Starting phenix.real_space_refine on Tue Aug 26 07:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvo_52440/08_2025/9hvo_52440.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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 86 5.49 5 Mg 1 5.21 5 S 199 5.16 5 C 21096 2.51 5 N 5972 2.21 5 O 6543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33905 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11266 Classifications: {'peptide': 1422} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 3 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9052 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1030 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} 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: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 769 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 257 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "O" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} 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 83.228 115.136 117.586 1.00 20.36 S ATOM 486 SG CYS A 74 86.688 115.196 115.850 1.00 21.49 S ATOM 533 SG CYS A 81 83.877 114.920 113.905 1.00 22.74 S ATOM 768 SG CYS A 111 78.204 67.656 121.957 1.00 55.44 S ATOM 1109 SG CYS A 154 81.260 65.676 121.512 1.00 81.27 S ATOM 1132 SG CYS A 184 78.896 65.386 124.907 1.00 66.29 S ATOM 19888 SG CYS B1119 96.332 101.783 115.687 1.00 21.10 S ATOM 19910 SG CYS B1122 93.034 99.712 115.397 1.00 31.74 S ATOM 20025 SG CYS B1137 92.878 102.380 117.529 1.00 45.95 S ATOM 20046 SG CYS B1140 94.944 98.946 118.167 1.00 46.08 S ATOM 21012 SG CYS C 88 73.657 162.510 68.442 1.00 32.08 S ATOM 21025 SG CYS C 90 72.198 161.351 71.614 1.00 34.96 S ATOM 21060 SG CYS C 94 70.711 163.929 69.255 1.00 33.72 S ATOM 21082 SG CYS C 97 70.693 159.975 68.557 1.00 21.78 S ATOM 28420 SG CYS I 17 23.404 49.792 88.487 1.00 28.76 S ATOM 28444 SG CYS I 20 24.691 52.164 90.583 1.00 29.69 S ATOM 28605 SG CYS I 39 27.349 50.151 89.992 1.00 27.06 S ATOM 28982 SG CYS I 86 22.944 70.315 47.443 1.00 11.22 S ATOM 29006 SG CYS I 89 19.726 71.061 47.760 1.00 14.07 S ATOM 29210 SG CYS I 114 22.739 72.998 49.834 1.00 9.64 S ATOM 29245 SG CYS I 119 21.082 69.600 51.063 1.00 12.07 S ATOM 29355 SG CYS J 7 56.259 136.551 53.547 1.00 9.24 S ATOM 29379 SG CYS J 10 57.657 138.741 50.939 1.00 3.96 S ATOM 29643 SG CYS J 44 56.857 134.994 49.959 1.00 11.82 S ATOM 29649 SG CYS J 45 54.385 138.052 50.254 1.00 5.55 S ATOM 30811 SG CYS L 19 36.987 141.678 93.138 1.00 7.96 S ATOM 30830 SG CYS L 22 34.780 144.648 92.476 1.00 10.05 S ATOM 30947 SG CYS L 36 36.009 143.863 95.847 1.00 22.09 S ATOM 30973 SG CYS L 39 33.656 141.557 94.535 1.00 28.78 S Time building chain proxies: 5.64, per 1000 atoms: 0.17 Number of scatterers: 33905 At special positions: 0 Unit cell: (154.035, 174.41, 168.705, 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 199 16.00 P 86 15.00 Mg 1 11.99 O 6543 8.00 N 5972 7.00 C 21096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 927.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 33 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7570 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 47 sheets defined 40.3% alpha, 18.2% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.795A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.634A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (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 434 through 439 removed outlier: 3.563A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' 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: 3.968A 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 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.133A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.660A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.608A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.079A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.538A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.033A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.606A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1295 removed outlier: 3.550A pdb=" N PHE A1284 " --> pdb=" O ASP A1280 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.877A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 removed outlier: 3.642A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.704A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.886A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 38 removed outlier: 4.441A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 4.526A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 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: 3.713A 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 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.593A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.513A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.647A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.525A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.608A 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 761 through 765 removed outlier: 3.670A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 971 through 976 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.872A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 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 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.074A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) 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 129 through 133 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 270 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.859A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 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 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.761A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 132 through 136 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 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.730A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 63 through 68 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 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.768A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'O' and resid 497 through 516 Processing helix chain 'O' and resid 546 through 569 Processing helix chain 'O' and resid 573 through 591 removed outlier: 3.615A pdb=" N ARG O 577 " --> pdb=" O GLU O 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 593 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.490A 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: 9.994A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 252 " --> 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 265 removed outlier: 3.694A pdb=" N VAL A 264 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.640A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 7.534A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.441A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.675A 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 579 through 581 removed outlier: 5.527A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.911A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 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 1307 through 1310 removed outlier: 3.913A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.642A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.824A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.004A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.004A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 93 removed outlier: 6.507A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.714A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.689A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 237 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 534 removed outlier: 4.471A pdb=" N ARG B 620 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 531 through 534 removed outlier: 4.471A pdb=" N ARG B 620 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.628A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.618A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.618A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.357A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD9, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.944A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.776A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.489A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.717A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE7, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.757A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 104 through 107 removed outlier: 3.509A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1448 hydrogen bonds defined for protein. 4044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 3.29 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: 9761 1.33 - 1.45: 5413 1.45 - 1.57: 19057 1.57 - 1.69: 169 1.69 - 1.81: 314 Bond restraints: 34714 Sorted by residual: bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.25e+00 bond pdb=" CB GLU O 559 " pdb=" CG GLU O 559 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.82e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 bond pdb=" C ALA B 308 " pdb=" N PHE B 309 " ideal model delta sigma weight residual 1.332 1.315 0.018 1.40e-02 5.10e+03 1.59e+00 ... (remaining 34709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 44939 0.99 - 1.99: 1860 1.99 - 2.98: 283 2.98 - 3.97: 157 3.97 - 4.96: 14 Bond angle restraints: 47253 Sorted by residual: angle pdb=" N VAL B 661 " pdb=" CA VAL B 661 " pdb=" C VAL B 661 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ILE A 883 " pdb=" CA ILE A 883 " pdb=" C ILE A 883 " ideal model delta sigma weight residual 113.00 109.66 3.34 1.30e+00 5.92e-01 6.60e+00 angle pdb=" C3' DC N 14 " pdb=" C2' DC N 14 " pdb=" C1' DC N 14 " ideal model delta sigma weight residual 101.60 105.36 -3.76 1.50e+00 4.44e-01 6.27e+00 angle pdb=" C3' DC N 30 " pdb=" C2' DC N 30 " pdb=" C1' DC N 30 " ideal model delta sigma weight residual 101.60 105.34 -3.74 1.50e+00 4.44e-01 6.23e+00 angle pdb=" C3' DC T 22 " pdb=" C2' DC T 22 " pdb=" C1' DC T 22 " ideal model delta sigma weight residual 101.60 105.08 -3.48 1.50e+00 4.44e-01 5.40e+00 ... (remaining 47248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 20486 35.82 - 71.64: 542 71.64 - 107.46: 55 107.46 - 143.28: 0 143.28 - 179.09: 5 Dihedral angle restraints: 21088 sinusoidal: 9395 harmonic: 11693 Sorted by residual: dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N ALA C 40 " pdb=" CA ALA C 40 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N LYS A 344 " pdb=" CA LYS A 344 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' G P 135 " pdb=" C3' G P 135 " pdb=" O3' G P 135 " pdb=" P G P 136 " ideal model delta sinusoidal sigma weight residual 250.00 70.91 179.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 21085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3537 0.034 - 0.068: 1190 0.068 - 0.102: 327 0.102 - 0.136: 208 0.136 - 0.170: 12 Chirality restraints: 5274 Sorted by residual: chirality pdb=" CA PRO A 478 " pdb=" N PRO A 478 " pdb=" C PRO A 478 " pdb=" CB PRO A 478 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE B 928 " pdb=" N ILE B 928 " pdb=" C ILE B 928 " pdb=" CB ILE B 928 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE H 40 " pdb=" N ILE H 40 " pdb=" C ILE H 40 " pdb=" CB ILE H 40 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 5271 not shown) Planarity restraints: 5837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS O 552 " -0.011 2.00e-02 2.50e+03 1.63e-02 4.00e+00 pdb=" CG HIS O 552 " 0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS O 552 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS O 552 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS O 552 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS O 552 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 458 " 0.016 2.00e-02 2.50e+03 1.38e-02 3.33e+00 pdb=" CG PHE A 458 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 458 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 458 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 458 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 458 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 458 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 35 " -0.019 2.00e-02 2.50e+03 1.03e-02 3.16e+00 pdb=" N9 DG T 35 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG T 35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG T 35 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG T 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG T 35 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG T 35 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG T 35 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG T 35 " -0.016 2.00e-02 2.50e+03 pdb=" N2 DG T 35 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DG T 35 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG T 35 " 0.002 2.00e-02 2.50e+03 ... (remaining 5834 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 136 2.45 - 3.06: 22451 3.06 - 3.68: 50946 3.68 - 4.29: 80103 4.29 - 4.90: 132570 Nonbonded interactions: 286206 Sorted by model distance: nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.838 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR A1314 " pdb=" OD1 ASN A1316 " model vdw 1.951 3.040 nonbonded pdb=" O3' U P 145 " pdb="MG MG A2003 " model vdw 1.958 2.170 nonbonded pdb=" OG1 THR E 29 " pdb=" OD1 ASP E 31 " model vdw 1.985 3.040 ... (remaining 286201 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: 4.830 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.630 34745 Z= 0.213 Angle : 0.555 19.491 47288 Z= 0.279 Chirality : 0.042 0.170 5274 Planarity : 0.004 0.040 5837 Dihedral : 16.154 179.094 13515 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.14), residues: 3974 helix: 1.59 (0.14), residues: 1441 sheet: -0.40 (0.20), residues: 612 loop : -0.20 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 47 TYR 0.025 0.001 TYR B1048 PHE 0.031 0.001 PHE A 458 TRP 0.011 0.001 TRP B 27 HIS 0.022 0.001 HIS O 552 Details of bonding type rmsd covalent geometry : bond 0.00370 (34714) covalent geometry : angle 0.49789 (47253) SS BOND : bond 0.00538 ( 1) SS BOND : angle 0.57525 ( 2) hydrogen bonds : bond 0.13459 ( 1504) hydrogen bonds : angle 5.84600 ( 4222) metal coordination : bond 0.14071 ( 30) metal coordination : angle 9.30616 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1279 MET cc_start: 0.4907 (tmm) cc_final: 0.4529 (tmm) REVERT: A 1440 MET cc_start: 0.8325 (mmt) cc_final: 0.7983 (mmt) REVERT: B 648 TYR cc_start: 0.6921 (m-10) cc_final: 0.6656 (m-10) REVERT: B 650 ASN cc_start: 0.8357 (t0) cc_final: 0.8156 (t0) REVERT: C 109 GLU cc_start: 0.7822 (mp0) cc_final: 0.7573 (pt0) REVERT: G 117 MET cc_start: 0.2242 (tpp) cc_final: 0.1883 (tmm) REVERT: O 535 LYS cc_start: 0.7201 (mttt) cc_final: 0.6715 (mmtm) REVERT: O 610 ARG cc_start: 0.5161 (mtp180) cc_final: 0.4832 (tpm170) outliers start: 0 outliers final: 2 residues processed: 613 average time/residue: 0.7405 time to fit residues: 525.0244 Evaluate side-chains 451 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 865 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 301 HIS A 485 ASN A 673 GLN A 905 ASN A1146 GLN A1236 ASN B 144 HIS B 582 GLN B1133 HIS C 55 ASN C 190 ASN E 92 GLN E 168 ASN G 60 GLN G 138 GLN H 76 ASN H 133 HIS I 46 GLN J 26 GLN K 89 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.160523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102987 restraints weight = 39810.256| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.45 r_work: 0.3231 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34745 Z= 0.153 Angle : 0.565 10.738 47288 Z= 0.294 Chirality : 0.044 0.204 5274 Planarity : 0.004 0.040 5837 Dihedral : 14.112 176.849 5343 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.86 % Allowed : 8.75 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.13), residues: 3974 helix: 1.57 (0.14), residues: 1455 sheet: -0.22 (0.21), residues: 581 loop : -0.20 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 186 TYR 0.015 0.001 TYR A 875 PHE 0.019 0.001 PHE A 234 TRP 0.017 0.001 TRP O 504 HIS 0.009 0.001 HIS O 609 Details of bonding type rmsd covalent geometry : bond 0.00355 (34714) covalent geometry : angle 0.55249 (47253) SS BOND : bond 0.01488 ( 1) SS BOND : angle 4.50411 ( 2) hydrogen bonds : bond 0.04460 ( 1504) hydrogen bonds : angle 4.88428 ( 4222) metal coordination : bond 0.00763 ( 30) metal coordination : angle 4.37371 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 486 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6572 (tmt170) cc_final: 0.6212 (tmt170) REVERT: A 423 ASN cc_start: 0.8265 (t0) cc_final: 0.7809 (m-40) REVERT: A 715 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: A 818 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 1031 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.6975 (mmt180) REVERT: A 1182 GLN cc_start: 0.7090 (mp10) cc_final: 0.6789 (pm20) REVERT: A 1199 MET cc_start: 0.3797 (pmm) cc_final: 0.2061 (ptp) REVERT: A 1215 GLU cc_start: 0.7458 (tt0) cc_final: 0.7136 (mt-10) REVERT: A 1233 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8169 (pt0) REVERT: A 1288 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (mp) REVERT: A 1302 GLU cc_start: 0.8496 (mp0) cc_final: 0.8293 (mp0) REVERT: A 1423 ASP cc_start: 0.7558 (t0) cc_final: 0.7270 (t0) REVERT: A 1437 ASP cc_start: 0.7973 (m-30) cc_final: 0.7414 (t0) REVERT: A 1440 MET cc_start: 0.7881 (mmt) cc_final: 0.7479 (mmt) REVERT: A 1479 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7245 (mmtm) REVERT: B 222 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7530 (mtp85) REVERT: B 233 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7494 (p) REVERT: B 254 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7441 (mm110) REVERT: B 298 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7065 (mmm) REVERT: B 333 GLU cc_start: 0.7638 (mp0) cc_final: 0.7316 (tm-30) REVERT: B 344 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: B 546 GLU cc_start: 0.8159 (tp30) cc_final: 0.7689 (mm-30) REVERT: B 606 ASP cc_start: 0.8090 (t70) cc_final: 0.7049 (t70) REVERT: B 608 ARG cc_start: 0.8452 (ttt180) cc_final: 0.7583 (tpp-160) REVERT: B 650 ASN cc_start: 0.8625 (t0) cc_final: 0.8341 (t0) REVERT: B 834 ARG cc_start: 0.6302 (mtt90) cc_final: 0.5886 (mtp85) REVERT: C 109 GLU cc_start: 0.8281 (mp0) cc_final: 0.6937 (pt0) REVERT: C 118 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8261 (ttm-80) REVERT: C 228 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: E 78 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7860 (mp0) REVERT: E 128 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7243 (mt-10) REVERT: H 31 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7625 (mt-10) REVERT: H 37 MET cc_start: 0.9106 (mmm) cc_final: 0.8887 (mmm) REVERT: K 2 ASN cc_start: 0.8946 (m-40) cc_final: 0.8546 (m110) REVERT: L 27 GLU cc_start: 0.8176 (tp30) cc_final: 0.7922 (tp30) REVERT: O 502 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6741 (mtm-85) REVERT: O 508 TYR cc_start: 0.8238 (t80) cc_final: 0.7978 (t80) REVERT: O 598 LYS cc_start: 0.7628 (tttt) cc_final: 0.6837 (ptpt) REVERT: O 603 LYS cc_start: 0.7754 (tppt) cc_final: 0.7511 (pptt) REVERT: O 610 ARG cc_start: 0.5390 (mtp180) cc_final: 0.5041 (tpm170) outliers start: 66 outliers final: 11 residues processed: 514 average time/residue: 0.7290 time to fit residues: 436.9191 Evaluate side-chains 454 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 435 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain G residue 147 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 157 optimal weight: 0.2980 chunk 271 optimal weight: 1.9990 chunk 335 optimal weight: 40.0000 chunk 380 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 310 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 367 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN A1236 ASN B 144 HIS B 518 HIS B 582 GLN D 34 ASN E 92 GLN G 60 GLN H 76 ASN I 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103365 restraints weight = 39695.769| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.18 r_work: 0.3264 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34745 Z= 0.130 Angle : 0.521 8.683 47288 Z= 0.271 Chirality : 0.042 0.184 5274 Planarity : 0.004 0.053 5837 Dihedral : 14.071 176.314 5339 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.94 % Allowed : 11.03 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.13), residues: 3974 helix: 1.65 (0.14), residues: 1459 sheet: -0.11 (0.22), residues: 560 loop : -0.21 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 35 TYR 0.014 0.001 TYR A 413 PHE 0.015 0.001 PHE A 592 TRP 0.014 0.001 TRP B 27 HIS 0.007 0.001 HIS O 552 Details of bonding type rmsd covalent geometry : bond 0.00302 (34714) covalent geometry : angle 0.51281 (47253) SS BOND : bond 0.00142 ( 1) SS BOND : angle 3.59907 ( 2) hydrogen bonds : bond 0.04014 ( 1504) hydrogen bonds : angle 4.66028 ( 4222) metal coordination : bond 0.00461 ( 30) metal coordination : angle 3.46576 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 463 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7617 (mmt180) cc_final: 0.7183 (mtp180) REVERT: A 223 GLU cc_start: 0.7989 (tp30) cc_final: 0.7564 (tp30) REVERT: A 423 ASN cc_start: 0.8304 (t0) cc_final: 0.7959 (m-40) REVERT: A 556 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 634 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 715 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 794 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: A 818 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 1031 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6920 (mmt180) REVERT: A 1135 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7962 (mmtm) REVERT: A 1182 GLN cc_start: 0.7058 (mp10) cc_final: 0.6682 (pm20) REVERT: A 1199 MET cc_start: 0.3842 (pmm) cc_final: 0.1998 (ptp) REVERT: A 1215 GLU cc_start: 0.7295 (tt0) cc_final: 0.7004 (mt-10) REVERT: A 1233 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: A 1287 CYS cc_start: 0.8255 (t) cc_final: 0.7788 (p) REVERT: A 1288 ILE cc_start: 0.7621 (mt) cc_final: 0.7254 (mp) REVERT: A 1423 ASP cc_start: 0.7543 (t0) cc_final: 0.7059 (t0) REVERT: A 1437 ASP cc_start: 0.7982 (m-30) cc_final: 0.7415 (t0) REVERT: A 1479 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7264 (mmtm) REVERT: B 24 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: B 214 LYS cc_start: 0.8468 (ttpt) cc_final: 0.7954 (ttpp) REVERT: B 222 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7360 (mtp85) REVERT: B 233 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7447 (p) REVERT: B 333 GLU cc_start: 0.7645 (mp0) cc_final: 0.7287 (tm-30) REVERT: B 546 GLU cc_start: 0.8110 (tp30) cc_final: 0.7657 (mm-30) REVERT: B 579 ASP cc_start: 0.7859 (t0) cc_final: 0.6982 (t0) REVERT: B 606 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7443 (t70) REVERT: B 608 ARG cc_start: 0.8418 (ttt180) cc_final: 0.7565 (tpp-160) REVERT: B 650 ASN cc_start: 0.8575 (t0) cc_final: 0.8240 (t0) REVERT: B 834 ARG cc_start: 0.6676 (mtt90) cc_final: 0.6348 (mtp85) REVERT: B 841 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6403 (mtt180) REVERT: B 1143 LYS cc_start: 0.8782 (mtmt) cc_final: 0.7935 (mtpt) REVERT: C 109 GLU cc_start: 0.8227 (mp0) cc_final: 0.7019 (pt0) REVERT: C 118 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8255 (ttm-80) REVERT: E 78 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7856 (mp0) REVERT: E 116 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7872 (tp40) REVERT: E 128 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7231 (mt-10) REVERT: F 86 GLU cc_start: 0.7991 (tp30) cc_final: 0.7767 (mm-30) REVERT: H 26 SER cc_start: 0.8889 (m) cc_final: 0.8642 (t) REVERT: H 36 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8187 (mmpt) REVERT: H 37 MET cc_start: 0.9064 (mmm) cc_final: 0.8856 (mmm) REVERT: H 103 GLU cc_start: 0.8823 (pm20) cc_final: 0.8327 (pm20) REVERT: K 2 ASN cc_start: 0.8902 (m-40) cc_final: 0.8543 (m110) REVERT: L 27 GLU cc_start: 0.8116 (tp30) cc_final: 0.7763 (tp30) REVERT: O 498 GLU cc_start: 0.5972 (pp20) cc_final: 0.5704 (pp20) REVERT: O 502 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6766 (mtm-85) REVERT: O 598 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6841 (ptmt) REVERT: O 603 LYS cc_start: 0.7752 (tppt) cc_final: 0.7487 (pptt) REVERT: O 609 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7275 (m-70) REVERT: O 610 ARG cc_start: 0.5460 (mtp180) cc_final: 0.5084 (tpm170) outliers start: 69 outliers final: 17 residues processed: 497 average time/residue: 0.6820 time to fit residues: 395.7182 Evaluate side-chains 468 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 439 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain O residue 509 GLN Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 331 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 320 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 485 ASN A 539 GLN A1146 GLN A1236 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 GLN B 639 HIS B1071 ASN E 92 GLN H 76 ASN I 46 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099321 restraints weight = 39732.657| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.39 r_work: 0.3176 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 34745 Z= 0.261 Angle : 0.604 10.823 47288 Z= 0.309 Chirality : 0.046 0.187 5274 Planarity : 0.004 0.043 5837 Dihedral : 14.102 176.475 5339 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.00 % Allowed : 12.52 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.13), residues: 3974 helix: 1.38 (0.14), residues: 1462 sheet: -0.19 (0.21), residues: 584 loop : -0.29 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 426 TYR 0.021 0.002 TYR B1048 PHE 0.025 0.002 PHE C 63 TRP 0.016 0.002 TRP B 27 HIS 0.010 0.001 HIS O 609 Details of bonding type rmsd covalent geometry : bond 0.00645 (34714) covalent geometry : angle 0.59462 (47253) SS BOND : bond 0.00512 ( 1) SS BOND : angle 2.70152 ( 2) hydrogen bonds : bond 0.04823 ( 1504) hydrogen bonds : angle 4.79339 ( 4222) metal coordination : bond 0.00724 ( 30) metal coordination : angle 4.02284 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 448 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7271 (mmm160) REVERT: A 70 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7884 (mtp180) REVERT: A 423 ASN cc_start: 0.8337 (t0) cc_final: 0.7978 (m-40) REVERT: A 524 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8126 (mmt) REVERT: A 556 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 634 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 715 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 818 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 1031 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.6949 (mpt90) REVERT: A 1182 GLN cc_start: 0.7050 (mp10) cc_final: 0.6758 (pm20) REVERT: A 1199 MET cc_start: 0.3957 (pmm) cc_final: 0.2293 (ptp) REVERT: A 1225 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: A 1233 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: A 1287 CYS cc_start: 0.8248 (t) cc_final: 0.7802 (p) REVERT: A 1423 ASP cc_start: 0.7754 (t0) cc_final: 0.7418 (t0) REVERT: A 1437 ASP cc_start: 0.8112 (m-30) cc_final: 0.7523 (t0) REVERT: A 1440 MET cc_start: 0.7858 (mmt) cc_final: 0.7525 (mmt) REVERT: A 1479 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7246 (mmtm) REVERT: B 24 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7064 (pp20) REVERT: B 222 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7391 (mtp85) REVERT: B 233 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7480 (p) REVERT: B 333 GLU cc_start: 0.7702 (mp0) cc_final: 0.7383 (tm-30) REVERT: B 546 GLU cc_start: 0.8200 (tp30) cc_final: 0.7848 (tp30) REVERT: B 552 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8253 (m110) REVERT: B 579 ASP cc_start: 0.7892 (t0) cc_final: 0.7595 (t70) REVERT: B 593 GLN cc_start: 0.7485 (mt0) cc_final: 0.7275 (mt0) REVERT: B 600 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: B 606 ASP cc_start: 0.8136 (t70) cc_final: 0.7484 (t70) REVERT: B 608 ARG cc_start: 0.8430 (tmt170) cc_final: 0.7595 (tpp-160) REVERT: B 650 ASN cc_start: 0.8609 (t0) cc_final: 0.8268 (t0) REVERT: B 834 ARG cc_start: 0.6729 (mtt90) cc_final: 0.6287 (mtp85) REVERT: B 841 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6434 (mtt180) REVERT: B 1143 LYS cc_start: 0.8770 (mtmt) cc_final: 0.7915 (mtpt) REVERT: C 118 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8300 (ttm-80) REVERT: E 116 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7871 (tp40) REVERT: E 128 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7277 (mt-10) REVERT: E 210 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6470 (pp30) REVERT: H 31 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7658 (mt-10) REVERT: H 74 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7275 (mm-30) REVERT: H 103 GLU cc_start: 0.8825 (pm20) cc_final: 0.8298 (pm20) REVERT: J 58 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7625 (mtpp) REVERT: L 27 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: O 502 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6669 (mtm-85) REVERT: O 582 GLU cc_start: 0.7356 (tp30) cc_final: 0.7110 (tp30) REVERT: O 598 LYS cc_start: 0.7628 (tttt) cc_final: 0.6862 (ptpt) REVERT: O 609 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7334 (m-70) REVERT: O 610 ARG cc_start: 0.5467 (mtp180) cc_final: 0.5078 (tpm170) outliers start: 71 outliers final: 22 residues processed: 488 average time/residue: 0.7676 time to fit residues: 435.1747 Evaluate side-chains 466 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain O residue 509 GLN Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 334 optimal weight: 20.0000 chunk 346 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1146 GLN A1236 ASN B 319 ASN B 518 HIS B 582 GLN B1071 ASN E 92 GLN H 76 ASN I 46 GLN O 609 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099064 restraints weight = 39951.093| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.17 r_work: 0.3198 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34745 Z= 0.220 Angle : 0.581 10.506 47288 Z= 0.298 Chirality : 0.045 0.185 5274 Planarity : 0.004 0.045 5837 Dihedral : 14.102 176.468 5339 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 13.37 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.13), residues: 3974 helix: 1.34 (0.14), residues: 1467 sheet: -0.27 (0.21), residues: 588 loop : -0.34 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 35 TYR 0.018 0.002 TYR O 508 PHE 0.019 0.002 PHE C 63 TRP 0.015 0.002 TRP B 27 HIS 0.010 0.001 HIS O 609 Details of bonding type rmsd covalent geometry : bond 0.00537 (34714) covalent geometry : angle 0.57171 (47253) SS BOND : bond 0.00139 ( 1) SS BOND : angle 4.59565 ( 2) hydrogen bonds : bond 0.04578 ( 1504) hydrogen bonds : angle 4.74997 ( 4222) metal coordination : bond 0.00612 ( 30) metal coordination : angle 3.85162 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 453 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7542 (mmm-85) REVERT: A 70 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7890 (mtp180) REVERT: A 127 LYS cc_start: 0.7288 (mptt) cc_final: 0.6951 (mptt) REVERT: A 223 GLU cc_start: 0.8039 (tp30) cc_final: 0.7540 (tp30) REVERT: A 423 ASN cc_start: 0.8324 (t0) cc_final: 0.7980 (m-40) REVERT: A 524 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8087 (mmt) REVERT: A 556 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7263 (mm-30) REVERT: A 562 ASN cc_start: 0.8104 (t0) cc_final: 0.7576 (t0) REVERT: A 634 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7495 (mt-10) REVERT: A 715 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 818 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 1182 GLN cc_start: 0.7011 (mp10) cc_final: 0.6732 (pm20) REVERT: A 1199 MET cc_start: 0.3875 (pmm) cc_final: 0.2275 (ptp) REVERT: A 1225 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7751 (ttmt) REVERT: A 1228 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7197 (mtt) REVERT: A 1233 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: A 1423 ASP cc_start: 0.7652 (t0) cc_final: 0.7279 (t0) REVERT: A 1437 ASP cc_start: 0.8083 (m-30) cc_final: 0.7484 (t0) REVERT: A 1440 MET cc_start: 0.7815 (mmt) cc_final: 0.7415 (mmt) REVERT: A 1479 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7210 (mmtm) REVERT: B 24 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: B 233 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7453 (p) REVERT: B 294 ASP cc_start: 0.8738 (t70) cc_final: 0.8525 (t70) REVERT: B 333 GLU cc_start: 0.7684 (mp0) cc_final: 0.7342 (tm-30) REVERT: B 473 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 546 GLU cc_start: 0.8202 (tp30) cc_final: 0.7890 (tp30) REVERT: B 552 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8197 (m110) REVERT: B 579 ASP cc_start: 0.7922 (t0) cc_final: 0.7588 (t70) REVERT: B 593 GLN cc_start: 0.7472 (mt0) cc_final: 0.7266 (mt0) REVERT: B 600 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 606 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7507 (t70) REVERT: B 608 ARG cc_start: 0.8418 (tmt170) cc_final: 0.7596 (tpp-160) REVERT: B 650 ASN cc_start: 0.8656 (t0) cc_final: 0.8272 (t0) REVERT: B 834 ARG cc_start: 0.6770 (mtt90) cc_final: 0.6425 (mtp85) REVERT: B 841 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6370 (mtt180) REVERT: B 1143 LYS cc_start: 0.8771 (mtmt) cc_final: 0.7904 (mtpt) REVERT: C 118 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (ttm-80) REVERT: E 116 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7888 (tp40) REVERT: E 128 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7166 (mt-10) REVERT: G 117 MET cc_start: -0.1031 (tmm) cc_final: -0.2948 (ptm) REVERT: H 31 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7615 (mt-10) REVERT: H 36 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7933 (mmpt) REVERT: H 103 GLU cc_start: 0.8834 (pm20) cc_final: 0.8291 (pm20) REVERT: J 58 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7617 (mtpp) REVERT: L 27 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: L 44 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8634 (mtp) REVERT: O 535 LYS cc_start: 0.6519 (mmtp) cc_final: 0.6175 (pptt) REVERT: O 536 GLU cc_start: 0.4992 (pp20) cc_final: 0.4233 (pp20) REVERT: O 598 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6866 (ptpt) REVERT: O 603 LYS cc_start: 0.7831 (tppt) cc_final: 0.7515 (pptt) REVERT: O 609 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7099 (m-70) REVERT: O 610 ARG cc_start: 0.5455 (mtp180) cc_final: 0.5054 (tpm170) outliers start: 79 outliers final: 23 residues processed: 492 average time/residue: 0.7704 time to fit residues: 440.8863 Evaluate side-chains 482 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 439 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 161 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 249 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1093 GLN A1146 GLN A1236 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS E 92 GLN F 46 GLN G 21 ASN G 60 GLN H 76 ASN H 87 GLN I 46 GLN O 509 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.159245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101429 restraints weight = 39628.008| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.18 r_work: 0.3241 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34745 Z= 0.135 Angle : 0.538 9.643 47288 Z= 0.278 Chirality : 0.042 0.187 5274 Planarity : 0.004 0.039 5837 Dihedral : 14.059 176.621 5339 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.94 % Allowed : 14.15 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.13), residues: 3974 helix: 1.50 (0.14), residues: 1467 sheet: -0.14 (0.22), residues: 549 loop : -0.30 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 35 TYR 0.018 0.001 TYR O 508 PHE 0.019 0.001 PHE A 234 TRP 0.014 0.001 TRP B 27 HIS 0.011 0.001 HIS O 609 Details of bonding type rmsd covalent geometry : bond 0.00318 (34714) covalent geometry : angle 0.53016 (47253) SS BOND : bond 0.00106 ( 1) SS BOND : angle 3.22970 ( 2) hydrogen bonds : bond 0.04002 ( 1504) hydrogen bonds : angle 4.61402 ( 4222) metal coordination : bond 0.00434 ( 30) metal coordination : angle 3.49996 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 455 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7549 (mmm-85) REVERT: A 70 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: A 223 GLU cc_start: 0.8071 (tp30) cc_final: 0.7634 (tp30) REVERT: A 423 ASN cc_start: 0.8291 (t0) cc_final: 0.7982 (m-40) REVERT: A 556 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 562 ASN cc_start: 0.8066 (t0) cc_final: 0.7539 (t0) REVERT: A 634 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 715 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 818 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: A 1031 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.6874 (mmt180) REVERT: A 1182 GLN cc_start: 0.6913 (mp10) cc_final: 0.6659 (pm20) REVERT: A 1199 MET cc_start: 0.3921 (pmm) cc_final: 0.1911 (ptt) REVERT: A 1225 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7712 (ttmt) REVERT: A 1228 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7184 (mtt) REVERT: A 1233 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: A 1423 ASP cc_start: 0.7633 (t0) cc_final: 0.7183 (t0) REVERT: A 1437 ASP cc_start: 0.8040 (m-30) cc_final: 0.7438 (t0) REVERT: A 1479 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7174 (mmtm) REVERT: B 156 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 222 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7520 (mtp85) REVERT: B 233 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7460 (p) REVERT: B 333 GLU cc_start: 0.7663 (mp0) cc_final: 0.7340 (tm-30) REVERT: B 546 GLU cc_start: 0.8138 (tp30) cc_final: 0.7852 (tp30) REVERT: B 552 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8163 (m110) REVERT: B 579 ASP cc_start: 0.7954 (t0) cc_final: 0.7637 (t70) REVERT: B 606 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7498 (t70) REVERT: B 608 ARG cc_start: 0.8387 (tmt170) cc_final: 0.7570 (tpp-160) REVERT: B 650 ASN cc_start: 0.8639 (t0) cc_final: 0.8283 (t0) REVERT: B 834 ARG cc_start: 0.6863 (mtt90) cc_final: 0.6514 (mmt180) REVERT: B 841 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6099 (mtt180) REVERT: B 1143 LYS cc_start: 0.8806 (mtmt) cc_final: 0.7963 (mtpt) REVERT: C 118 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8221 (ttm-80) REVERT: E 95 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8498 (tt0) REVERT: E 116 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7943 (tp40) REVERT: E 128 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7163 (mt-10) REVERT: F 122 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7953 (mt-10) REVERT: G 117 MET cc_start: -0.0922 (tmm) cc_final: -0.2967 (ptm) REVERT: H 36 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7953 (mmpt) REVERT: J 58 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7666 (mtpp) REVERT: K 2 ASN cc_start: 0.8936 (m-40) cc_final: 0.8560 (m110) REVERT: L 27 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: L 44 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: O 582 GLU cc_start: 0.6954 (tp30) cc_final: 0.6679 (tp30) REVERT: O 598 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6834 (ptpt) REVERT: O 603 LYS cc_start: 0.7693 (tppt) cc_final: 0.7432 (pptt) REVERT: O 610 ARG cc_start: 0.5411 (mtp180) cc_final: 0.5005 (tpm170) outliers start: 69 outliers final: 20 residues processed: 490 average time/residue: 0.7728 time to fit residues: 440.8860 Evaluate side-chains 455 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 419 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 598 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 219 optimal weight: 2.9990 chunk 393 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 529 GLN A1146 GLN A1236 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 518 HIS B 593 GLN E 92 GLN F 46 GLN G 21 ASN H 76 ASN H 87 GLN I 46 GLN ** O 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 609 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097859 restraints weight = 40129.917| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.17 r_work: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 34745 Z= 0.278 Angle : 0.630 11.593 47288 Z= 0.323 Chirality : 0.047 0.221 5274 Planarity : 0.005 0.047 5837 Dihedral : 14.094 176.580 5339 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.11 % Allowed : 15.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 3974 helix: 1.21 (0.14), residues: 1468 sheet: -0.37 (0.21), residues: 599 loop : -0.34 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 583 TYR 0.017 0.002 TYR B1048 PHE 0.021 0.002 PHE C 63 TRP 0.016 0.002 TRP B 27 HIS 0.014 0.001 HIS O 609 Details of bonding type rmsd covalent geometry : bond 0.00688 (34714) covalent geometry : angle 0.62153 (47253) SS BOND : bond 0.00517 ( 1) SS BOND : angle 3.08024 ( 2) hydrogen bonds : bond 0.04952 ( 1504) hydrogen bonds : angle 4.80569 ( 4222) metal coordination : bond 0.00743 ( 30) metal coordination : angle 3.94207 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 427 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7550 (mmm-85) REVERT: A 70 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7877 (mtp180) REVERT: A 127 LYS cc_start: 0.7313 (mptt) cc_final: 0.6991 (mptt) REVERT: A 223 GLU cc_start: 0.8071 (tp30) cc_final: 0.7870 (tp30) REVERT: A 423 ASN cc_start: 0.8355 (t0) cc_final: 0.8003 (m-40) REVERT: A 556 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 562 ASN cc_start: 0.8123 (t0) cc_final: 0.7646 (t0) REVERT: A 634 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 678 ASN cc_start: 0.8887 (m-40) cc_final: 0.8661 (m110) REVERT: A 715 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 1031 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6879 (mmt90) REVERT: A 1182 GLN cc_start: 0.6873 (mp10) cc_final: 0.6628 (pm20) REVERT: A 1199 MET cc_start: 0.4165 (pmm) cc_final: 0.2239 (ptp) REVERT: A 1225 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7771 (ttmt) REVERT: A 1228 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7231 (mtt) REVERT: A 1233 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 1423 ASP cc_start: 0.7794 (t0) cc_final: 0.7463 (t0) REVERT: A 1437 ASP cc_start: 0.8126 (m-30) cc_final: 0.7516 (t0) REVERT: A 1440 MET cc_start: 0.7886 (mmt) cc_final: 0.7467 (mmt) REVERT: A 1479 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7165 (mmtm) REVERT: B 156 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 233 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7443 (p) REVERT: B 333 GLU cc_start: 0.7671 (mp0) cc_final: 0.7346 (tm-30) REVERT: B 546 GLU cc_start: 0.8231 (tp30) cc_final: 0.7991 (tp30) REVERT: B 552 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8155 (m110) REVERT: B 579 ASP cc_start: 0.8100 (t0) cc_final: 0.7694 (t70) REVERT: B 600 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: B 606 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7654 (t70) REVERT: B 608 ARG cc_start: 0.8399 (tmt170) cc_final: 0.7582 (tpp-160) REVERT: B 650 ASN cc_start: 0.8671 (t0) cc_final: 0.8300 (t0) REVERT: B 834 ARG cc_start: 0.6789 (mtt90) cc_final: 0.6392 (mmt180) REVERT: B 841 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6058 (mtt180) REVERT: C 118 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8234 (ttm-80) REVERT: D 62 MET cc_start: 0.6782 (mmt) cc_final: 0.6415 (mpt) REVERT: E 95 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8471 (tt0) REVERT: E 116 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7931 (tp40) REVERT: E 128 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7230 (mt-10) REVERT: F 100 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7645 (mtt-85) REVERT: F 122 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7940 (mt-10) REVERT: J 58 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7689 (mtpp) REVERT: O 598 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6894 (ptpt) REVERT: O 613 LYS cc_start: 0.5448 (mmtt) cc_final: 0.5132 (pptt) outliers start: 75 outliers final: 29 residues processed: 470 average time/residue: 0.7629 time to fit residues: 418.0248 Evaluate side-chains 445 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 401 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain O residue 551 GLU Chi-restraints excluded: chain O residue 598 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 364 optimal weight: 0.9980 chunk 366 optimal weight: 0.7980 chunk 325 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.0270 chunk 402 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 353 ASN A1146 GLN A1236 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B1073 GLN E 92 GLN F 46 GLN G 21 ASN H 76 ASN H 87 GLN I 46 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102235 restraints weight = 39620.113| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.17 r_work: 0.3257 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34745 Z= 0.121 Angle : 0.550 12.120 47288 Z= 0.285 Chirality : 0.042 0.338 5274 Planarity : 0.004 0.043 5837 Dihedral : 14.055 176.751 5339 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.13), residues: 3974 helix: 1.50 (0.14), residues: 1463 sheet: -0.12 (0.22), residues: 554 loop : -0.28 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 589 TYR 0.015 0.001 TYR O 508 PHE 0.020 0.001 PHE A 234 TRP 0.013 0.001 TRP B 27 HIS 0.006 0.001 HIS O 552 Details of bonding type rmsd covalent geometry : bond 0.00275 (34714) covalent geometry : angle 0.54215 (47253) SS BOND : bond 0.01124 ( 1) SS BOND : angle 5.36444 ( 2) hydrogen bonds : bond 0.03875 ( 1504) hydrogen bonds : angle 4.58281 ( 4222) metal coordination : bond 0.00388 ( 30) metal coordination : angle 3.34126 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 431 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7587 (mmm-85) REVERT: A 70 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7853 (mtp180) REVERT: A 127 LYS cc_start: 0.7283 (mptt) cc_final: 0.6925 (mptt) REVERT: A 223 GLU cc_start: 0.8053 (tp30) cc_final: 0.7850 (tp30) REVERT: A 423 ASN cc_start: 0.8301 (t0) cc_final: 0.7986 (m-40) REVERT: A 556 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 562 ASN cc_start: 0.8073 (t0) cc_final: 0.7562 (t0) REVERT: A 634 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 678 ASN cc_start: 0.8833 (m-40) cc_final: 0.8580 (m110) REVERT: A 715 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: A 1031 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6850 (mmt90) REVERT: A 1182 GLN cc_start: 0.6798 (mp10) cc_final: 0.6571 (pm20) REVERT: A 1199 MET cc_start: 0.4027 (pmm) cc_final: 0.2138 (ptp) REVERT: A 1225 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: A 1228 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7164 (mtt) REVERT: A 1233 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: A 1287 CYS cc_start: 0.8144 (t) cc_final: 0.7832 (m) REVERT: A 1423 ASP cc_start: 0.7652 (t0) cc_final: 0.7361 (t0) REVERT: A 1437 ASP cc_start: 0.8022 (m-30) cc_final: 0.7420 (t0) REVERT: A 1479 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7153 (mmtm) REVERT: B 108 MET cc_start: 0.8580 (ttp) cc_final: 0.8222 (ptp) REVERT: B 233 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7420 (p) REVERT: B 333 GLU cc_start: 0.7651 (mp0) cc_final: 0.7328 (tm-30) REVERT: B 546 GLU cc_start: 0.8132 (tp30) cc_final: 0.7886 (tp30) REVERT: B 552 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (m110) REVERT: B 579 ASP cc_start: 0.8028 (t0) cc_final: 0.7660 (t70) REVERT: B 606 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7641 (t70) REVERT: B 608 ARG cc_start: 0.8302 (tmt170) cc_final: 0.7516 (tpp-160) REVERT: B 650 ASN cc_start: 0.8659 (t0) cc_final: 0.8285 (t0) REVERT: B 834 ARG cc_start: 0.6897 (mtt90) cc_final: 0.6551 (mmt180) REVERT: B 841 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6086 (mtt180) REVERT: B 1143 LYS cc_start: 0.8796 (mtmt) cc_final: 0.7940 (mtpt) REVERT: B 1172 MET cc_start: 0.8597 (mmt) cc_final: 0.8186 (mmm) REVERT: C 118 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8207 (ttm-80) REVERT: D 62 MET cc_start: 0.6841 (mmt) cc_final: 0.6473 (mpt) REVERT: E 95 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8480 (tt0) REVERT: E 116 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7938 (tp40) REVERT: E 128 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7176 (mt-10) REVERT: F 122 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7936 (mt-10) REVERT: J 28 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8443 (mt-10) REVERT: J 58 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7632 (mtpp) REVERT: K 2 ASN cc_start: 0.8907 (m-40) cc_final: 0.8547 (m110) REVERT: L 47 LYS cc_start: 0.8510 (mtpp) cc_final: 0.7931 (mttp) REVERT: O 598 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6974 (ptpt) REVERT: O 603 LYS cc_start: 0.7711 (tppt) cc_final: 0.7397 (pptt) REVERT: O 609 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7511 (m-70) REVERT: O 613 LYS cc_start: 0.5580 (mmtt) cc_final: 0.5217 (pptt) outliers start: 55 outliers final: 17 residues processed: 458 average time/residue: 0.7347 time to fit residues: 393.5480 Evaluate side-chains 448 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 418 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain O residue 551 GLU Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 315 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 290 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 394 optimal weight: 0.0040 chunk 236 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1236 ASN B 518 HIS E 92 GLN G 21 ASN G 60 GLN H 76 ASN H 87 GLN I 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101311 restraints weight = 39823.430| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.37 r_work: 0.3213 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34745 Z= 0.183 Angle : 0.577 13.247 47288 Z= 0.296 Chirality : 0.044 0.261 5274 Planarity : 0.004 0.043 5837 Dihedral : 14.026 176.754 5339 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 16.01 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.13), residues: 3974 helix: 1.45 (0.14), residues: 1464 sheet: -0.20 (0.21), residues: 575 loop : -0.29 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 589 TYR 0.015 0.001 TYR B 766 PHE 0.015 0.001 PHE A 592 TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00446 (34714) covalent geometry : angle 0.56923 (47253) SS BOND : bond 0.00180 ( 1) SS BOND : angle 4.81078 ( 2) hydrogen bonds : bond 0.04237 ( 1504) hydrogen bonds : angle 4.63101 ( 4222) metal coordination : bond 0.00514 ( 30) metal coordination : angle 3.44393 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 425 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7596 (mmm-85) REVERT: A 67 ARG cc_start: 0.7604 (mmt180) cc_final: 0.7298 (mmm160) REVERT: A 70 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7916 (mtp180) REVERT: A 127 LYS cc_start: 0.7302 (mptt) cc_final: 0.6913 (mptt) REVERT: A 223 GLU cc_start: 0.8043 (tp30) cc_final: 0.7839 (tp30) REVERT: A 423 ASN cc_start: 0.8324 (t0) cc_final: 0.7993 (m-40) REVERT: A 556 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 562 ASN cc_start: 0.8079 (t0) cc_final: 0.7552 (t0) REVERT: A 634 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7386 (mt-10) REVERT: A 678 ASN cc_start: 0.8865 (m-40) cc_final: 0.8614 (m110) REVERT: A 715 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 1031 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6859 (mmt180) REVERT: A 1101 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: A 1182 GLN cc_start: 0.6792 (mp10) cc_final: 0.6548 (pm20) REVERT: A 1225 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7722 (ttmt) REVERT: A 1228 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: A 1233 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: A 1287 CYS cc_start: 0.8141 (t) cc_final: 0.7823 (m) REVERT: A 1351 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8194 (t0) REVERT: A 1423 ASP cc_start: 0.7737 (t0) cc_final: 0.7440 (t0) REVERT: A 1437 ASP cc_start: 0.8058 (m-30) cc_final: 0.7452 (t0) REVERT: A 1440 MET cc_start: 0.7921 (mmt) cc_final: 0.7511 (mmt) REVERT: A 1479 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7130 (mmtm) REVERT: B 108 MET cc_start: 0.8558 (ttp) cc_final: 0.8226 (ptp) REVERT: B 156 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 222 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7759 (mtp85) REVERT: B 233 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7458 (p) REVERT: B 333 GLU cc_start: 0.7649 (mp0) cc_final: 0.7323 (tm-30) REVERT: B 335 ARG cc_start: 0.6438 (mtm180) cc_final: 0.6200 (mtm180) REVERT: B 546 GLU cc_start: 0.8161 (tp30) cc_final: 0.7940 (tp30) REVERT: B 552 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8100 (m110) REVERT: B 579 ASP cc_start: 0.8074 (t0) cc_final: 0.7662 (t70) REVERT: B 600 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: B 606 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7674 (t70) REVERT: B 608 ARG cc_start: 0.8340 (tmt170) cc_final: 0.7539 (tpp-160) REVERT: B 650 ASN cc_start: 0.8663 (t0) cc_final: 0.8295 (t0) REVERT: B 834 ARG cc_start: 0.6951 (mtt90) cc_final: 0.6628 (mmt180) REVERT: B 841 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6104 (mtt180) REVERT: C 118 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (ttm-80) REVERT: D 62 MET cc_start: 0.6823 (mmt) cc_final: 0.6448 (mpt) REVERT: E 95 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8484 (tt0) REVERT: E 116 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7952 (tp40) REVERT: E 128 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7204 (mt-10) REVERT: F 86 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7726 (mm-30) REVERT: F 122 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7957 (mt-10) REVERT: J 58 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7703 (mtpp) REVERT: K 2 ASN cc_start: 0.8927 (m-40) cc_final: 0.8566 (m110) REVERT: L 47 LYS cc_start: 0.8516 (mtpp) cc_final: 0.7929 (mttp) REVERT: O 598 LYS cc_start: 0.7637 (tttt) cc_final: 0.7238 (ptpt) REVERT: O 603 LYS cc_start: 0.7759 (tppt) cc_final: 0.7411 (pptt) REVERT: O 613 LYS cc_start: 0.5664 (mmtt) cc_final: 0.5379 (pptt) outliers start: 52 outliers final: 24 residues processed: 456 average time/residue: 0.7114 time to fit residues: 379.2492 Evaluate side-chains 454 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 415 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 141 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1236 ASN B 518 HIS E 92 GLN E 108 GLN G 21 ASN H 76 ASN H 87 GLN I 46 GLN O 585 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102057 restraints weight = 39865.908| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.17 r_work: 0.3251 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34745 Z= 0.138 Angle : 0.557 12.339 47288 Z= 0.288 Chirality : 0.042 0.201 5274 Planarity : 0.004 0.045 5837 Dihedral : 14.010 176.814 5339 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.32 % Allowed : 16.24 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.13), residues: 3974 helix: 1.53 (0.14), residues: 1462 sheet: -0.05 (0.22), residues: 550 loop : -0.27 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 583 TYR 0.015 0.001 TYR O 508 PHE 0.021 0.001 PHE A 234 TRP 0.012 0.001 TRP B 27 HIS 0.007 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00326 (34714) covalent geometry : angle 0.55009 (47253) SS BOND : bond 0.00169 ( 1) SS BOND : angle 4.11423 ( 2) hydrogen bonds : bond 0.03893 ( 1504) hydrogen bonds : angle 4.56534 ( 4222) metal coordination : bond 0.00397 ( 30) metal coordination : angle 3.18938 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 427 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7581 (mmm-85) REVERT: A 70 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7922 (mtp180) REVERT: A 223 GLU cc_start: 0.7980 (tp30) cc_final: 0.7778 (tp30) REVERT: A 423 ASN cc_start: 0.8330 (t0) cc_final: 0.8005 (m-40) REVERT: A 556 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 562 ASN cc_start: 0.8043 (t0) cc_final: 0.7518 (t0) REVERT: A 634 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 678 ASN cc_start: 0.8814 (m-40) cc_final: 0.8561 (m110) REVERT: A 715 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: A 1031 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.6895 (mmt180) REVERT: A 1101 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: A 1182 GLN cc_start: 0.6781 (mp10) cc_final: 0.6531 (pm20) REVERT: A 1199 MET cc_start: 0.3937 (pmm) cc_final: 0.1812 (ptp) REVERT: A 1228 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: A 1233 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8225 (pt0) REVERT: A 1279 MET cc_start: 0.4083 (tmm) cc_final: 0.3372 (ttm) REVERT: A 1280 ASP cc_start: 0.7863 (t0) cc_final: 0.7621 (t0) REVERT: A 1287 CYS cc_start: 0.8131 (t) cc_final: 0.7813 (m) REVERT: A 1351 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 1423 ASP cc_start: 0.7650 (t0) cc_final: 0.7388 (t0) REVERT: A 1437 ASP cc_start: 0.8031 (m-30) cc_final: 0.7440 (t0) REVERT: A 1479 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7150 (mppt) REVERT: B 108 MET cc_start: 0.8533 (ttp) cc_final: 0.8206 (ptp) REVERT: B 156 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 233 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7390 (p) REVERT: B 324 ARG cc_start: 0.7075 (mmm-85) cc_final: 0.6871 (mmm-85) REVERT: B 333 GLU cc_start: 0.7644 (mp0) cc_final: 0.7330 (tm-30) REVERT: B 335 ARG cc_start: 0.6436 (mtm180) cc_final: 0.6190 (mtm180) REVERT: B 546 GLU cc_start: 0.8125 (tp30) cc_final: 0.7877 (tp30) REVERT: B 552 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8059 (m-40) REVERT: B 554 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 579 ASP cc_start: 0.8025 (t0) cc_final: 0.7670 (t70) REVERT: B 606 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7712 (t70) REVERT: B 608 ARG cc_start: 0.8292 (tmt170) cc_final: 0.7520 (tpp-160) REVERT: B 650 ASN cc_start: 0.8660 (t0) cc_final: 0.8296 (t0) REVERT: B 834 ARG cc_start: 0.6999 (mtt90) cc_final: 0.6699 (mmt180) REVERT: B 841 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6076 (mtt180) REVERT: C 118 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8203 (ttm-80) REVERT: D 62 MET cc_start: 0.6825 (mmt) cc_final: 0.6448 (mpt) REVERT: E 95 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8486 (tt0) REVERT: E 116 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7828 (tp40) REVERT: E 128 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7146 (mt-10) REVERT: F 122 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7873 (mt-10) REVERT: H 36 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8063 (mmmt) REVERT: J 28 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8369 (mt-10) REVERT: J 58 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7628 (mtpp) REVERT: K 2 ASN cc_start: 0.8898 (m-40) cc_final: 0.8522 (m110) REVERT: L 47 LYS cc_start: 0.8514 (mtpp) cc_final: 0.7932 (mttp) REVERT: O 598 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7062 (ptpt) REVERT: O 603 LYS cc_start: 0.7733 (tppt) cc_final: 0.7362 (pptt) REVERT: O 609 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7532 (m90) REVERT: O 613 LYS cc_start: 0.5777 (mmtt) cc_final: 0.5454 (pptt) outliers start: 47 outliers final: 23 residues processed: 453 average time/residue: 0.8469 time to fit residues: 449.2230 Evaluate side-chains 452 residues out of total 3554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 415 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain O residue 598 LYS Chi-restraints excluded: chain O residue 609 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 359 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 260 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 385 optimal weight: 10.0000 chunk 234 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1236 ASN B 344 GLN B 518 HIS E 92 GLN E 108 GLN G 21 ASN G 60 GLN H 76 ASN H 87 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101836 restraints weight = 39555.642| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.17 r_work: 0.3246 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34745 Z= 0.142 Angle : 0.556 11.751 47288 Z= 0.287 Chirality : 0.043 0.208 5274 Planarity : 0.004 0.062 5837 Dihedral : 13.989 176.881 5339 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.29 % Allowed : 16.40 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.13), residues: 3974 helix: 1.55 (0.14), residues: 1461 sheet: -0.09 (0.22), residues: 562 loop : -0.25 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 583 TYR 0.014 0.001 TYR O 508 PHE 0.015 0.001 PHE A 592 TRP 0.014 0.001 TRP B 27 HIS 0.008 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00338 (34714) covalent geometry : angle 0.54923 (47253) SS BOND : bond 0.00085 ( 1) SS BOND : angle 3.93167 ( 2) hydrogen bonds : bond 0.03914 ( 1504) hydrogen bonds : angle 4.54610 ( 4222) metal coordination : bond 0.00410 ( 30) metal coordination : angle 3.17353 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14225.91 seconds wall clock time: 241 minutes 57.04 seconds (14517.04 seconds total)