G 10 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6967 (pm20) REVERT: H 92 MET cc_start: 0.8847 (mtm) cc_final: 0.8515 (mtm) REVERT: I 34 ILE cc_start: 0.7264 (tp) cc_final: 0.6876 (pp) REVERT: I 54 TYR cc_start: 0.8200 (t80) cc_final: 0.7814 (t80) REVERT: I 56 ASN cc_start: 0.8352 (t0) cc_final: 0.7603 (t0) REVERT: J 1 MET cc_start: 0.8596 (mpp) cc_final: 0.8261 (mpm) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 1.7549 time to fit residues: 778.2409 Evaluate side-chains 250 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 20.0000 chunk 294 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 185 optimal weight: 0.4980 chunk 226 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 301 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 83 GLN C 217 GLN C 260 GLN D 66 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 50 ASN K 69 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.108764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063755 restraints weight = 64462.192| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.69 r_work: 0.2795 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33310 Z= 0.188 Angle : 0.659 14.948 45307 Z= 0.342 Chirality : 0.046 0.190 5068 Planarity : 0.005 0.052 5617 Dihedral : 13.518 168.414 5092 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.96 % Allowed : 9.40 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3848 helix: 1.38 (0.14), residues: 1361 sheet: 0.15 (0.21), residues: 581 loop : -0.31 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 49 HIS 0.009 0.001 HIS A 301 PHE 0.023 0.002 PHE A 994 TYR 0.032 0.002 TYR G 3 ARG 0.010 0.001 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 1407) hydrogen bonds : angle 5.03813 ( 3932) metal coordination : bond 0.01064 ( 31) metal coordination : angle 5.31875 ( 39) covalent geometry : bond 0.00445 (33279) covalent geometry : angle 0.64020 (45268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: A 266 MET cc_start: 0.0286 (mmm) cc_final: -0.0458 (tpt) REVERT: A 1038 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 1221 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7894 (mmm) REVERT: A 1244 ASN cc_start: 0.8726 (t0) cc_final: 0.8130 (m-40) REVERT: A 1262 MET cc_start: 0.7584 (ttt) cc_final: 0.7322 (ttm) REVERT: A 1484 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.4732 (mtt) REVERT: B 108 MET cc_start: 0.9041 (ttp) cc_final: 0.8759 (ttm) REVERT: B 225 LEU cc_start: 0.7814 (tp) cc_final: 0.7597 (tp) REVERT: B 494 LYS cc_start: 0.7958 (mptt) cc_final: 0.7601 (pmtt) REVERT: B 650 ASN cc_start: 0.8480 (p0) cc_final: 0.8269 (p0) REVERT: B 927 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8757 (mtt90) REVERT: B 1163 MET cc_start: 0.9071 (mtp) cc_final: 0.8750 (mtp) REVERT: C 51 GLN cc_start: 0.9138 (tt0) cc_final: 0.8888 (tt0) REVERT: C 83 GLN cc_start: 0.8730 (mt0) cc_final: 0.8388 (mm110) REVERT: E 97 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: F 80 MET cc_start: 0.8335 (mmm) cc_final: 0.8002 (mmm) REVERT: F 83 LEU cc_start: 0.8699 (pt) cc_final: 0.8489 (pp) REVERT: F 86 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7847 (mm-30) REVERT: G 71 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7497 (mmpt) REVERT: G 104 MET cc_start: 0.0128 (OUTLIER) cc_final: -0.0566 (mpp) REVERT: G 164 MET cc_start: 0.4118 (mmp) cc_final: 0.3300 (pmm) REVERT: H 84 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7313 (ttp-110) REVERT: I 23 MET cc_start: 0.7519 (ppp) cc_final: 0.7095 (ttp) REVERT: I 34 ILE cc_start: 0.7128 (tp) cc_final: 0.6731 (pp) REVERT: I 35 LEU cc_start: 0.6594 (pt) cc_final: 0.6181 (tp) REVERT: I 54 TYR cc_start: 0.8207 (t80) cc_final: 0.7664 (t80) REVERT: I 56 ASN cc_start: 0.8502 (t0) cc_final: 0.7861 (t0) REVERT: I 58 ILE cc_start: 0.8524 (mt) cc_final: 0.8268 (mt) REVERT: J 1 MET cc_start: 0.8978 (mpp) cc_final: 0.8753 (mmp) REVERT: K 8 GLU cc_start: 0.8079 (mp0) cc_final: 0.7575 (mp0) REVERT: L 32 ASP cc_start: 0.5853 (m-30) cc_final: 0.5543 (m-30) outliers start: 67 outliers final: 12 residues processed: 309 average time/residue: 1.5675 time to fit residues: 568.6315 Evaluate side-chains 256 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 107 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 98 HIS B 500 GLN B 817 GLN B 968 ASN B1120 ASN I 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062688 restraints weight = 64785.209| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.93 r_work: 0.2774 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33310 Z= 0.170 Angle : 0.602 13.525 45307 Z= 0.314 Chirality : 0.045 0.185 5068 Planarity : 0.004 0.049 5617 Dihedral : 13.429 168.590 5092 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.60 % Allowed : 10.01 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3848 helix: 1.61 (0.14), residues: 1361 sheet: 0.16 (0.20), residues: 607 loop : -0.28 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 49 HIS 0.009 0.001 HIS A 301 PHE 0.021 0.002 PHE A 994 TYR 0.021 0.002 TYR G 3 ARG 0.011 0.001 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 1407) hydrogen bonds : angle 4.70812 ( 3932) metal coordination : bond 0.00737 ( 31) metal coordination : angle 4.40059 ( 39) covalent geometry : bond 0.00403 (33279) covalent geometry : angle 0.58868 (45268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 254 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: A 743 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7950 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8507 (t0) cc_final: 0.7925 (m-40) REVERT: B 108 MET cc_start: 0.9014 (ttp) cc_final: 0.8742 (ttp) REVERT: B 494 LYS cc_start: 0.7952 (mptt) cc_final: 0.7604 (pmtt) REVERT: B 581 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: B 817 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7609 (tp40) REVERT: B 927 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8757 (mtt90) REVERT: B 1163 MET cc_start: 0.9057 (mtp) cc_final: 0.8789 (mtp) REVERT: C 27 ASP cc_start: 0.8405 (t0) cc_final: 0.8182 (t0) REVERT: C 51 GLN cc_start: 0.9189 (tt0) cc_final: 0.8918 (tt0) REVERT: C 83 GLN cc_start: 0.8867 (mt0) cc_final: 0.8419 (mm110) REVERT: C 111 GLN cc_start: 0.8467 (pm20) cc_final: 0.8245 (pm20) REVERT: E 97 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: F 80 MET cc_start: 0.8436 (mmm) cc_final: 0.8235 (mmm) REVERT: F 86 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8081 (mm-30) REVERT: G 10 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6979 (pm20) REVERT: G 71 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7358 (mmpt) REVERT: G 104 MET cc_start: 0.0873 (OUTLIER) cc_final: 0.0093 (mpp) REVERT: G 117 MET cc_start: 0.3076 (mmm) cc_final: 0.2449 (ttt) REVERT: G 164 MET cc_start: 0.3720 (mmp) cc_final: 0.3273 (pmm) REVERT: H 107 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: I 15 ARG cc_start: 0.7352 (mpp80) cc_final: 0.7133 (mpp80) REVERT: I 25 TYR cc_start: 0.7912 (p90) cc_final: 0.7635 (p90) REVERT: I 34 ILE cc_start: 0.6988 (tp) cc_final: 0.6607 (pp) REVERT: I 35 LEU cc_start: 0.6534 (pt) cc_final: 0.6049 (tp) REVERT: I 54 TYR cc_start: 0.8067 (t80) cc_final: 0.7575 (t80) REVERT: I 56 ASN cc_start: 0.8562 (t0) cc_final: 0.7954 (t0) REVERT: I 122 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: J 57 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8776 (mm-30) REVERT: K 8 GLU cc_start: 0.7971 (mp0) cc_final: 0.7361 (mp0) REVERT: K 24 ASP cc_start: 0.8748 (t0) cc_final: 0.8336 (t0) REVERT: L 32 ASP cc_start: 0.5970 (m-30) cc_final: 0.5646 (m-30) outliers start: 89 outliers final: 30 residues processed: 317 average time/residue: 1.4913 time to fit residues: 563.3106 Evaluate side-chains 272 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain B residue 1125 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 113 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 274 optimal weight: 0.0870 chunk 241 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 336 optimal weight: 40.0000 chunk 362 optimal weight: 7.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A1082 HIS A1093 GLN A1236 ASN B 98 HIS B 731 GLN B 968 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.107021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062352 restraints weight = 64406.117| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.60 r_work: 0.2732 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33310 Z= 0.221 Angle : 0.624 14.799 45307 Z= 0.321 Chirality : 0.046 0.193 5068 Planarity : 0.004 0.046 5617 Dihedral : 13.383 168.801 5092 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.77 % Allowed : 10.69 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 3848 helix: 1.65 (0.14), residues: 1356 sheet: 0.13 (0.20), residues: 616 loop : -0.31 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.010 0.001 HIS A 301 PHE 0.021 0.002 PHE A 800 TYR 0.022 0.002 TYR G 72 ARG 0.013 0.001 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 1407) hydrogen bonds : angle 4.69873 ( 3932) metal coordination : bond 0.00824 ( 31) metal coordination : angle 4.91212 ( 39) covalent geometry : bond 0.00532 (33279) covalent geometry : angle 0.60790 (45268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 242 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: A 743 ARG cc_start: 0.8338 (tpp-160) cc_final: 0.8035 (tmm-80) REVERT: A 959 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: A 1221 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: A 1244 ASN cc_start: 0.8624 (t0) cc_final: 0.8009 (m-40) REVERT: B 108 MET cc_start: 0.9024 (ttp) cc_final: 0.8773 (ttp) REVERT: B 494 LYS cc_start: 0.8035 (mptt) cc_final: 0.7603 (pmtt) REVERT: B 927 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8837 (mtt90) REVERT: B 1163 MET cc_start: 0.9084 (mtp) cc_final: 0.8837 (mtp) REVERT: C 27 ASP cc_start: 0.8528 (t0) cc_final: 0.8278 (t0) REVERT: C 51 GLN cc_start: 0.9235 (tt0) cc_final: 0.8987 (tt0) REVERT: C 83 GLN cc_start: 0.8901 (mt0) cc_final: 0.8427 (mm110) REVERT: E 97 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: F 86 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8303 (mm-30) REVERT: G 10 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6992 (pm20) REVERT: G 71 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7457 (mmpt) REVERT: G 104 MET cc_start: 0.0427 (OUTLIER) cc_final: -0.0244 (mpp) REVERT: G 164 MET cc_start: 0.4048 (mmp) cc_final: 0.3325 (pmm) REVERT: H 84 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7573 (ttp-110) REVERT: I 15 ARG cc_start: 0.7351 (mpp80) cc_final: 0.6968 (mpp80) REVERT: I 25 TYR cc_start: 0.7831 (p90) cc_final: 0.7575 (p90) REVERT: I 34 ILE cc_start: 0.7031 (tp) cc_final: 0.6511 (pp) REVERT: I 35 LEU cc_start: 0.6610 (pt) cc_final: 0.6076 (tp) REVERT: I 54 TYR cc_start: 0.8160 (t80) cc_final: 0.7692 (t80) REVERT: I 56 ASN cc_start: 0.8569 (t0) cc_final: 0.7883 (t0) REVERT: I 122 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7889 (mtm-85) REVERT: J 26 GLN cc_start: 0.8987 (tt0) cc_final: 0.8586 (tm-30) REVERT: J 57 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8790 (mm-30) REVERT: K 16 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8125 (mt-10) REVERT: K 24 ASP cc_start: 0.8786 (t0) cc_final: 0.8368 (t0) REVERT: L 32 ASP cc_start: 0.5978 (m-30) cc_final: 0.5625 (m-30) outliers start: 95 outliers final: 41 residues processed: 306 average time/residue: 1.4351 time to fit residues: 524.1575 Evaluate side-chains 277 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 332 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 378 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.107604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062053 restraints weight = 64633.822| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.86 r_work: 0.2748 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33310 Z= 0.166 Angle : 0.582 14.190 45307 Z= 0.299 Chirality : 0.044 0.172 5068 Planarity : 0.004 0.046 5617 Dihedral : 13.264 167.937 5092 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 11.65 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 3848 helix: 1.75 (0.14), residues: 1357 sheet: 0.15 (0.20), residues: 608 loop : -0.31 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 49 HIS 0.012 0.001 HIS A 301 PHE 0.016 0.002 PHE A 800 TYR 0.023 0.001 TYR G 72 ARG 0.008 0.000 ARG L 37 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1407) hydrogen bonds : angle 4.58225 ( 3932) metal coordination : bond 0.00724 ( 31) metal coordination : angle 4.83525 ( 39) covalent geometry : bond 0.00395 (33279) covalent geometry : angle 0.56486 (45268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 243 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: A 743 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.8036 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8557 (t0) cc_final: 0.8041 (m-40) REVERT: B 108 MET cc_start: 0.9032 (ttp) cc_final: 0.8794 (ttp) REVERT: B 840 MET cc_start: 0.1738 (tmt) cc_final: 0.1212 (mmm) REVERT: B 927 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8724 (mtt90) REVERT: B 1163 MET cc_start: 0.9071 (mtp) cc_final: 0.8809 (mtp) REVERT: C 27 ASP cc_start: 0.8530 (t0) cc_final: 0.8282 (t0) REVERT: C 51 GLN cc_start: 0.9222 (tt0) cc_final: 0.8978 (tt0) REVERT: C 83 GLN cc_start: 0.8860 (mt0) cc_final: 0.8393 (mm110) REVERT: E 97 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: F 86 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8345 (mm-30) REVERT: G 1 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7795 (pp-130) REVERT: G 10 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6921 (pm20) REVERT: G 104 MET cc_start: 0.0511 (OUTLIER) cc_final: -0.0168 (mpp) REVERT: G 117 MET cc_start: 0.2842 (OUTLIER) cc_final: 0.2099 (ttt) REVERT: G 164 MET cc_start: 0.3942 (mmp) cc_final: 0.3407 (pmm) REVERT: H 84 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7599 (ttp-110) REVERT: I 15 ARG cc_start: 0.7456 (mpp80) cc_final: 0.7046 (mpp80) REVERT: I 25 TYR cc_start: 0.7707 (p90) cc_final: 0.7399 (p90) REVERT: I 35 LEU cc_start: 0.6614 (pt) cc_final: 0.6116 (tp) REVERT: I 54 TYR cc_start: 0.8111 (t80) cc_final: 0.7589 (t80) REVERT: I 56 ASN cc_start: 0.8530 (t0) cc_final: 0.7819 (t0) REVERT: I 122 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: J 26 GLN cc_start: 0.8982 (tt0) cc_final: 0.8577 (tm-30) REVERT: J 48 MET cc_start: 0.9435 (mmt) cc_final: 0.9177 (mmm) REVERT: J 57 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8829 (mm-30) REVERT: K 24 ASP cc_start: 0.8762 (t0) cc_final: 0.8331 (t0) REVERT: L 32 ASP cc_start: 0.5994 (m-30) cc_final: 0.5693 (m-30) outliers start: 82 outliers final: 39 residues processed: 299 average time/residue: 1.4560 time to fit residues: 520.6850 Evaluate side-chains 275 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 218 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 368 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 449 HIS B 500 GLN B 790 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.105909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060138 restraints weight = 64790.350| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.78 r_work: 0.2696 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 33310 Z= 0.283 Angle : 0.667 15.556 45307 Z= 0.341 Chirality : 0.047 0.206 5068 Planarity : 0.005 0.056 5617 Dihedral : 13.303 167.724 5092 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.04 % Allowed : 11.56 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 3848 helix: 1.63 (0.14), residues: 1362 sheet: 0.15 (0.20), residues: 599 loop : -0.41 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 49 HIS 0.011 0.001 HIS A 301 PHE 0.025 0.002 PHE A 800 TYR 0.017 0.002 TYR B 811 ARG 0.007 0.001 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 1407) hydrogen bonds : angle 4.70770 ( 3932) metal coordination : bond 0.00927 ( 31) metal coordination : angle 5.16857 ( 39) covalent geometry : bond 0.00685 (33279) covalent geometry : angle 0.64981 (45268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 231 time to evaluate : 3.854 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: A 959 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8621 (mtt) REVERT: A 1244 ASN cc_start: 0.8560 (t0) cc_final: 0.7914 (m-40) REVERT: B 108 MET cc_start: 0.9019 (ttp) cc_final: 0.8806 (ttp) REVERT: B 298 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8645 (mmt) REVERT: B 581 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: B 840 MET cc_start: 0.1762 (tmt) cc_final: 0.1248 (mmm) REVERT: B 890 ARG cc_start: 0.6535 (ttt90) cc_final: 0.6239 (mtp180) REVERT: B 927 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8803 (mtt90) REVERT: B 1163 MET cc_start: 0.9177 (mtp) cc_final: 0.8896 (mtp) REVERT: C 27 ASP cc_start: 0.8596 (t0) cc_final: 0.8325 (t0) REVERT: C 83 GLN cc_start: 0.8856 (mt0) cc_final: 0.8459 (mp-120) REVERT: C 147 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8576 (t0) REVERT: E 97 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 137 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8933 (pp) REVERT: F 86 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8414 (mm-30) REVERT: G 1 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (pp-130) REVERT: G 10 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6934 (pm20) REVERT: G 104 MET cc_start: 0.0392 (OUTLIER) cc_final: -0.0349 (mpp) REVERT: G 117 MET cc_start: 0.2753 (mmm) cc_final: 0.1941 (ttt) REVERT: G 164 MET cc_start: 0.3972 (mmp) cc_final: 0.3318 (pmm) REVERT: H 84 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7651 (ttp-110) REVERT: H 107 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: I 15 ARG cc_start: 0.7508 (mpp80) cc_final: 0.7052 (mpp80) REVERT: I 25 TYR cc_start: 0.7689 (p90) cc_final: 0.7363 (p90) REVERT: I 34 ILE cc_start: 0.7697 (tp) cc_final: 0.7349 (pp) REVERT: I 35 LEU cc_start: 0.6730 (pt) cc_final: 0.6122 (tp) REVERT: I 54 TYR cc_start: 0.8152 (t80) cc_final: 0.7654 (t80) REVERT: I 56 ASN cc_start: 0.8524 (t0) cc_final: 0.7833 (t0) REVERT: I 122 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: J 57 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8813 (mm-30) REVERT: K 24 ASP cc_start: 0.8791 (t0) cc_final: 0.8365 (t0) REVERT: L 32 ASP cc_start: 0.5962 (m-30) cc_final: 0.5654 (m-30) REVERT: L 42 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7492 (mtp85) outliers start: 104 outliers final: 44 residues processed: 305 average time/residue: 1.4598 time to fit residues: 529.9476 Evaluate side-chains 285 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 304 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 369 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 671 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.106834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061088 restraints weight = 64460.383| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.88 r_work: 0.2726 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.004 0.067 33310 Z= 0.187 Angle : 0.615 17.707 45307 Z= 0.312 Chirality : 0.044 0.176 5068 Planarity : 0.004 0.046 5617 Dihedral : 13.238 167.346 5092 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.22 % Allowed : 12.47 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 3848 helix: 1.73 (0.14), residues: 1357 sheet: 0.17 (0.20), residues: 591 loop : -0.39 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 49 HIS 0.011 0.001 HIS A 301 PHE 0.016 0.002 PHE A 800 TYR 0.020 0.001 TYR I 25 ARG 0.012 0.000 ARG B1141 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 1407) hydrogen bonds : angle 4.57624 ( 3932) metal coordination : bond 0.00846 ( 31) metal coordination : angle 5.49429 ( 39) covalent geometry : bond 0.00449 (33279) covalent geometry : angle 0.59379 (45268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 3.938 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: A 743 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.8061 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8514 (t0) cc_final: 0.7975 (m-40) REVERT: A 1484 MET cc_start: 0.5611 (OUTLIER) cc_final: 0.4371 (ppp) REVERT: B 108 MET cc_start: 0.9031 (ttp) cc_final: 0.8799 (ttp) REVERT: B 298 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8607 (mmt) REVERT: B 840 MET cc_start: 0.1803 (tmt) cc_final: 0.1250 (mmm) REVERT: B 890 ARG cc_start: 0.6548 (ttt90) cc_final: 0.6212 (mtp180) REVERT: B 927 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8762 (mtt180) REVERT: B 1163 MET cc_start: 0.9106 (mtp) cc_final: 0.8811 (mtp) REVERT: C 27 ASP cc_start: 0.8547 (t0) cc_final: 0.8327 (t0) REVERT: C 83 GLN cc_start: 0.8838 (mt0) cc_final: 0.8420 (mm110) REVERT: C 147 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8579 (t0) REVERT: D 125 GLU cc_start: 0.6373 (pm20) cc_final: 0.6137 (mp0) REVERT: E 97 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: E 137 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8925 (pp) REVERT: F 79 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8661 (t) REVERT: F 86 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8465 (mm-30) REVERT: G 1 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7821 (pp-130) REVERT: G 10 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6896 (pm20) REVERT: G 27 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7464 (ptpt) REVERT: G 104 MET cc_start: 0.0499 (OUTLIER) cc_final: -0.0148 (mpp) REVERT: G 117 MET cc_start: 0.2874 (mmm) cc_final: 0.2146 (ttt) REVERT: G 164 MET cc_start: 0.3953 (mmp) cc_final: 0.3395 (pmm) REVERT: H 84 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7674 (ttp-110) REVERT: H 107 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: I 15 ARG cc_start: 0.7550 (mpp80) cc_final: 0.7185 (mpp80) REVERT: I 25 TYR cc_start: 0.7546 (p90) cc_final: 0.7193 (p90) REVERT: I 54 TYR cc_start: 0.8102 (t80) cc_final: 0.7632 (t80) REVERT: I 56 ASN cc_start: 0.8495 (t0) cc_final: 0.7832 (t0) REVERT: I 121 HIS cc_start: 0.7976 (t-90) cc_final: 0.7758 (t-170) REVERT: J 48 MET cc_start: 0.9450 (mmt) cc_final: 0.9193 (mmm) REVERT: J 57 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8850 (mm-30) REVERT: K 24 ASP cc_start: 0.8764 (t0) cc_final: 0.8325 (t0) REVERT: L 32 ASP cc_start: 0.6022 (m-30) cc_final: 0.5719 (m-30) REVERT: L 42 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7464 (mtp85) outliers start: 76 outliers final: 38 residues processed: 289 average time/residue: 1.5203 time to fit residues: 521.6647 Evaluate side-chains 278 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 344 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 chunk 39 optimal weight: 0.0470 chunk 334 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 232 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.109016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064253 restraints weight = 64374.811| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.65 r_work: 0.2805 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 33310 Z= 0.106 Angle : 0.561 19.001 45307 Z= 0.285 Chirality : 0.042 0.160 5068 Planarity : 0.004 0.047 5617 Dihedral : 13.092 167.415 5092 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 13.31 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3848 helix: 1.84 (0.15), residues: 1363 sheet: 0.24 (0.20), residues: 620 loop : -0.32 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.011 0.001 HIS A 301 PHE 0.014 0.001 PHE A 548 TYR 0.023 0.001 TYR G 72 ARG 0.010 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 1407) hydrogen bonds : angle 4.36284 ( 3932) metal coordination : bond 0.00665 ( 31) metal coordination : angle 4.92459 ( 39) covalent geometry : bond 0.00236 (33279) covalent geometry : angle 0.54180 (45268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: A 743 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.8025 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8534 (t0) cc_final: 0.8067 (m-40) REVERT: A 1279 MET cc_start: 0.5285 (tmm) cc_final: 0.4982 (ppp) REVERT: B 108 MET cc_start: 0.9033 (ttp) cc_final: 0.8801 (ttp) REVERT: B 794 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9081 (m) REVERT: B 817 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (tp-100) REVERT: B 840 MET cc_start: 0.1655 (tmt) cc_final: 0.1224 (mmm) REVERT: B 890 ARG cc_start: 0.6535 (ttt90) cc_final: 0.6207 (mtp180) REVERT: B 927 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8701 (mtt180) REVERT: B 1112 ASP cc_start: 0.7819 (p0) cc_final: 0.7556 (p0) REVERT: B 1163 MET cc_start: 0.9027 (mtp) cc_final: 0.8764 (mtp) REVERT: C 27 ASP cc_start: 0.8423 (t0) cc_final: 0.8220 (t0) REVERT: C 83 GLN cc_start: 0.8844 (mt0) cc_final: 0.8351 (mm110) REVERT: E 97 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: E 137 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8908 (pp) REVERT: F 79 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8833 (t) REVERT: G 1 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7675 (pp-130) REVERT: G 10 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6991 (pm20) REVERT: G 104 MET cc_start: 0.0198 (OUTLIER) cc_final: -0.0490 (mpp) REVERT: G 117 MET cc_start: 0.1853 (OUTLIER) cc_final: 0.0812 (ttt) REVERT: G 164 MET cc_start: 0.3997 (mmp) cc_final: 0.3151 (pmm) REVERT: H 84 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7592 (ttp-110) REVERT: H 107 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: I 25 TYR cc_start: 0.7810 (p90) cc_final: 0.7502 (p90) REVERT: I 54 TYR cc_start: 0.8120 (t80) cc_final: 0.7734 (t80) REVERT: I 56 ASN cc_start: 0.8511 (t0) cc_final: 0.7854 (t0) REVERT: J 48 MET cc_start: 0.9374 (mmt) cc_final: 0.9123 (mmm) REVERT: J 57 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8807 (mm-30) REVERT: K 16 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7957 (mt-10) REVERT: K 24 ASP cc_start: 0.8729 (t0) cc_final: 0.8271 (t0) REVERT: L 32 ASP cc_start: 0.6042 (m-30) cc_final: 0.5727 (m-30) REVERT: L 35 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7407 (tmm160) REVERT: L 42 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7535 (mtp85) outliers start: 58 outliers final: 22 residues processed: 285 average time/residue: 1.5673 time to fit residues: 529.7821 Evaluate side-chains 261 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 338 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 363 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** L 23 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 = 0.3811 r_free = 0.3811 target = 0.107532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.062043 restraints weight = 64177.787| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.78 r_work: 0.2755 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33310 Z= 0.162 Angle : 0.588 15.024 45307 Z= 0.298 Chirality : 0.043 0.174 5068 Planarity : 0.004 0.044 5617 Dihedral : 13.071 166.806 5092 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.52 % Allowed : 13.31 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3848 helix: 1.87 (0.15), residues: 1358 sheet: 0.27 (0.20), residues: 619 loop : -0.32 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 49 HIS 0.012 0.001 HIS A 301 PHE 0.018 0.001 PHE B 422 TYR 0.019 0.001 TYR G 72 ARG 0.011 0.000 ARG B1141 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1407) hydrogen bonds : angle 4.40214 ( 3932) metal coordination : bond 0.00694 ( 31) metal coordination : angle 5.08413 ( 39) covalent geometry : bond 0.00387 (33279) covalent geometry : angle 0.56950 (45268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: A 743 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.8048 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8469 (t0) cc_final: 0.8035 (m-40) REVERT: A 1279 MET cc_start: 0.5360 (tmm) cc_final: 0.5004 (ppp) REVERT: A 1321 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8886 (pp) REVERT: B 108 MET cc_start: 0.9023 (ttp) cc_final: 0.8798 (ttp) REVERT: B 817 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8012 (tp-100) REVERT: B 840 MET cc_start: 0.1704 (tmt) cc_final: 0.1285 (mmm) REVERT: B 890 ARG cc_start: 0.6606 (ttt90) cc_final: 0.6277 (mtp180) REVERT: B 927 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8775 (mtt180) REVERT: B 1112 ASP cc_start: 0.8014 (p0) cc_final: 0.7767 (p0) REVERT: B 1163 MET cc_start: 0.9141 (mtp) cc_final: 0.8902 (mtp) REVERT: C 27 ASP cc_start: 0.8481 (t0) cc_final: 0.8275 (t0) REVERT: C 83 GLN cc_start: 0.8832 (mt0) cc_final: 0.8315 (mm110) REVERT: D 125 GLU cc_start: 0.6428 (pm20) cc_final: 0.6185 (mp0) REVERT: E 97 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: E 137 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8911 (pp) REVERT: G 1 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7867 (pp-130) REVERT: G 10 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6990 (pm20) REVERT: G 27 LYS cc_start: 0.7589 (mtmm) cc_final: 0.7326 (ptpt) REVERT: G 104 MET cc_start: 0.0395 (OUTLIER) cc_final: -0.0268 (mpp) REVERT: G 164 MET cc_start: 0.3577 (mmp) cc_final: 0.3052 (pmm) REVERT: H 84 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7619 (ttp-110) REVERT: H 107 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: I 25 TYR cc_start: 0.7761 (p90) cc_final: 0.7443 (p90) REVERT: I 54 TYR cc_start: 0.8201 (t80) cc_final: 0.7686 (t80) REVERT: I 56 ASN cc_start: 0.8571 (t0) cc_final: 0.7891 (t0) REVERT: I 122 ARG cc_start: 0.8379 (mpp-170) cc_final: 0.8126 (mtm-85) REVERT: J 57 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8810 (mm-30) REVERT: K 16 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7867 (mt-10) REVERT: K 24 ASP cc_start: 0.8750 (t0) cc_final: 0.8307 (t0) REVERT: K 114 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7621 (mp0) REVERT: L 32 ASP cc_start: 0.6041 (m-30) cc_final: 0.5746 (m-30) REVERT: L 35 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7433 (tmm160) REVERT: L 42 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7593 (mtp85) outliers start: 52 outliers final: 27 residues processed: 273 average time/residue: 1.5923 time to fit residues: 511.9171 Evaluate side-chains 267 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 4.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 348 optimal weight: 2.9990 chunk 314 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.062993 restraints weight = 64262.790| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.96 r_work: 0.2779 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33310 Z= 0.123 Angle : 0.559 12.167 45307 Z= 0.285 Chirality : 0.042 0.160 5068 Planarity : 0.004 0.045 5617 Dihedral : 13.034 166.305 5092 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.31 % Allowed : 13.78 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3848 helix: 1.93 (0.15), residues: 1360 sheet: 0.28 (0.20), residues: 618 loop : -0.27 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 49 HIS 0.013 0.001 HIS A 301 PHE 0.023 0.001 PHE B 422 TYR 0.020 0.001 TYR G 72 ARG 0.014 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1407) hydrogen bonds : angle 4.32253 ( 3932) metal coordination : bond 0.00588 ( 31) metal coordination : angle 4.31369 ( 39) covalent geometry : bond 0.00289 (33279) covalent geometry : angle 0.54431 (45268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: A 743 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.8049 (tmm-80) REVERT: A 1244 ASN cc_start: 0.8477 (t0) cc_final: 0.8061 (m-40) REVERT: A 1279 MET cc_start: 0.5359 (tmm) cc_final: 0.5027 (ppp) REVERT: B 108 MET cc_start: 0.9032 (ttp) cc_final: 0.8795 (ttp) REVERT: B 494 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7480 (ptpt) REVERT: B 817 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8009 (tp-100) REVERT: B 840 MET cc_start: 0.1492 (tmt) cc_final: 0.1085 (mmm) REVERT: B 890 ARG cc_start: 0.6596 (ttt90) cc_final: 0.6269 (mtp180) REVERT: B 927 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8739 (mtt180) REVERT: B 1112 ASP cc_start: 0.7882 (p0) cc_final: 0.7630 (p0) REVERT: B 1163 MET cc_start: 0.9150 (mtp) cc_final: 0.8911 (mtp) REVERT: C 27 ASP cc_start: 0.8457 (t0) cc_final: 0.8252 (t0) REVERT: C 83 GLN cc_start: 0.8864 (mt0) cc_final: 0.8286 (mp-120) REVERT: C 147 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8557 (t0) REVERT: D 125 GLU cc_start: 0.6363 (pm20) cc_final: 0.6137 (mp0) REVERT: E 137 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8906 (pp) REVERT: G 1 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7813 (ppp) REVERT: G 10 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6899 (pm20) REVERT: G 27 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7287 (ptpt) REVERT: G 104 MET cc_start: 0.0656 (OUTLIER) cc_final: 0.0037 (mpp) REVERT: G 117 MET cc_start: 0.3694 (mmm) cc_final: 0.3094 (ttt) REVERT: G 164 MET cc_start: 0.3527 (mmp) cc_final: 0.3116 (pmm) REVERT: H 84 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7608 (ttp-110) REVERT: H 107 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: I 15 ARG cc_start: 0.7422 (mpp80) cc_final: 0.7088 (mpp80) REVERT: I 25 TYR cc_start: 0.7726 (p90) cc_final: 0.7433 (p90) REVERT: I 54 TYR cc_start: 0.8168 (t80) cc_final: 0.7645 (t80) REVERT: I 56 ASN cc_start: 0.8661 (t0) cc_final: 0.8038 (t0) REVERT: J 57 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8786 (mm-30) REVERT: K 16 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7914 (mt-10) REVERT: K 24 ASP cc_start: 0.8735 (t0) cc_final: 0.8286 (t0) REVERT: K 114 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7745 (pp20) REVERT: L 32 ASP cc_start: 0.6045 (m-30) cc_final: 0.5766 (m-30) REVERT: L 35 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7380 (tmm160) REVERT: L 42 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8146 (mtp85) outliers start: 45 outliers final: 21 residues processed: 267 average time/residue: 1.5510 time to fit residues: 492.5304 Evaluate side-chains 257 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 927 ARG Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 112 optimal weight: 9.9990 chunk 289 optimal weight: 30.0000 chunk 5 optimal weight: 0.4980 chunk 259 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 59 optimal weight: 0.0030 chunk 213 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN L 23 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064024 restraints weight = 63969.872| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.72 r_work: 0.2797 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33310 Z= 0.111 Angle : 0.553 16.247 45307 Z= 0.281 Chirality : 0.042 0.157 5068 Planarity : 0.004 0.066 5617 Dihedral : 12.980 166.015 5092 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 13.87 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3848 helix: 1.97 (0.15), residues: 1360 sheet: 0.30 (0.20), residues: 620 loop : -0.24 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.013 0.001 HIS A 301 PHE 0.028 0.001 PHE B 422 TYR 0.024 0.001 TYR G 72 ARG 0.014 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1407) hydrogen bonds : angle 4.26336 ( 3932) metal coordination : bond 0.00509 ( 31) metal coordination : angle 3.98415 ( 39) covalent geometry : bond 0.00257 (33279) covalent geometry : angle 0.54074 (45268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34163.24 seconds wall clock time: 587 minutes 6.49 seconds (35226.49 seconds total)