Starting phenix.real_space_refine on Tue Aug 26 23:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_38717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_38717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_38717.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_38717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvs_38717/08_2025/8xvs_38717.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.12, per 1000 atoms: 0.19 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: 3.20 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 5.62 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: 14.55 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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=" 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=" N MET a 120 " pdb=" CA MET a 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" N MET e 120 " pdb=" CA MET e 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" CB THR A 511 " pdb=" OG1 THR A 511 " ideal model delta sigma weight residual 1.433 1.373 0.060 1.60e-02 3.91e+03 1.42e+01 ... (remaining 44923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 56286 2.41 - 4.83: 5376 4.83 - 7.24: 409 7.24 - 9.65: 13 9.65 - 12.07: 2 Bond angle restraints: 62086 Sorted by residual: 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 angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 112.90 106.68 6.22 9.60e-01 1.09e+00 4.20e+01 angle pdb=" C MET A 520 " pdb=" N VAL A 521 " pdb=" CA VAL A 521 " ideal model delta sigma weight residual 120.33 125.50 -5.17 8.00e-01 1.56e+00 4.18e+01 angle pdb=" C GLY B1065 " pdb=" N PRO B1066 " pdb=" CA PRO B1066 " ideal model delta sigma weight residual 119.78 126.25 -6.47 1.03e+00 9.43e-01 3.94e+01 angle pdb=" C GLU I 82 " pdb=" N ASP I 83 " pdb=" CA ASP I 83 " ideal model delta sigma weight residual 120.65 128.84 -8.19 1.32e+00 5.74e-01 3.85e+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: 5979 0.114 - 0.228: 883 0.228 - 0.343: 95 0.343 - 0.457: 13 0.457 - 0.571: 15 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=" CA LYS A 910 " pdb=" N LYS A 910 " pdb=" C LYS A 910 " pdb=" CB LYS A 910 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 48.210 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.461 44959 Z= 0.615 Angle : 1.382 20.929 62125 Z= 0.917 Chirality : 0.084 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 aren 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 covalent geometry : bond 0.00940 (44928) covalent geometry : angle 1.36332 (62086) hydrogen bonds : bond 0.14965 ( 2096) hydrogen bonds : angle 6.51606 ( 5706) metal coordination : bond 0.17243 ( 31) metal coordination : angle 9.20883 ( 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 : 1.365 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: 0.6936 (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: 0.2826 (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: 0.4397 (mmp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2317 time to fit residues: 97.3269 Evaluate side-chains 158 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 620 HIS A 671 ASN A 982 ASN ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 98 HIS B 790 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 g 73 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.054370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.044118 restraints weight = 536474.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.043788 restraints weight = 356990.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.043955 restraints weight = 272938.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.043955 restraints weight = 209033.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.043957 restraints weight = 191907.081| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 44959 Z= 0.236 Angle : 0.709 15.286 62125 Z= 0.385 Chirality : 0.046 0.188 6985 Planarity : 0.005 0.047 6873 Dihedral : 23.715 179.746 8650 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % 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 aren not related in a simple way. whole: 0.47 (0.12), residues: 4562 helix: 1.30 (0.12), residues: 1884 sheet: 0.01 (0.21), residues: 595 loop : -0.45 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG c 20 TYR 0.025 0.002 TYR f 51 PHE 0.023 0.003 PHE C 93 TRP 0.018 0.003 TRP B 548 HIS 0.014 0.002 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00492 (44928) covalent geometry : angle 0.69718 (62086) hydrogen bonds : bond 0.05697 ( 2096) hydrogen bonds : angle 4.82538 ( 5706) metal coordination : bond 0.01226 ( 31) metal coordination : angle 5.12978 ( 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 166 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 1.042 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 467 MET cc_start: 0.7509 (mpp) cc_final: 0.7272 (mmt) REVERT: A 1279 MET cc_start: 0.1856 (ttt) cc_final: 0.0935 (ttt) REVERT: B 368 MET cc_start: 0.7630 (mtp) cc_final: 0.7394 (ttm) REVERT: B 508 MET cc_start: 0.7371 (mpp) cc_final: 0.6989 (mpp) REVERT: B 603 MET cc_start: 0.7436 (ptp) cc_final: 0.7185 (ptt) REVERT: E 151 MET cc_start: 0.7548 (mtp) cc_final: 0.7119 (ttm) REVERT: G 53 ASN cc_start: 0.8176 (t0) cc_final: 0.7800 (p0) REVERT: G 119 PHE cc_start: 0.4065 (t80) cc_final: 0.3845 (p90) REVERT: H 78 THR cc_start: 0.8315 (p) cc_final: 0.7747 (t) REVERT: I 108 MET cc_start: 0.6076 (mmm) cc_final: 0.5868 (mmt) REVERT: J 48 MET cc_start: 0.8878 (mmm) cc_final: 0.8170 (mmm) REVERT: L 27 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7531 (mp0) REVERT: L 44 MET cc_start: 0.6779 (tpp) cc_final: 0.6488 (tpt) REVERT: e 90 MET cc_start: 0.5747 (mmm) cc_final: 0.4998 (mmp) outliers start: 4 outliers final: 1 residues processed: 166 average time/residue: 0.2037 time to fit residues: 57.7179 Evaluate side-chains 149 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 10.0000 chunk 226 optimal weight: 30.0000 chunk 307 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 265 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS I 41 ASN I 84 HIS K 40 HIS K 69 HIS c 24 GLN e 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.053630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.043442 restraints weight = 533314.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.043149 restraints weight = 349678.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.043097 restraints weight = 279878.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.043129 restraints weight = 239542.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.043126 restraints weight = 214251.872| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 44959 Z= 0.193 Angle : 0.634 11.903 62125 Z= 0.346 Chirality : 0.044 0.185 6985 Planarity : 0.005 0.109 6873 Dihedral : 23.577 174.922 8650 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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 aren not related in a simple way. whole: 0.57 (0.12), residues: 4562 helix: 1.44 (0.12), residues: 1882 sheet: -0.03 (0.21), residues: 581 loop : -0.42 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.023 0.002 TYR B 752 PHE 0.046 0.003 PHE A 458 TRP 0.012 0.002 TRP B 548 HIS 0.010 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (44928) covalent geometry : angle 0.62505 (62086) hydrogen bonds : bond 0.04721 ( 2096) hydrogen bonds : angle 4.62837 ( 5706) metal coordination : bond 0.00877 ( 31) metal coordination : angle 4.38783 ( 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 156 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.284 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: 0.7375 (tpp) cc_final: 0.7062 (tpp) REVERT: A 524 MET cc_start: 0.7548 (mmm) cc_final: 0.6569 (mmp) REVERT: A 1086 MET cc_start: 0.8657 (mmm) cc_final: 0.8253 (mpp) REVERT: B 108 MET cc_start: 0.3200 (ttt) cc_final: 0.2932 (ttt) REVERT: B 200 MET cc_start: 0.8137 (tpp) cc_final: 0.7898 (tpp) REVERT: B 508 MET cc_start: 0.7344 (mpp) cc_final: 0.6982 (mpp) REVERT: B 550 MET cc_start: 0.6631 (tmm) cc_final: 0.6227 (tmm) REVERT: B 603 MET cc_start: 0.7373 (ptp) cc_final: 0.6888 (ptt) REVERT: E 151 MET cc_start: 0.7762 (mtp) cc_final: 0.7215 (ttm) REVERT: G 53 ASN cc_start: 0.8243 (t0) cc_final: 0.7934 (p0) REVERT: H 78 THR cc_start: 0.8437 (p) cc_final: 0.8086 (t) REVERT: I 108 MET cc_start: 0.6469 (mmm) cc_final: 0.6258 (mmm) REVERT: J 48 MET cc_start: 0.9006 (mmm) cc_final: 0.7608 (mmm) REVERT: L 27 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7615 (mp0) REVERT: e 90 MET cc_start: 0.5789 (mmm) cc_final: 0.5111 (mmp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2080 time to fit residues: 56.7424 Evaluate side-chains 144 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 8.9990 chunk 460 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 354 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 272 ASN A 313 HIS A 387 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.052832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.042862 restraints weight = 534070.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042503 restraints weight = 360067.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.042593 restraints weight = 271470.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.042613 restraints weight = 251402.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.042665 restraints weight = 207343.773| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 44959 Z= 0.229 Angle : 0.661 15.051 62125 Z= 0.355 Chirality : 0.044 0.191 6985 Planarity : 0.005 0.057 6873 Dihedral : 23.630 177.573 8650 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 aren not related in a simple way. whole: 0.32 (0.12), residues: 4562 helix: 1.24 (0.12), residues: 1886 sheet: -0.21 (0.20), residues: 612 loop : -0.56 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 54 TYR 0.021 0.002 TYR f 51 PHE 0.024 0.002 PHE A 234 TRP 0.024 0.002 TRP C 176 HIS 0.010 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00510 (44928) covalent geometry : angle 0.64915 (62086) hydrogen bonds : bond 0.04989 ( 2096) hydrogen bonds : angle 4.69671 ( 5706) metal coordination : bond 0.00962 ( 31) metal coordination : angle 4.92040 ( 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 149 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8108 (m90) cc_final: 0.7847 (m-70) REVERT: A 329 MET cc_start: 0.7435 (tpp) cc_final: 0.6628 (tpp) REVERT: A 467 MET cc_start: 0.7926 (mmt) cc_final: 0.7502 (mmt) REVERT: A 524 MET cc_start: 0.7431 (mmm) cc_final: 0.6617 (mmt) REVERT: A 959 MET cc_start: 0.8442 (mmm) cc_final: 0.8238 (mmp) REVERT: A 1279 MET cc_start: 0.1792 (ttt) cc_final: 0.1313 (ttt) REVERT: B 508 MET cc_start: 0.7252 (mpp) cc_final: 0.6888 (mpp) REVERT: B 550 MET cc_start: 0.6849 (tmm) cc_final: 0.5976 (tmm) REVERT: B 603 MET cc_start: 0.7657 (ptp) cc_final: 0.7104 (ptt) REVERT: E 94 MET cc_start: 0.7697 (tmm) cc_final: 0.7158 (tmm) REVERT: E 151 MET cc_start: 0.7662 (mtp) cc_final: 0.7223 (ttm) REVERT: F 75 MET cc_start: 0.8221 (mtt) cc_final: 0.8015 (mtp) REVERT: G 53 ASN cc_start: 0.8199 (t0) cc_final: 0.7849 (p0) REVERT: G 98 PHE cc_start: -0.4457 (m-10) cc_final: -0.5859 (m-80) REVERT: H 78 THR cc_start: 0.8663 (p) cc_final: 0.8353 (t) REVERT: I 14 ILE cc_start: 0.5064 (tt) cc_final: 0.4232 (tt) REVERT: K 1 MET cc_start: 0.2222 (pmm) cc_final: 0.1306 (tpp) REVERT: L 27 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7642 (mp0) REVERT: e 90 MET cc_start: 0.5930 (mmm) cc_final: 0.5178 (mmp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1860 time to fit residues: 49.4665 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 : 0.952 ------------------------------------------------------------------------------- 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: 9.9990 chunk 283 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** g 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.052546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.042469 restraints weight = 537457.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.042030 restraints weight = 372573.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042336 restraints weight = 286388.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.042286 restraints weight = 208928.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.042262 restraints weight = 202923.073| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 44959 Z= 0.209 Angle : 0.650 13.004 62125 Z= 0.350 Chirality : 0.044 0.167 6985 Planarity : 0.005 0.075 6873 Dihedral : 23.662 179.179 8650 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 aren not related in a simple way. whole: 0.24 (0.12), residues: 4562 helix: 1.19 (0.12), residues: 1890 sheet: -0.36 (0.21), residues: 560 loop : -0.58 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 108 TYR 0.026 0.002 TYR L 41 PHE 0.046 0.002 PHE a 104 TRP 0.018 0.002 TRP C 176 HIS 0.009 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (44928) covalent geometry : angle 0.63705 (62086) hydrogen bonds : bond 0.04654 ( 2096) hydrogen bonds : angle 4.70311 ( 5706) metal coordination : bond 0.01468 ( 31) metal coordination : angle 5.14466 ( 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 148 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8191 (m90) cc_final: 0.7926 (m-70) REVERT: A 329 MET cc_start: 0.7482 (tpp) cc_final: 0.6786 (tpp) REVERT: A 467 MET cc_start: 0.8029 (mmt) cc_final: 0.7595 (mmt) REVERT: A 524 MET cc_start: 0.7476 (mmm) cc_final: 0.6734 (mmp) REVERT: B 508 MET cc_start: 0.7361 (mpp) cc_final: 0.7020 (mpp) REVERT: B 550 MET cc_start: 0.6884 (tmm) cc_final: 0.5878 (tmm) REVERT: B 603 MET cc_start: 0.7717 (ptp) cc_final: 0.7129 (ptt) REVERT: E 151 MET cc_start: 0.7704 (mtp) cc_final: 0.7290 (ttm) REVERT: G 53 ASN cc_start: 0.8136 (t0) cc_final: 0.7731 (p0) REVERT: G 107 PHE cc_start: 0.3028 (t80) cc_final: 0.2197 (m-80) REVERT: G 117 MET cc_start: -0.1668 (tpp) cc_final: -0.1975 (tpp) REVERT: H 78 THR cc_start: 0.8893 (p) cc_final: 0.8623 (t) REVERT: I 14 ILE cc_start: 0.4803 (tt) cc_final: 0.4262 (tt) REVERT: I 108 MET cc_start: 0.6252 (mmt) cc_final: 0.5236 (mpp) REVERT: K 1 MET cc_start: 0.2321 (pmm) cc_final: 0.2079 (tpp) REVERT: e 90 MET cc_start: 0.6012 (mmm) cc_final: 0.5356 (mmp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2029 time to fit residues: 53.1044 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 : 1.049 ------------------------------------------------------------------------------- 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: 5.9990 chunk 180 optimal weight: 7.9990 chunk 184 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 331 optimal weight: 20.0000 chunk 467 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 overall best weight: 4.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 387 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.052529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.042369 restraints weight = 538181.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.042006 restraints weight = 342762.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.042000 restraints weight = 284021.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.041955 restraints weight = 236052.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.041896 restraints weight = 188728.843| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44959 Z= 0.175 Angle : 0.605 11.734 62125 Z= 0.327 Chirality : 0.042 0.182 6985 Planarity : 0.004 0.071 6873 Dihedral : 23.610 178.419 8650 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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 aren not related in a simple way. whole: 0.34 (0.12), residues: 4562 helix: 1.33 (0.12), residues: 1902 sheet: -0.33 (0.21), residues: 576 loop : -0.60 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 190 TYR 0.020 0.001 TYR L 41 PHE 0.019 0.002 PHE A 458 TRP 0.017 0.002 TRP B 27 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (44928) covalent geometry : angle 0.59454 (62086) hydrogen bonds : bond 0.04366 ( 2096) hydrogen bonds : angle 4.56450 ( 5706) metal coordination : bond 0.00769 ( 31) metal coordination : angle 4.48616 ( 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 148 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8252 (m90) cc_final: 0.7962 (m-70) REVERT: A 329 MET cc_start: 0.7344 (tpp) cc_final: 0.6591 (tpp) REVERT: A 467 MET cc_start: 0.7972 (mmt) cc_final: 0.7475 (mmt) REVERT: A 524 MET cc_start: 0.7469 (mmm) cc_final: 0.6673 (mmt) REVERT: A 1221 MET cc_start: 0.7759 (mmt) cc_final: 0.7334 (tmm) REVERT: A 1279 MET cc_start: 0.1528 (ttt) cc_final: 0.0950 (ttt) REVERT: B 508 MET cc_start: 0.7328 (mpp) cc_final: 0.6932 (mpp) REVERT: B 550 MET cc_start: 0.6877 (tmm) cc_final: 0.5800 (tmm) REVERT: B 584 MET cc_start: 0.7265 (tpt) cc_final: 0.6974 (mmm) REVERT: B 603 MET cc_start: 0.7680 (ptp) cc_final: 0.6883 (ptt) REVERT: E 94 MET cc_start: 0.7573 (tmm) cc_final: 0.7260 (ppp) REVERT: E 151 MET cc_start: 0.7622 (mtp) cc_final: 0.7265 (ttm) REVERT: G 107 PHE cc_start: 0.2861 (t80) cc_final: 0.2041 (m-80) REVERT: H 78 THR cc_start: 0.8890 (p) cc_final: 0.8635 (t) REVERT: I 108 MET cc_start: 0.6274 (mmt) cc_final: 0.5302 (mpp) REVERT: J 48 MET cc_start: 0.8515 (mmm) cc_final: 0.8293 (mtp) REVERT: L 44 MET cc_start: 0.6009 (tpp) cc_final: 0.5645 (tpt) REVERT: e 90 MET cc_start: 0.5776 (mmm) cc_final: 0.5316 (mmp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2005 time to fit residues: 53.0386 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 : 1.207 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 403 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 232 optimal weight: 7.9990 chunk 199 optimal weight: 0.0470 chunk 320 optimal weight: 5.9990 chunk 370 optimal weight: 0.8980 overall best weight: 3.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 410 ASN ** 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 ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** 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 = 0.3998 r_free = 0.3998 target = 0.052790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.042761 restraints weight = 529252.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.042334 restraints weight = 372380.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.042298 restraints weight = 303681.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.042387 restraints weight = 255587.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.042393 restraints weight = 216497.802| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44959 Z= 0.162 Angle : 0.588 10.335 62125 Z= 0.318 Chirality : 0.042 0.184 6985 Planarity : 0.004 0.058 6873 Dihedral : 23.548 176.845 8650 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 aren not related in a simple way. whole: 0.43 (0.13), residues: 4562 helix: 1.43 (0.12), residues: 1905 sheet: -0.38 (0.21), residues: 582 loop : -0.54 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 358 TYR 0.016 0.001 TYR L 41 PHE 0.019 0.002 PHE a 104 TRP 0.014 0.002 TRP B 27 HIS 0.020 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00360 (44928) covalent geometry : angle 0.57885 (62086) hydrogen bonds : bond 0.04166 ( 2096) hydrogen bonds : angle 4.46384 ( 5706) metal coordination : bond 0.00786 ( 31) metal coordination : angle 4.13670 ( 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 144 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8175 (m90) cc_final: 0.7894 (m-70) REVERT: A 329 MET cc_start: 0.7164 (tpp) cc_final: 0.6416 (tpp) REVERT: A 524 MET cc_start: 0.7433 (mmm) cc_final: 0.6809 (mmt) REVERT: A 1086 MET cc_start: 0.8412 (mpp) cc_final: 0.8032 (mpp) REVERT: A 1221 MET cc_start: 0.7832 (mmt) cc_final: 0.7337 (tmm) REVERT: B 297 MET cc_start: 0.7087 (mmt) cc_final: 0.6784 (mmt) REVERT: B 508 MET cc_start: 0.7268 (mpp) cc_final: 0.6889 (mpp) REVERT: B 550 MET cc_start: 0.6963 (tmm) cc_final: 0.5848 (tmm) REVERT: B 603 MET cc_start: 0.7248 (ptp) cc_final: 0.6940 (ptt) REVERT: B 976 MET cc_start: 0.8232 (mtp) cc_final: 0.8023 (mtm) REVERT: E 110 MET cc_start: 0.8209 (tmm) cc_final: 0.7719 (tmm) REVERT: E 151 MET cc_start: 0.7560 (mtp) cc_final: 0.7167 (ttm) REVERT: G 107 PHE cc_start: 0.2848 (t80) cc_final: 0.1968 (m-80) REVERT: H 78 THR cc_start: 0.8828 (p) cc_final: 0.8589 (t) REVERT: I 49 ASP cc_start: 0.7460 (m-30) cc_final: 0.7149 (p0) REVERT: I 108 MET cc_start: 0.6373 (mmt) cc_final: 0.5388 (mpp) REVERT: J 48 MET cc_start: 0.8694 (mmm) cc_final: 0.8181 (mmm) REVERT: e 90 MET cc_start: 0.5940 (mmm) cc_final: 0.5317 (mmp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1914 time to fit residues: 49.1423 Evaluate side-chains 139 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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: 6.9990 chunk 474 optimal weight: 50.0000 chunk 301 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 297 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 359 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 overall best weight: 4.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.052590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.042590 restraints weight = 532910.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042165 restraints weight = 382297.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.042024 restraints weight = 312019.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.042297 restraints weight = 258126.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.042199 restraints weight = 216376.379| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 44959 Z= 0.177 Angle : 0.607 10.630 62125 Z= 0.326 Chirality : 0.042 0.193 6985 Planarity : 0.004 0.059 6873 Dihedral : 23.544 174.556 8650 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: 0.37 (0.13), residues: 4562 helix: 1.39 (0.12), residues: 1896 sheet: -0.39 (0.21), residues: 585 loop : -0.59 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 35 TYR 0.020 0.001 TYR A 827 PHE 0.020 0.002 PHE A 458 TRP 0.014 0.002 TRP B 27 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (44928) covalent geometry : angle 0.59743 (62086) hydrogen bonds : bond 0.04306 ( 2096) hydrogen bonds : angle 4.51021 ( 5706) metal coordination : bond 0.00784 ( 31) metal coordination : angle 4.24750 ( 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 142 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8239 (m90) cc_final: 0.7958 (m-70) REVERT: A 467 MET cc_start: 0.8048 (mmt) cc_final: 0.7457 (mmt) REVERT: A 524 MET cc_start: 0.7483 (mmm) cc_final: 0.6583 (mmt) REVERT: A 1086 MET cc_start: 0.8509 (mpp) cc_final: 0.8082 (mpp) REVERT: A 1221 MET cc_start: 0.7912 (mmt) cc_final: 0.7556 (tmm) REVERT: A 1279 MET cc_start: 0.2393 (ttt) cc_final: 0.1334 (ttt) REVERT: A 1412 MET cc_start: 0.7438 (ttt) cc_final: 0.7128 (ttt) REVERT: B 297 MET cc_start: 0.7027 (mmt) cc_final: 0.6708 (mmt) REVERT: B 508 MET cc_start: 0.7294 (mpp) cc_final: 0.6904 (mpp) REVERT: B 550 MET cc_start: 0.6966 (tmm) cc_final: 0.5904 (tmm) REVERT: B 603 MET cc_start: 0.7809 (ptp) cc_final: 0.7007 (ptt) REVERT: E 110 MET cc_start: 0.8235 (tmm) cc_final: 0.7422 (tmm) REVERT: E 151 MET cc_start: 0.7576 (mtp) cc_final: 0.7262 (ttm) REVERT: G 107 PHE cc_start: 0.2825 (t80) cc_final: 0.1918 (m-80) REVERT: H 78 THR cc_start: 0.8836 (p) cc_final: 0.8608 (t) REVERT: I 49 ASP cc_start: 0.7485 (m-30) cc_final: 0.7168 (p0) REVERT: I 108 MET cc_start: 0.6465 (mmt) cc_final: 0.5480 (mpp) REVERT: J 48 MET cc_start: 0.8724 (mmm) cc_final: 0.8061 (mmm) REVERT: e 90 MET cc_start: 0.5882 (mmm) cc_final: 0.5318 (mmp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1976 time to fit residues: 49.8221 Evaluate side-chains 138 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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: 20.0000 chunk 117 optimal weight: 0.4980 chunk 153 optimal weight: 8.9990 chunk 346 optimal weight: 0.0570 chunk 393 optimal weight: 30.0000 chunk 234 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 459 optimal weight: 20.0000 chunk 342 optimal weight: 0.6980 chunk 159 optimal weight: 20.0000 overall best weight: 2.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.052920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.042753 restraints weight = 529659.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.042389 restraints weight = 358298.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.042375 restraints weight = 290410.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.042404 restraints weight = 242795.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.042407 restraints weight = 216568.574| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44959 Z= 0.135 Angle : 0.564 10.355 62125 Z= 0.305 Chirality : 0.041 0.207 6985 Planarity : 0.004 0.058 6873 Dihedral : 23.429 170.409 8650 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 aren not related in a simple way. whole: 0.62 (0.13), residues: 4562 helix: 1.62 (0.12), residues: 1891 sheet: -0.29 (0.21), residues: 577 loop : -0.46 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.025 0.001 TYR f 72 PHE 0.021 0.001 PHE A 458 TRP 0.018 0.001 TRP B 27 HIS 0.006 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00298 (44928) covalent geometry : angle 0.55651 (62086) hydrogen bonds : bond 0.03829 ( 2096) hydrogen bonds : angle 4.34942 ( 5706) metal coordination : bond 0.00716 ( 31) metal coordination : angle 3.72540 ( 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 145 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8244 (m90) cc_final: 0.7962 (m-70) REVERT: A 467 MET cc_start: 0.7984 (mmt) cc_final: 0.7505 (mmt) REVERT: A 524 MET cc_start: 0.7297 (mmm) cc_final: 0.6528 (mmt) REVERT: A 1086 MET cc_start: 0.8414 (mpp) cc_final: 0.8004 (mpp) REVERT: A 1221 MET cc_start: 0.8008 (mmt) cc_final: 0.7655 (tmm) REVERT: A 1279 MET cc_start: 0.2493 (ttt) cc_final: 0.1303 (ttt) REVERT: A 1292 MET cc_start: 0.7582 (ptp) cc_final: 0.7255 (ppp) REVERT: A 1412 MET cc_start: 0.7526 (ttt) cc_final: 0.7231 (ttt) REVERT: B 508 MET cc_start: 0.7108 (mpp) cc_final: 0.6812 (mpp) REVERT: B 550 MET cc_start: 0.7057 (tmm) cc_final: 0.6096 (tmm) REVERT: B 603 MET cc_start: 0.7215 (ptp) cc_final: 0.6545 (ptt) REVERT: E 110 MET cc_start: 0.8344 (tmm) cc_final: 0.7572 (tmm) REVERT: E 151 MET cc_start: 0.7595 (mtp) cc_final: 0.7299 (ttm) REVERT: G 107 PHE cc_start: 0.2868 (t80) cc_final: 0.1961 (m-80) REVERT: G 117 MET cc_start: 0.0388 (tpp) cc_final: 0.0172 (tpp) REVERT: H 78 THR cc_start: 0.8781 (p) cc_final: 0.8549 (t) REVERT: I 108 MET cc_start: 0.6382 (mmt) cc_final: 0.5375 (mpp) REVERT: e 90 MET cc_start: 0.6022 (mmm) cc_final: 0.5423 (mmp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2125 time to fit residues: 54.6251 Evaluate side-chains 137 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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: 10.0000 chunk 276 optimal weight: 9.9990 chunk 445 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 475 optimal weight: 30.0000 chunk 460 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 382 optimal weight: 20.0000 chunk 314 optimal weight: 0.0050 chunk 329 optimal weight: 8.9990 overall best weight: 6.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 790 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 790 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** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN h 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.052125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.042015 restraints weight = 535742.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.041845 restraints weight = 379857.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.041529 restraints weight = 319918.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.041630 restraints weight = 314733.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.041601 restraints weight = 255752.711| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 44959 Z= 0.229 Angle : 0.674 12.718 62125 Z= 0.358 Chirality : 0.044 0.201 6985 Planarity : 0.005 0.062 6873 Dihedral : 23.553 166.275 8650 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 aren not related in a simple way. whole: 0.08 (0.12), residues: 4562 helix: 1.09 (0.12), residues: 1907 sheet: -0.51 (0.20), residues: 603 loop : -0.71 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1258 TYR 0.027 0.002 TYR A 827 PHE 0.025 0.002 PHE A 23 TRP 0.025 0.002 TRP A1210 HIS 0.009 0.001 HIS B 741 Details of bonding type rmsd covalent geometry : bond 0.00513 (44928) covalent geometry : angle 0.66246 (62086) hydrogen bonds : bond 0.04977 ( 2096) hydrogen bonds : angle 4.69177 ( 5706) metal coordination : bond 0.01032 ( 31) metal coordination : angle 5.10163 ( 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 143 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.8308 (m90) cc_final: 0.8025 (m-70) REVERT: A 467 MET cc_start: 0.7955 (mmt) cc_final: 0.7379 (mmt) REVERT: A 524 MET cc_start: 0.7596 (mmm) cc_final: 0.6581 (mmp) REVERT: A 1086 MET cc_start: 0.8487 (mpp) cc_final: 0.7891 (mpp) REVERT: A 1221 MET cc_start: 0.8024 (mmt) cc_final: 0.7819 (tmm) REVERT: A 1279 MET cc_start: 0.2662 (ttt) cc_final: 0.1735 (ttt) REVERT: B 297 MET cc_start: 0.6849 (mmt) cc_final: 0.6606 (mmt) REVERT: B 508 MET cc_start: 0.7302 (mpp) cc_final: 0.6975 (mpp) REVERT: B 550 MET cc_start: 0.7088 (tmm) cc_final: 0.6084 (tmm) REVERT: B 603 MET cc_start: 0.7674 (ptp) cc_final: 0.7009 (ptt) REVERT: E 110 MET cc_start: 0.8619 (tmm) cc_final: 0.7751 (tmm) REVERT: E 151 MET cc_start: 0.7725 (mtp) cc_final: 0.7374 (ttm) REVERT: G 107 PHE cc_start: 0.2892 (t80) cc_final: 0.2018 (m-80) REVERT: H 78 THR cc_start: 0.8897 (p) cc_final: 0.8683 (t) REVERT: I 108 MET cc_start: 0.6420 (mmt) cc_final: 0.5284 (mpp) REVERT: e 90 MET cc_start: 0.5987 (mmm) cc_final: 0.5365 (mmp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2069 time to fit residues: 52.8862 Evaluate side-chains 138 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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: 2.9990 chunk 458 optimal weight: 30.0000 chunk 273 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 368 optimal weight: 8.9990 chunk 431 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 286 optimal weight: 20.0000 chunk 237 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.052461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.042318 restraints weight = 534603.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.042343 restraints weight = 352713.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.042012 restraints weight = 278908.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.042079 restraints weight = 278491.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.042104 restraints weight = 226567.376| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 44959 Z= 0.162 Angle : 0.592 8.668 62125 Z= 0.319 Chirality : 0.042 0.196 6985 Planarity : 0.004 0.059 6873 Dihedral : 23.479 166.801 8650 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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 : 0.02 % 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 aren not related in a simple way. whole: 0.29 (0.12), residues: 4562 helix: 1.33 (0.12), residues: 1902 sheet: -0.42 (0.21), residues: 575 loop : -0.64 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1050 TYR 0.015 0.001 TYR B 752 PHE 0.020 0.002 PHE A 458 TRP 0.017 0.002 TRP B 27 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (44928) covalent geometry : angle 0.58423 (62086) hydrogen bonds : bond 0.04085 ( 2096) hydrogen bonds : angle 4.49245 ( 5706) metal coordination : bond 0.00739 ( 31) metal coordination : angle 3.97495 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5574.28 seconds wall clock time: 97 minutes 53.35 seconds (5873.35 seconds total)