Starting phenix.real_space_refine on Mon Aug 10 05:44:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2026/8xvs_38717.map" } resolution = 4.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 324 5.49 5 Mg 1 5.21 5 S 211 5.16 5 C 26395 2.51 5 N 7750 2.21 5 O 8775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 339 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43464 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11237 Classifications: {'peptide': 1418} Link IDs: {'PTRANS': 69, 'TRANS': 1348} Chain breaks: 4 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 15, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1337 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3107 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain breaks: 1 Chain: "T" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3325 Classifications: {'DNA': 163} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 162} Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "a" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "b" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "d" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "e" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "h" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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 71 157.537 42.472 121.994 1.00144.43 S ATOM 486 SG CYS A 74 159.265 44.852 120.132 1.00140.44 S ATOM 533 SG CYS A 81 156.388 45.958 122.007 1.00133.68 S ATOM 768 SG CYS A 111 125.509 47.613 84.203 1.00212.58 S ATOM 796 SG CYS A 114 127.937 45.748 82.601 1.00210.70 S ATOM 1142 SG CYS A 184 124.262 45.086 82.060 1.00207.63 S ATOM 19869 SG CYS B1119 158.546 50.943 104.890 1.00135.04 S ATOM 19891 SG CYS B1122 154.780 50.397 105.367 1.00134.67 S ATOM 20006 SG CYS B1137 157.140 47.905 106.175 1.00141.46 S ATOM 20027 SG CYS B1140 157.211 47.663 102.886 1.00148.99 S ATOM 20994 SG CYS C 88 169.252 77.510 180.827 1.00223.53 S ATOM 21007 SG CYS C 90 168.788 74.016 180.607 1.00209.09 S ATOM 21042 SG CYS C 94 167.953 74.758 184.024 1.00194.44 S ATOM 21064 SG CYS C 97 165.939 76.084 181.351 1.00201.35 S ATOM 28278 SG CYS I 17 65.753 61.556 110.684 1.00128.86 S ATOM 28302 SG CYS I 20 67.728 58.905 111.963 1.00124.30 S ATOM 28463 SG CYS I 39 69.109 61.155 109.329 1.00131.47 S ATOM 28488 SG CYS I 42 66.348 58.837 108.760 1.00125.65 S ATOM 28840 SG CYS I 86 70.473 95.999 139.203 1.00126.10 S ATOM 28864 SG CYS I 89 68.866 95.565 142.091 1.00122.53 S ATOM 29068 SG CYS I 114 72.467 94.218 141.830 1.00124.93 S ATOM 29103 SG CYS I 119 69.374 92.695 140.490 1.00126.75 S ATOM 29213 SG CYS J 7 137.526 90.081 174.849 1.00115.24 S ATOM 29237 SG CYS J 10 139.725 92.562 176.489 1.00123.59 S ATOM 29501 SG CYS J 44 136.636 93.707 174.582 1.00113.88 S ATOM 29507 SG CYS J 45 136.533 92.230 177.749 1.00116.99 S ATOM 30653 SG CYS L 19 132.172 45.798 175.874 1.00256.75 S ATOM 30672 SG CYS L 22 131.938 45.158 179.243 1.00283.54 S ATOM 30789 SG CYS L 36 133.159 42.569 177.103 1.00234.04 S ATOM 30815 SG CYS L 39 129.448 43.441 177.078 1.00258.08 S Time building chain proxies: 7.85, per 1000 atoms: 0.18 Number of scatterers: 43464 At special positions: 0 Unit cell: (216.24, 159, 207.76, 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 211 16.00 P 324 15.00 Mg 1 11.99 O 8775 8.00 N 7750 7.00 C 26395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 39 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8670 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 59 sheets defined 44.8% alpha, 17.2% beta 141 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.072A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.932A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.635A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.520A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.751A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.575A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.853A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.630A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.736A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.511A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.512A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.959A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.802A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.716A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.251A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 3.595A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.296A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.062A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.939A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.594A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.133A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.644A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1263 through 1267 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.025A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.551A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.967A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.623A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.656A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.626A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1470 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.729A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.703A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 251 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: 3.776A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.797A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.008A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.578A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.501A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.840A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.536A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.688A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.055A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.680A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.897A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 124 through 128 removed outlier: 4.132A pdb=" N VAL C 127 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE C 128 " --> pdb=" O PRO C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 128' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.716A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.947A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.001A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.978A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.029A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.846A pdb=" N GLU K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 56 Processing helix chain 'a' and resid 63 through 77 removed outlier: 4.093A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 removed outlier: 3.541A pdb=" N LEU d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 removed outlier: 3.512A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.910A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.369A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 122 removed outlier: 3.546A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.673A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.022A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.666A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.648A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.978A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.783A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.888A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.748A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.644A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.754A 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 'F' and resid 115 through 119 removed outlier: 5.207A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.207A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.895A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.944A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 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 removed outlier: 3.541A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.684A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.273A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.967A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.967A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS L 46 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=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: 6.999A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=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: 4.056A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 894 " --> pdb=" O ILE B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.712A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.760A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.759A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.087A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.556A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE7, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE8, first strand: chain 'G' and resid 84 through 93 removed outlier: 5.537A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.805A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 25 through 29 removed outlier: 4.619A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.840A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF7, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF8, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.395A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG1, first strand: chain 'c' and resid 100 through 102 removed outlier: 6.485A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.836A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.088A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'g' and resid 77 through 78 1785 hydrogen bonds defined for protein. 5010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 19.13 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8928 1.33 - 1.45: 11497 1.45 - 1.58: 23522 1.58 - 1.70: 645 1.70 - 1.83: 336 Bond restraints: 44928 Sorted by residual: bond pdb=" C3' DC T 53 " pdb=" C2' DC T 53 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.35e+01 bond pdb=" C3' DA N 77 " pdb=" C2' DA N 77 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.19e+01 bond pdb=" CA GLN A 461 " pdb=" C GLN A 461 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.26e-02 6.30e+03 2.03e+01 bond pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.58e-02 4.01e+03 1.98e+01 bond pdb=" C3' DC N 43 " pdb=" C2' DC N 43 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.97e+01 ... (remaining 44923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 56129 2.41 - 4.83: 5489 4.83 - 7.24: 452 7.24 - 9.65: 14 9.65 - 12.07: 2 Bond angle restraints: 62086 Sorted by residual: angle pdb=" O5' DG T 39 " pdb=" C5' DG T 39 " pdb=" C4' DG T 39 " ideal model delta sigma weight residual 109.40 116.56 -7.16 8.00e-01 1.56e+00 8.01e+01 angle pdb=" O5' DC N 37 " pdb=" C5' DC N 37 " pdb=" C4' DC N 37 " ideal model delta sigma weight residual 109.40 115.11 -5.71 8.00e-01 1.56e+00 5.09e+01 angle pdb=" O5' DA N 150 " pdb=" C5' DA N 150 " pdb=" C4' DA N 150 " ideal model delta sigma weight residual 109.40 114.91 -5.51 8.00e-01 1.56e+00 4.74e+01 angle pdb=" O5' DC N 152 " pdb=" C5' DC N 152 " pdb=" C4' DC N 152 " ideal model delta sigma weight residual 109.40 114.88 -5.48 8.00e-01 1.56e+00 4.70e+01 angle pdb=" N VAL e 117 " pdb=" CA VAL e 117 " pdb=" C VAL e 117 " ideal model delta sigma weight residual 112.90 106.63 6.27 9.60e-01 1.09e+00 4.27e+01 ... (remaining 62081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 24791 35.99 - 71.99: 1709 71.99 - 107.98: 85 107.98 - 143.97: 4 143.97 - 179.96: 4 Dihedral angle restraints: 26593 sinusoidal: 13177 harmonic: 13416 Sorted by residual: dihedral pdb=" CA GLN B 825 " pdb=" C GLN B 825 " pdb=" N GLU B 826 " pdb=" CA GLU B 826 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU B 135 " pdb=" C GLU B 135 " pdb=" N GLY B 136 " pdb=" CA GLY B 136 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 26590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 5932 0.114 - 0.228: 928 0.228 - 0.343: 96 0.343 - 0.457: 12 0.457 - 0.571: 17 Chirality restraints: 6985 Sorted by residual: chirality pdb=" P A P 1 " pdb=" OP1 A P 1 " pdb=" OP2 A P 1 " pdb=" O5' A P 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.15e+00 chirality pdb=" CA GLN A 461 " pdb=" N GLN A 461 " pdb=" C GLN A 461 " pdb=" CB GLN A 461 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" P DT N 106 " pdb=" OP1 DT N 106 " pdb=" OP2 DT N 106 " pdb=" O5' DT N 106 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 6982 not shown) Planarity restraints: 6873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 548 " -0.207 2.00e-02 2.50e+03 9.87e-02 2.43e+02 pdb=" CG TRP B 548 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 548 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP B 548 " 0.099 2.00e-02 2.50e+03 pdb=" NE1 TRP B 548 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP B 548 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 548 " 0.119 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 548 " -0.107 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 548 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP B 548 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 49 " 0.134 2.00e-02 2.50e+03 6.71e-02 1.13e+02 pdb=" CG TRP C 49 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 49 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 49 " -0.077 2.00e-02 2.50e+03 pdb=" NE1 TRP C 49 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP C 49 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP C 49 " -0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 49 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 49 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 49 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 42 " -0.075 2.00e-02 2.50e+03 5.92e-02 1.05e+02 pdb=" N9 DG N 42 " 0.002 2.00e-02 2.50e+03 pdb=" C8 DG N 42 " -0.051 2.00e-02 2.50e+03 pdb=" N7 DG N 42 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DG N 42 " 0.037 2.00e-02 2.50e+03 pdb=" C6 DG N 42 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG N 42 " -0.056 2.00e-02 2.50e+03 pdb=" N1 DG N 42 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DG N 42 " 0.050 2.00e-02 2.50e+03 pdb=" N2 DG N 42 " -0.103 2.00e-02 2.50e+03 pdb=" N3 DG N 42 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DG N 42 " 0.081 2.00e-02 2.50e+03 ... (remaining 6870 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 15 2.40 - 3.03: 22825 3.03 - 3.65: 66112 3.65 - 4.28: 102624 4.28 - 4.90: 164045 Nonbonded interactions: 355621 Sorted by model distance: nonbonded pdb=" OP1 U P 11 " pdb="MG MG A2003 " model vdw 1.775 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.183 2.170 nonbonded pdb=" OG SER B 31 " pdb=" OH TYR B 766 " model vdw 2.205 3.040 nonbonded pdb=" O2 DT N 31 " pdb=" N1 DA T 133 " model vdw 2.282 3.120 ... (remaining 355616 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 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 34 through 122) selection = (chain 'h' and resid 34 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 56.660 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 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 : 0.011 0.461 44959 Z= 0.691 Angle : 1.398 20.929 62125 Z= 0.979 Chirality : 0.085 0.571 6985 Planarity : 0.011 0.133 6873 Dihedral : 19.822 179.963 17923 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4562 helix: 0.43 (0.11), residues: 1870 sheet: 0.06 (0.22), residues: 546 loop : -0.53 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 551 TYR 0.118 0.009 TYR K 81 PHE 0.101 0.007 PHE C 229 TRP 0.207 0.015 TRP B 548 HIS 0.032 0.002 HIS H 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00959 / 0.67 (44928) covalent geometry : angle 1.37916 / 0.98 (62086) hydrogen bonds : bond 0.14965 / 10.00 ( 2096) hydrogen bonds : angle 6.51606 / 4.61 ( 5706) metal coordination : bond 0.17243 / 13.23 ( 31) metal coordination : angle 9.20883 / 6.40 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.327 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 58 MET cc_start: 0.8120 (ttt) cc_final: 0.7713 (mtt) REVERT: A 266 MET cc_start: -0.5296 (mmm) cc_final: -0.5814 (ttt) REVERT: A 329 MET cc_start: 0.7231 (mmt) cc_final: 0.6935 (tpp) REVERT: A 467 MET cc_start: 0.7653 (mpp) cc_final: 0.7269 (mmt) REVERT: A 524 MET cc_start: 0.8068 (mmp) cc_final: 0.6986 (mmt) REVERT: A 1221 MET cc_start: 0.8109 (mmm) cc_final: 0.7859 (mmm) REVERT: A 1292 MET cc_start: 0.6898 (mtm) cc_final: 0.6654 (mtm) REVERT: B 53 MET cc_start: 0.8508 (mmp) cc_final: 0.7784 (mmm) REVERT: F 49 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7347 (pm20) REVERT: G 98 PHE cc_start: -0.4952 (m-10) cc_final: -0.5283 (m-80) REVERT: G 107 PHE cc_start: 0.4042 (m-80) cc_final: 0.3578 (t80) REVERT: G 119 PHE cc_start: 0.3104 (t80) cc_final: 0.2825 (p90) REVERT: I 108 MET cc_start: 0.6433 (mmm) cc_final: 0.6081 (mmm) REVERT: K 114 GLU cc_start: 0.7330 (pm20) cc_final: 0.7065 (mp0) REVERT: L 27 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7992 (mp0) REVERT: e 90 MET cc_start: 0.5142 (mmm) cc_final: 0.4396 (mmp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2600 time to fit residues: 110.2964 Evaluate side-chains 159 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 671 ASN A 982 ASN A1462 GLN B 98 HIS B 265 GLN B 790 GLN C 25 ASN C 51 GLN C 66 HIS C 217 GLN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS J 52 HIS K 69 HIS a 85 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN f 25 ASN g 73 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.055051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.044679 restraints weight = 531691.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.044490 restraints weight = 353019.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.044409 restraints weight = 268283.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.044473 restraints weight = 244235.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.044428 restraints weight = 211431.856| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 44959 Z= 0.224 Angle : 0.752 14.895 62125 Z= 0.406 Chirality : 0.051 0.342 6985 Planarity : 0.005 0.061 6873 Dihedral : 23.803 176.925 8650 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4562 helix: 1.26 (0.12), residues: 1887 sheet: -0.01 (0.20), residues: 595 loop : -0.44 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1260 TYR 0.025 0.002 TYR f 51 PHE 0.027 0.002 PHE C 93 TRP 0.018 0.002 TRP A1210 HIS 0.013 0.002 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (44928) covalent geometry : angle 0.73877 / 0.40 (62086) hydrogen bonds : bond 0.06091 / 4.12 ( 2096) hydrogen bonds : angle 4.93344 / 3.47 ( 5706) metal coordination : bond 0.01494 / 1.10 ( 31) metal coordination : angle 5.66077 / 3.85 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.6944 (mmt) cc_final: 0.6727 (tpp) REVERT: A 467 MET cc_start: 0.7534 (mpp) cc_final: 0.7290 (mmt) REVERT: B 200 MET cc_start: 0.8027 (tpp) cc_final: 0.7777 (tpp) REVERT: G 53 ASN cc_start: 0.8324 (t0) cc_final: 0.7906 (p0) REVERT: H 78 THR cc_start: 0.8299 (p) cc_final: 0.7702 (t) REVERT: I 14 ILE cc_start: 0.6068 (tt) cc_final: 0.5773 (tt) REVERT: I 108 MET cc_start: 0.6071 (mmm) cc_final: 0.5713 (mmt) REVERT: L 27 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7616 (mp0) REVERT: L 44 MET cc_start: 0.6687 (tpp) cc_final: 0.6292 (tpt) REVERT: e 90 MET cc_start: 0.5621 (mmm) cc_final: 0.4960 (mmp) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2351 time to fit residues: 68.0835 Evaluate side-chains 149 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 159 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 226 optimal weight: 40.0000 chunk 307 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 84 HIS K 69 HIS a 113 HIS c 24 GLN f 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.053632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.043584 restraints weight = 534277.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.043177 restraints weight = 363714.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.043327 restraints weight = 292478.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.043208 restraints weight = 265659.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.043149 restraints weight = 227519.939| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 44959 Z= 0.223 Angle : 0.713 13.202 62125 Z= 0.386 Chirality : 0.049 0.406 6985 Planarity : 0.005 0.054 6873 Dihedral : 23.827 174.902 8650 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.12), residues: 4562 helix: 1.24 (0.12), residues: 1871 sheet: -0.15 (0.21), residues: 601 loop : -0.50 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG I 109 TYR 0.025 0.002 TYR B 752 PHE 0.041 0.003 PHE A 458 TRP 0.021 0.003 TRP A1210 HIS 0.014 0.002 HIS A1220 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (44928) covalent geometry : angle 0.70298 / 0.39 (62086) hydrogen bonds : bond 0.05352 / 3.56 ( 2096) hydrogen bonds : angle 4.76950 / 3.39 ( 5706) metal coordination : bond 0.01089 / 0.73 ( 31) metal coordination : angle 4.72748 / 3.57 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7196 (mmt) cc_final: 0.6753 (tpp) REVERT: A 1428 MET cc_start: 0.8104 (mmm) cc_final: 0.7883 (mmm) REVERT: B 200 MET cc_start: 0.8074 (tpp) cc_final: 0.7850 (tpp) REVERT: B 297 MET cc_start: 0.7005 (mmt) cc_final: 0.6754 (mmt) REVERT: B 508 MET cc_start: 0.7293 (mpp) cc_final: 0.6865 (mpp) REVERT: G 53 ASN cc_start: 0.8298 (t0) cc_final: 0.7957 (p0) REVERT: H 78 THR cc_start: 0.8393 (p) cc_final: 0.7962 (t) REVERT: I 108 MET cc_start: 0.6293 (mmm) cc_final: 0.5998 (mmt) REVERT: L 27 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7520 (mp0) REVERT: e 90 MET cc_start: 0.5788 (mmm) cc_final: 0.5099 (mmp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2356 time to fit residues: 64.9319 Evaluate side-chains 146 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 125 optimal weight: 7.9990 chunk 460 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 371 optimal weight: 0.0070 chunk 47 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 overall best weight: 4.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 265 GLN B1094 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.053671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.043686 restraints weight = 531405.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.043227 restraints weight = 374896.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.043181 restraints weight = 299128.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.043255 restraints weight = 292248.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.043274 restraints weight = 231305.261| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44959 Z= 0.163 Angle : 0.631 12.449 62125 Z= 0.341 Chirality : 0.046 0.378 6985 Planarity : 0.004 0.083 6873 Dihedral : 23.755 177.710 8650 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4562 helix: 1.51 (0.12), residues: 1877 sheet: -0.23 (0.20), residues: 596 loop : -0.46 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 483 TYR 0.017 0.002 TYR f 51 PHE 0.026 0.002 PHE A 458 TRP 0.033 0.002 TRP C 176 HIS 0.009 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (44928) covalent geometry : angle 0.62079 / 0.34 (62086) hydrogen bonds : bond 0.04554 / 3.02 ( 2096) hydrogen bonds : angle 4.56171 / 3.25 ( 5706) metal coordination : bond 0.00763 / 0.52 ( 31) metal coordination : angle 4.50031 / 3.20 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8247 (m90) cc_final: 0.7958 (m-70) REVERT: A 329 MET cc_start: 0.7349 (mmt) cc_final: 0.6857 (tpp) REVERT: A 1086 MET cc_start: 0.8716 (mmm) cc_final: 0.8478 (mpp) REVERT: A 1428 MET cc_start: 0.8119 (mmm) cc_final: 0.7878 (mmm) REVERT: B 550 MET cc_start: 0.6734 (tmm) cc_final: 0.6273 (tmm) REVERT: B 594 MET cc_start: 0.7785 (mpp) cc_final: 0.7553 (mpp) REVERT: E 151 MET cc_start: 0.7643 (mtp) cc_final: 0.7168 (ttm) REVERT: G 53 ASN cc_start: 0.8248 (t0) cc_final: 0.7873 (p0) REVERT: G 98 PHE cc_start: -0.5047 (m-10) cc_final: -0.6322 (m-80) REVERT: H 78 THR cc_start: 0.8479 (p) cc_final: 0.8117 (t) REVERT: J 48 MET cc_start: 0.8703 (mmm) cc_final: 0.7865 (mmm) REVERT: L 27 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7451 (mp0) REVERT: e 90 MET cc_start: 0.5767 (mmm) cc_final: 0.5082 (mmp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2369 time to fit residues: 65.5084 Evaluate side-chains 146 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 318 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 403 optimal weight: 50.0000 chunk 339 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.053505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.043249 restraints weight = 530543.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.042887 restraints weight = 354678.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.042967 restraints weight = 316150.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.042988 restraints weight = 233965.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.042950 restraints weight = 216581.349| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 44959 Z= 0.151 Angle : 0.600 11.559 62125 Z= 0.327 Chirality : 0.045 0.356 6985 Planarity : 0.004 0.052 6873 Dihedral : 23.624 175.641 8650 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 4562 helix: 1.59 (0.12), residues: 1888 sheet: -0.23 (0.20), residues: 598 loop : -0.41 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 109 TYR 0.015 0.001 TYR f 51 PHE 0.034 0.002 PHE a 104 TRP 0.016 0.002 TRP C 176 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (44928) covalent geometry : angle 0.59165 / 0.33 (62086) hydrogen bonds : bond 0.04359 / 2.88 ( 2096) hydrogen bonds : angle 4.46640 / 3.18 ( 5706) metal coordination : bond 0.00700 / 0.48 ( 31) metal coordination : angle 4.08601 / 2.89 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8289 (m90) cc_final: 0.7993 (m-70) REVERT: A 329 MET cc_start: 0.7296 (mmt) cc_final: 0.6952 (tpp) REVERT: A 1428 MET cc_start: 0.8178 (mmm) cc_final: 0.7939 (mmm) REVERT: B 508 MET cc_start: 0.7187 (mpp) cc_final: 0.6742 (mpp) REVERT: B 550 MET cc_start: 0.6762 (tmm) cc_final: 0.6216 (tmm) REVERT: E 151 MET cc_start: 0.7640 (mtp) cc_final: 0.7193 (ttm) REVERT: G 53 ASN cc_start: 0.8253 (t0) cc_final: 0.7856 (p0) REVERT: G 107 PHE cc_start: 0.3186 (t80) cc_final: 0.2506 (m-80) REVERT: H 78 THR cc_start: 0.8561 (p) cc_final: 0.8213 (t) REVERT: I 108 MET cc_start: 0.5911 (mmt) cc_final: 0.4678 (mmt) REVERT: J 48 MET cc_start: 0.8850 (mmm) cc_final: 0.7890 (mmm) REVERT: K 111 ASP cc_start: 0.7671 (m-30) cc_final: 0.7415 (m-30) REVERT: L 27 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7599 (mp0) REVERT: e 90 MET cc_start: 0.5742 (mmm) cc_final: 0.5159 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2273 time to fit residues: 61.6255 Evaluate side-chains 143 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 152 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 184 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 331 optimal weight: 20.0000 chunk 467 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 322 optimal weight: 40.0000 chunk 30 optimal weight: 7.9990 chunk 365 optimal weight: 0.9980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.053522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.043403 restraints weight = 531264.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.042970 restraints weight = 358690.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043242 restraints weight = 296038.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.043172 restraints weight = 228544.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043163 restraints weight = 218177.016| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44959 Z= 0.135 Angle : 0.580 10.122 62125 Z= 0.315 Chirality : 0.044 0.330 6985 Planarity : 0.004 0.062 6873 Dihedral : 23.530 174.620 8650 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 4562 helix: 1.69 (0.12), residues: 1888 sheet: -0.25 (0.20), residues: 587 loop : -0.38 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.024 0.001 TYR L 41 PHE 0.024 0.001 PHE A 458 TRP 0.014 0.001 TRP B 27 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (44928) covalent geometry : angle 0.57173 / 0.31 (62086) hydrogen bonds : bond 0.04095 / 2.70 ( 2096) hydrogen bonds : angle 4.38306 / 3.13 ( 5706) metal coordination : bond 0.00635 / 0.44 ( 31) metal coordination : angle 3.89904 / 2.85 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8232 (m90) cc_final: 0.7934 (m-70) REVERT: A 329 MET cc_start: 0.7356 (mmt) cc_final: 0.6962 (tpp) REVERT: A 1086 MET cc_start: 0.8381 (mpp) cc_final: 0.8107 (mpp) REVERT: A 1428 MET cc_start: 0.8131 (mmm) cc_final: 0.7875 (mmm) REVERT: B 550 MET cc_start: 0.6788 (tmm) cc_final: 0.5854 (tmm) REVERT: E 110 MET cc_start: 0.8137 (tmm) cc_final: 0.7599 (tmm) REVERT: E 151 MET cc_start: 0.7576 (mtp) cc_final: 0.7186 (ttm) REVERT: G 53 ASN cc_start: 0.8109 (t0) cc_final: 0.7751 (p0) REVERT: G 107 PHE cc_start: 0.3219 (t80) cc_final: 0.2484 (m-80) REVERT: H 78 THR cc_start: 0.8565 (p) cc_final: 0.8234 (t) REVERT: I 108 MET cc_start: 0.5894 (mmt) cc_final: 0.4695 (mmt) REVERT: J 48 MET cc_start: 0.8790 (mmm) cc_final: 0.7938 (mmm) REVERT: K 111 ASP cc_start: 0.7723 (m-30) cc_final: 0.7387 (m-30) REVERT: L 27 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7629 (mp0) REVERT: e 90 MET cc_start: 0.5923 (mmm) cc_final: 0.5267 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2249 time to fit residues: 60.5755 Evaluate side-chains 143 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 159 optimal weight: 0.0060 chunk 71 optimal weight: 20.0000 chunk 413 optimal weight: 30.0000 chunk 300 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 403 optimal weight: 50.0000 chunk 110 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 370 optimal weight: 0.4980 overall best weight: 2.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS A 387 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 265 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.053445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.043257 restraints weight = 528816.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.042944 restraints weight = 350511.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043193 restraints weight = 253937.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043165 restraints weight = 200149.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.043150 restraints weight = 192741.087| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44959 Z= 0.126 Angle : 0.564 9.415 62125 Z= 0.307 Chirality : 0.044 0.309 6985 Planarity : 0.004 0.056 6873 Dihedral : 23.397 172.277 8650 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.13), residues: 4562 helix: 1.83 (0.12), residues: 1882 sheet: -0.22 (0.21), residues: 587 loop : -0.32 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG f 92 TYR 0.022 0.001 TYR L 41 PHE 0.020 0.001 PHE A 458 TRP 0.013 0.001 TRP B 27 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (44928) covalent geometry : angle 0.55664 / 0.31 (62086) hydrogen bonds : bond 0.03933 / 2.59 ( 2096) hydrogen bonds : angle 4.31013 / 3.07 ( 5706) metal coordination : bond 0.01295 / 0.69 ( 31) metal coordination : angle 3.77414 / 2.63 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8259 (m90) cc_final: 0.7945 (m-70) REVERT: A 329 MET cc_start: 0.7519 (mmt) cc_final: 0.7037 (tpp) REVERT: A 470 MET cc_start: 0.8418 (mtt) cc_final: 0.8102 (mtt) REVERT: A 1086 MET cc_start: 0.8350 (mpp) cc_final: 0.8041 (mpp) REVERT: A 1428 MET cc_start: 0.8087 (mmm) cc_final: 0.7836 (mmm) REVERT: B 550 MET cc_start: 0.6823 (tmm) cc_final: 0.5840 (tmm) REVERT: E 110 MET cc_start: 0.8133 (tmm) cc_final: 0.7267 (tmm) REVERT: E 151 MET cc_start: 0.7481 (mtp) cc_final: 0.7134 (ttm) REVERT: G 107 PHE cc_start: 0.3127 (t80) cc_final: 0.2410 (m-80) REVERT: H 78 THR cc_start: 0.8629 (p) cc_final: 0.8326 (t) REVERT: I 23 MET cc_start: 0.2934 (tmm) cc_final: 0.1355 (ttp) REVERT: I 108 MET cc_start: 0.5897 (mmt) cc_final: 0.4708 (mmt) REVERT: J 48 MET cc_start: 0.8783 (mmm) cc_final: 0.7981 (mmm) REVERT: K 111 ASP cc_start: 0.7537 (m-30) cc_final: 0.7322 (m-30) REVERT: L 27 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7594 (mp0) REVERT: e 90 MET cc_start: 0.5920 (mmm) cc_final: 0.5280 (mmp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2158 time to fit residues: 59.0269 Evaluate side-chains 141 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 177 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 359 optimal weight: 2.9990 chunk 448 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.053332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.043138 restraints weight = 528996.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.042777 restraints weight = 353844.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.042726 restraints weight = 276451.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.042762 restraints weight = 235696.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.042788 restraints weight = 211982.146| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 44959 Z= 0.159 Angle : 0.602 10.760 62125 Z= 0.325 Chirality : 0.044 0.296 6985 Planarity : 0.004 0.053 6873 Dihedral : 23.336 171.246 8650 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4562 helix: 1.77 (0.12), residues: 1878 sheet: -0.36 (0.20), residues: 593 loop : -0.34 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 483 TYR 0.021 0.001 TYR B 752 PHE 0.031 0.002 PHE H 56 TRP 0.012 0.002 TRP A1192 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (44928) covalent geometry : angle 0.59381 / 0.32 (62086) hydrogen bonds : bond 0.04279 / 2.81 ( 2096) hydrogen bonds : angle 4.36758 / 3.12 ( 5706) metal coordination : bond 0.01100 / 0.63 ( 31) metal coordination : angle 3.94659 / 2.82 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8327 (m90) cc_final: 0.7977 (m-70) REVERT: A 329 MET cc_start: 0.7482 (mmt) cc_final: 0.7012 (tpp) REVERT: A 524 MET cc_start: 0.7689 (mmm) cc_final: 0.6720 (mmt) REVERT: A 1086 MET cc_start: 0.8462 (mpp) cc_final: 0.8167 (mpp) REVERT: A 1428 MET cc_start: 0.8083 (mmm) cc_final: 0.7857 (mmm) REVERT: A 1484 MET cc_start: 0.3185 (ptp) cc_final: 0.2671 (ptp) REVERT: B 550 MET cc_start: 0.6985 (tmm) cc_final: 0.6142 (tmm) REVERT: B 603 MET cc_start: 0.7689 (ptt) cc_final: 0.7242 (ptp) REVERT: E 110 MET cc_start: 0.8240 (tmm) cc_final: 0.7454 (tmm) REVERT: E 151 MET cc_start: 0.7617 (mtp) cc_final: 0.7156 (ttm) REVERT: G 107 PHE cc_start: 0.3127 (t80) cc_final: 0.2317 (m-80) REVERT: H 78 THR cc_start: 0.8697 (p) cc_final: 0.8408 (t) REVERT: I 108 MET cc_start: 0.5884 (mmt) cc_final: 0.4727 (mmt) REVERT: J 48 MET cc_start: 0.8933 (mmm) cc_final: 0.8084 (mmm) REVERT: K 1 MET cc_start: 0.1594 (ptp) cc_final: 0.1012 (tpp) REVERT: K 111 ASP cc_start: 0.7676 (m-30) cc_final: 0.7335 (m-30) REVERT: L 27 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7508 (mp0) REVERT: L 44 MET cc_start: 0.6067 (tpp) cc_final: 0.5775 (tpp) REVERT: e 90 MET cc_start: 0.5985 (mmm) cc_final: 0.5396 (mmp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2104 time to fit residues: 56.5703 Evaluate side-chains 143 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 124 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 346 optimal weight: 40.0000 chunk 393 optimal weight: 50.0000 chunk 234 optimal weight: 0.9980 chunk 403 optimal weight: 50.0000 chunk 245 optimal weight: 4.9990 chunk 459 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 731 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.052962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.042512 restraints weight = 528392.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.042454 restraints weight = 347621.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.042310 restraints weight = 242297.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.042341 restraints weight = 224168.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.042342 restraints weight = 203506.655| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 44959 Z= 0.208 Angle : 0.650 12.466 62125 Z= 0.347 Chirality : 0.046 0.295 6985 Planarity : 0.005 0.058 6873 Dihedral : 23.418 172.328 8650 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.12), residues: 4562 helix: 1.54 (0.12), residues: 1882 sheet: -0.48 (0.20), residues: 579 loop : -0.46 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 358 TYR 0.028 0.002 TYR A 827 PHE 0.020 0.002 PHE A 458 TRP 0.012 0.002 TRP A1210 HIS 0.009 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (44928) covalent geometry : angle 0.64108 / 0.35 (62086) hydrogen bonds : bond 0.04666 / 3.06 ( 2096) hydrogen bonds : angle 4.52763 / 3.23 ( 5706) metal coordination : bond 0.00921 / 0.60 ( 31) metal coordination : angle 4.39337 / 3.13 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8360 (m90) cc_final: 0.8026 (m-70) REVERT: A 329 MET cc_start: 0.7414 (mmt) cc_final: 0.6990 (tpp) REVERT: A 1086 MET cc_start: 0.8503 (mpp) cc_final: 0.8112 (mpp) REVERT: A 1428 MET cc_start: 0.8074 (mmm) cc_final: 0.7805 (mmm) REVERT: A 1484 MET cc_start: 0.3028 (ptp) cc_final: 0.2529 (ptp) REVERT: E 110 MET cc_start: 0.8261 (tmm) cc_final: 0.7512 (tmm) REVERT: E 151 MET cc_start: 0.7735 (mtp) cc_final: 0.7208 (ttm) REVERT: G 107 PHE cc_start: 0.3004 (t80) cc_final: 0.2161 (m-80) REVERT: H 78 THR cc_start: 0.8855 (p) cc_final: 0.8571 (t) REVERT: I 108 MET cc_start: 0.5803 (mmt) cc_final: 0.4741 (mpp) REVERT: J 48 MET cc_start: 0.9008 (mmm) cc_final: 0.8062 (mmm) REVERT: K 1 MET cc_start: 0.1943 (ptp) cc_final: 0.1493 (tpp) REVERT: K 111 ASP cc_start: 0.7629 (m-30) cc_final: 0.7365 (m-30) REVERT: e 90 MET cc_start: 0.5867 (mmm) cc_final: 0.5343 (mmp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2258 time to fit residues: 60.4537 Evaluate side-chains 140 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 205 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 475 optimal weight: 40.0000 chunk 460 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 208 optimal weight: 0.0870 chunk 382 optimal weight: 50.0000 chunk 314 optimal weight: 30.0000 chunk 329 optimal weight: 8.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 HIS A 387 ASN A 685 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.052852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042646 restraints weight = 530207.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042457 restraints weight = 360000.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.042436 restraints weight = 272205.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.042463 restraints weight = 269802.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.042449 restraints weight = 223405.322| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44959 Z= 0.196 Angle : 0.649 13.032 62125 Z= 0.347 Chirality : 0.046 0.352 6985 Planarity : 0.005 0.075 6873 Dihedral : 23.478 173.585 8650 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.12), residues: 4562 helix: 1.40 (0.12), residues: 1884 sheet: -0.48 (0.21), residues: 565 loop : -0.56 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 35 TYR 0.023 0.002 TYR A 827 PHE 0.028 0.002 PHE B 956 TRP 0.011 0.002 TRP A1210 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (44928) covalent geometry : angle 0.63904 / 0.35 (62086) hydrogen bonds : bond 0.04590 / 3.01 ( 2096) hydrogen bonds : angle 4.60017 / 3.28 ( 5706) metal coordination : bond 0.00863 / 0.57 ( 31) metal coordination : angle 4.54505 / 3.14 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8206 (m90) cc_final: 0.7901 (m-70) REVERT: A 329 MET cc_start: 0.7399 (mmt) cc_final: 0.6974 (tpp) REVERT: A 1086 MET cc_start: 0.8474 (mpp) cc_final: 0.8031 (mpp) REVERT: A 1428 MET cc_start: 0.8159 (mmm) cc_final: 0.7876 (mmm) REVERT: A 1484 MET cc_start: 0.3056 (ptp) cc_final: 0.2577 (ptp) REVERT: B 407 MET cc_start: 0.5825 (tmm) cc_final: 0.5432 (tmm) REVERT: B 550 MET cc_start: 0.6954 (tmm) cc_final: 0.6174 (tmm) REVERT: E 110 MET cc_start: 0.8284 (tmm) cc_final: 0.7583 (tmm) REVERT: E 151 MET cc_start: 0.7678 (mtp) cc_final: 0.7218 (ttm) REVERT: G 107 PHE cc_start: 0.2864 (t80) cc_final: 0.2081 (m-80) REVERT: H 78 THR cc_start: 0.8955 (p) cc_final: 0.8697 (t) REVERT: I 108 MET cc_start: 0.6102 (mmt) cc_final: 0.5010 (mpp) REVERT: J 48 MET cc_start: 0.8970 (mmm) cc_final: 0.8054 (mmm) REVERT: K 1 MET cc_start: 0.2029 (ptp) cc_final: 0.1668 (tpp) REVERT: e 90 MET cc_start: 0.6023 (mmm) cc_final: 0.5371 (mmp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2290 time to fit residues: 61.2682 Evaluate side-chains 141 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 175 optimal weight: 3.9990 chunk 458 optimal weight: 8.9990 chunk 273 optimal weight: 0.0070 chunk 39 optimal weight: 0.0020 chunk 355 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 431 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 286 optimal weight: 30.0000 chunk 237 optimal weight: 0.2980 overall best weight: 0.8610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 809 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B1094 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN I 41 ASN e 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.053533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.043319 restraints weight = 530367.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.043205 restraints weight = 344655.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.042979 restraints weight = 268329.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.043072 restraints weight = 283674.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.043058 restraints weight = 222643.651| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 44959 Z= 0.114 Angle : 0.578 13.982 62125 Z= 0.312 Chirality : 0.044 0.301 6985 Planarity : 0.004 0.059 6873 Dihedral : 23.308 173.368 8650 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4562 helix: 1.71 (0.12), residues: 1891 sheet: -0.37 (0.21), residues: 585 loop : -0.36 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 110 TYR 0.025 0.001 TYR B 752 PHE 0.021 0.001 PHE A 458 TRP 0.022 0.002 TRP B 27 HIS 0.006 0.001 HIS J 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (44928) covalent geometry : angle 0.57234 / 0.31 (62086) hydrogen bonds : bond 0.03776 / 2.48 ( 2096) hydrogen bonds : angle 4.31435 / 3.08 ( 5706) metal coordination : bond 0.00815 / 0.46 ( 31) metal coordination : angle 3.34708 / 2.34 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6210.61 seconds wall clock time: 108 minutes 37.59 seconds (6517.59 seconds total)