Starting phenix.real_space_refine on Tue Jul 7 03:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvs_12611/07_2026/7nvs_12611.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.983 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 10 6.06 5 P 97 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 27521 2.51 5 N 7749 2.21 5 O 8446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44073 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} 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: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1015 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 991 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" 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 98.166 109.141 65.442 1.00 36.59 S ATOM 486 SG CYS A 74 98.322 106.733 62.483 1.00 32.93 S ATOM 533 SG CYS A 81 97.116 105.659 65.968 1.00 32.64 S ATOM 768 SG CYS A 111 139.703 84.440 71.079 1.00 41.00 S ATOM 796 SG CYS A 114 140.380 85.182 67.577 1.00 39.75 S ATOM 1109 SG CYS A 154 141.683 81.961 69.042 1.00 43.42 S ATOM 1132 SG CYS A 184 143.176 85.300 70.104 1.00 43.18 S ATOM 19919 SG CYS B1119 108.255 98.089 53.780 1.00 30.25 S ATOM 19941 SG CYS B1122 109.764 97.316 57.180 1.00 31.60 S ATOM 20056 SG CYS B1137 108.382 100.763 56.517 1.00 34.76 S ATOM 20077 SG CYS B1140 111.595 99.393 54.859 1.00 38.31 S ATOM 21044 SG CYS C 88 33.175 100.180 74.559 1.00 18.87 S ATOM 21057 SG CYS C 90 35.927 102.069 76.668 1.00 26.31 S ATOM 21092 SG CYS C 94 32.382 101.838 77.640 1.00 15.72 S ATOM 21114 SG CYS C 97 34.650 98.877 77.700 1.00 10.58 S ATOM 28400 SG CYS I 17 126.553 40.816 129.107 1.00 33.14 S ATOM 28424 SG CYS I 20 126.480 44.421 128.005 1.00 33.49 S ATOM 28585 SG CYS I 39 127.607 41.774 125.639 1.00 34.19 S ATOM 28610 SG CYS I 42 129.698 42.819 128.869 1.00 34.83 S ATOM 28962 SG CYS I 86 86.245 22.618 125.283 1.00 26.52 S ATOM 28986 SG CYS I 89 84.186 22.883 128.439 1.00 31.10 S ATOM 29190 SG CYS I 114 84.331 25.742 126.139 1.00 21.10 S ATOM 29225 SG CYS I 119 87.316 24.762 128.202 1.00 31.99 S ATOM 29336 SG CYS J 7 41.531 71.544 91.749 1.00 18.97 S ATOM 29360 SG CYS J 10 38.474 71.270 89.607 1.00 7.95 S ATOM 29624 SG CYS J 44 40.427 68.169 90.633 1.00 5.14 S ATOM 29630 SG CYS J 45 38.239 70.070 92.851 1.00 1.13 S ATOM 30750 SG CYS L 19 62.051 103.685 113.305 1.00 14.72 S ATOM 30769 SG CYS L 22 59.170 105.057 115.274 1.00 18.98 S ATOM 30886 SG CYS L 36 61.919 107.334 114.227 1.00 16.67 S ATOM 30912 SG CYS L 39 62.420 104.051 117.254 1.00 22.10 S ATOM 31094 SG CYS M 15 77.323 113.848 60.849 1.00 31.21 S ATOM 31241 SG CYS M 34 74.681 113.553 63.654 1.00 28.75 S ATOM 31263 SG CYS M 37 74.016 111.785 59.528 1.00 29.82 S ATOM 42122 SG CYS W 129 108.001 126.965 63.563 1.00 43.06 S ATOM 42142 SG CYS W 132 108.654 123.538 65.073 1.00 45.33 S ATOM 42314 SG CYS W 154 106.706 123.899 61.793 1.00 46.26 S ATOM 42338 SG CYS W 157 105.157 124.978 65.143 1.00 44.19 S Time building chain proxies: 7.11, per 1000 atoms: 0.16 Number of scatterers: 44073 At special positions: 0 Unit cell: (176.4, 170.1, 183.75, 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 10 29.99 S 249 16.00 P 97 15.00 Mg 1 11.99 O 8446 8.00 N 7749 7.00 C 27521 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " Number of angles added : 54 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9910 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 0 sheets defined 36.3% alpha, 0.0% beta 44 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.613A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.773A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.518A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.533A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.568A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.008A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.518A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 683 removed outlier: 8.135A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.642A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.626A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.381A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1187 through 1196 removed outlier: 4.104A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.577A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.571A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.573A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.476A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.679A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.529A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.773A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.790A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.291A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.888A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.636A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.502A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.536A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 removed outlier: 3.866A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.893A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.540A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.521A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.819A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.691A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.859A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 128 removed outlier: 3.533A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 183 removed outlier: 3.682A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'M' and resid 226 through 241 Processing helix chain 'M' and resid 250 through 263 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 6 through 9 Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 165 removed outlier: 3.852A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.277A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 14 Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.898A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 122 through 136 removed outlier: 3.944A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 192 removed outlier: 3.893A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.549A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.398A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.557A pdb=" N LYS U 43 " --> pdb=" O MET U 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 45 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 329 No H-bonds generated for 'chain 'U' and resid 326 through 329' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.799A pdb=" N GLY W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 removed outlier: 3.648A pdb=" N ILE W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.907A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG W 119 " --> pdb=" O GLU W 115 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN W 123 " --> pdb=" O ARG W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 removed outlier: 3.799A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 183 removed outlier: 4.098A pdb=" N MET W 168 " --> pdb=" O GLU W 165 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.677A pdb=" N ALA W 178 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG W 179 " --> pdb=" O LEU W 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN W 183 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 194 Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.503A pdb=" N GLN X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG X 91 " --> pdb=" O THR X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.766A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 removed outlier: 3.727A pdb=" N GLN X 117 " --> pdb=" O LEU X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 removed outlier: 3.583A pdb=" N ALA X 174 " --> pdb=" O ASP X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 188 removed outlier: 6.009A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 4.109A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14383 1.34 - 1.46: 9657 1.46 - 1.58: 20458 1.58 - 1.70: 193 1.70 - 1.83: 392 Bond restraints: 45083 Sorted by residual: bond pdb=" C1' DC T -20 " pdb=" N1 DC T -20 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.85e+00 bond pdb=" C3' DC T -12 " pdb=" C2' DC T -12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.60e+00 bond pdb=" C3' DT N 39 " pdb=" C2' DT N 39 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.56e+00 bond pdb=" C3' DT T -32 " pdb=" C2' DT T -32 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.26e+00 bond pdb=" C3' DG N 16 " pdb=" C2' DG N 16 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.21e+00 ... (remaining 45078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 60058 1.36 - 2.73: 880 2.73 - 4.09: 329 4.09 - 5.46: 12 5.46 - 6.82: 2 Bond angle restraints: 61281 Sorted by residual: angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT N 1 " pdb=" C4 DT N 1 " pdb=" O4 DT N 1 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT N 30 " pdb=" C4 DT N 30 " pdb=" O4 DT N 30 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT N 24 " pdb=" C4 DT N 24 " pdb=" O4 DT N 24 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT T 7 " pdb=" C4 DT T 7 " pdb=" O4 DT T 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 61276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24228 17.97 - 35.95: 2387 35.95 - 53.92: 564 53.92 - 71.89: 155 71.89 - 89.86: 47 Dihedral angle restraints: 27381 sinusoidal: 12083 harmonic: 15298 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA TRP B 453 " pdb=" C TRP B 453 " pdb=" N GLY B 454 " pdb=" CA GLY B 454 " ideal model delta harmonic sigma weight residual 180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 27378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4819 0.033 - 0.067: 1257 0.067 - 0.100: 374 0.100 - 0.133: 303 0.133 - 0.167: 83 Chirality restraints: 6836 Sorted by residual: chirality pdb=" CA PRO A 478 " pdb=" N PRO A 478 " pdb=" C PRO A 478 " pdb=" CB PRO A 478 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" C3' DG N 10 " pdb=" C4' DG N 10 " pdb=" O3' DG N 10 " pdb=" C2' DG N 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C3' DG T -19 " pdb=" C4' DG T -19 " pdb=" O3' DG T -19 " pdb=" C2' DG T -19 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 6833 not shown) Planarity restraints: 7603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO O 298 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1379 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CD GLU A1379 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A1379 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A1379 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 396 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.022 5.00e-02 4.00e+02 ... (remaining 7600 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 366 2.55 - 3.14: 35614 3.14 - 3.72: 72456 3.72 - 4.31: 104434 4.31 - 4.90: 168291 Nonbonded interactions: 381161 Sorted by model distance: nonbonded pdb=" OH TYR B 814 " pdb=" OE1 GLU B 900 " model vdw 1.961 3.040 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 1.977 3.040 nonbonded pdb=" OE1 GLU A 893 " pdb=" OG SER E 197 " model vdw 1.989 3.040 nonbonded pdb=" OG SER A1147 " pdb=" OD2 ASP A1351 " model vdw 2.045 3.040 nonbonded pdb=" OH TYR A 875 " pdb=" OE2 GLU F 61 " model vdw 2.075 3.040 ... (remaining 381156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.420 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: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 43.830 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.004 0.327 45123 Z= 0.226 Angle : 0.499 15.244 61335 Z= 0.313 Chirality : 0.042 0.167 6836 Planarity : 0.003 0.066 7603 Dihedral : 15.533 89.862 17471 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5187 helix: 1.94 (0.12), residues: 1908 sheet: 0.79 (0.18), residues: 864 loop : 0.24 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 52 TYR 0.015 0.001 TYR B1048 PHE 0.018 0.001 PHE C 63 TRP 0.016 0.001 TRP B 453 HIS 0.006 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.20 (45083) covalent geometry : angle 0.48138 / 0.31 (61281) hydrogen bonds : bond 0.21165 / 14.25 ( 1164) hydrogen bonds : angle 5.43332 / 3.92 ( 3285) metal coordination : bond 0.10607 / 6.56 ( 40) metal coordination : angle 4.45769 / 2.87 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 926 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 MET cc_start: 0.8904 (mmm) cc_final: 0.8471 (mmt) REVERT: A 1231 ILE cc_start: 0.7803 (mt) cc_final: 0.7399 (mt) REVERT: A 1451 MET cc_start: 0.8394 (mmm) cc_final: 0.8180 (mmm) REVERT: C 61 ASP cc_start: 0.7982 (m-30) cc_final: 0.7771 (m-30) REVERT: C 89 THR cc_start: 0.8545 (p) cc_final: 0.8270 (p) REVERT: I 111 TYR cc_start: 0.8363 (m-80) cc_final: 0.8034 (m-80) REVERT: K 22 ASN cc_start: 0.7958 (m-40) cc_final: 0.7624 (m-40) REVERT: M 35 PRO cc_start: 0.5794 (Cg_endo) cc_final: 0.5591 (Cg_exo) REVERT: U 51 MET cc_start: 0.2977 (mmp) cc_final: 0.2021 (mpp) outliers start: 0 outliers final: 1 residues processed: 926 average time/residue: 0.7741 time to fit residues: 865.6659 Evaluate side-chains 667 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 666 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 0.1980 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 516 optimal weight: 40.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS A 465 HIS A 671 ASN A 757 GLN A 804 HIS A1190 GLN B 52 GLN B 503 ASN B 537 GLN B 913 GLN B 968 ASN B1115 GLN C 51 GLN C 217 GLN H 76 ASN I 46 GLN I 91 HIS J 52 HIS K 89 ASN L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 140 ASN M 263 GLN M 287 GLN O 166 GLN Q 129 GLN R 194 HIS R 208 GLN W 109 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.220214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161701 restraints weight = 50099.957| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.28 r_work: 0.3083 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 45123 Z= 0.198 Angle : 0.629 18.167 61335 Z= 0.325 Chirality : 0.045 0.271 6836 Planarity : 0.005 0.066 7603 Dihedral : 12.675 122.691 6792 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.26 % Allowed : 10.61 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 5187 helix: 1.41 (0.12), residues: 1947 sheet: 0.61 (0.18), residues: 850 loop : 0.13 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 863 TYR 0.020 0.002 TYR I 54 PHE 0.025 0.002 PHE G 44 TRP 0.024 0.002 TRP B 453 HIS 0.009 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (45083) covalent geometry : angle 0.61410 / 0.32 (61281) hydrogen bonds : bond 0.05743 / 3.86 ( 1164) hydrogen bonds : angle 4.12413 / 3.00 ( 3285) metal coordination : bond 0.01475 / 1.07 ( 40) metal coordination : angle 4.64496 / 3.02 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 682 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7886 (mmtp) REVERT: A 244 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7892 (mmm-85) REVERT: A 248 MET cc_start: 0.8127 (mtm) cc_final: 0.7769 (ttm) REVERT: A 266 MET cc_start: 0.3267 (ppp) cc_final: 0.2808 (pmt) REVERT: A 514 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: A 1015 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: A 1146 GLN cc_start: 0.7491 (tp40) cc_final: 0.7245 (tp40) REVERT: A 1153 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8120 (ttm110) REVERT: A 1258 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7735 (mtp-110) REVERT: A 1279 MET cc_start: 0.3799 (tmt) cc_final: 0.2705 (mpt) REVERT: A 1303 GLN cc_start: 0.8441 (mp10) cc_final: 0.8134 (mp10) REVERT: A 1313 GLN cc_start: 0.7901 (mp10) cc_final: 0.7226 (tp40) REVERT: A 1411 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8168 (mt) REVERT: A 1428 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6203 (tmt) REVERT: A 1437 ASP cc_start: 0.8061 (m-30) cc_final: 0.7768 (p0) REVERT: A 1447 GLU cc_start: 0.7943 (pt0) cc_final: 0.7673 (pm20) REVERT: B 297 MET cc_start: 0.8531 (mmt) cc_final: 0.8083 (mmt) REVERT: B 332 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7537 (tmmt) REVERT: B 358 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: B 442 ASP cc_start: 0.8450 (m-30) cc_final: 0.8226 (m-30) REVERT: B 764 MET cc_start: 0.8999 (mtt) cc_final: 0.8564 (mtp) REVERT: B 851 ASP cc_start: 0.8072 (p0) cc_final: 0.7779 (p0) REVERT: C 61 ASP cc_start: 0.8560 (m-30) cc_final: 0.8349 (m-30) REVERT: C 210 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: E 23 ASP cc_start: 0.8418 (m-30) cc_final: 0.8184 (m-30) REVERT: E 116 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8097 (tp-100) REVERT: E 120 ASP cc_start: 0.8276 (m-30) cc_final: 0.7791 (m-30) REVERT: G 1 MET cc_start: 0.5732 (pp-130) cc_final: 0.5272 (pp-130) REVERT: G 10 GLU cc_start: 0.7922 (mp0) cc_final: 0.7575 (mm-30) REVERT: I 15 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7379 (mtt90) REVERT: I 18 GLN cc_start: 0.8116 (mm110) cc_final: 0.7886 (mm110) REVERT: K 22 ASN cc_start: 0.8512 (m-40) cc_final: 0.8090 (m-40) REVERT: M 31 ASP cc_start: 0.8273 (p0) cc_final: 0.7874 (p0) REVERT: M 44 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7133 (mtt180) REVERT: M 238 LYS cc_start: 0.8663 (tppp) cc_final: 0.8370 (ttmm) REVERT: M 263 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7128 (mm-40) REVERT: M 286 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: M 287 GLN cc_start: 0.8811 (mt0) cc_final: 0.8536 (mm-40) REVERT: M 289 TYR cc_start: 0.8881 (t80) cc_final: 0.8653 (t80) REVERT: O 167 ASN cc_start: 0.6791 (t0) cc_final: 0.6386 (t160) REVERT: R 160 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7724 (tp40) REVERT: U 51 MET cc_start: 0.4670 (mmp) cc_final: 0.3106 (mpp) REVERT: W 76 MET cc_start: 0.4732 (mmp) cc_final: 0.4371 (mmm) REVERT: X 167 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4437 (tm) outliers start: 105 outliers final: 25 residues processed: 733 average time/residue: 0.7290 time to fit residues: 652.5069 Evaluate side-chains 647 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 612 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 286 ARG Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain X residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 431 optimal weight: 5.9990 chunk 372 optimal weight: 0.0980 chunk 403 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 0.0000 chunk 217 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 501 optimal weight: 3.9990 chunk 341 optimal weight: 0.8980 chunk 343 optimal weight: 0.0010 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 HIS A1093 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 582 GLN B 649 ASN B1115 GLN C 217 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.221519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162574 restraints weight = 50422.866| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.18 r_work: 0.3128 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45123 Z= 0.131 Angle : 0.557 15.907 61335 Z= 0.289 Chirality : 0.042 0.238 6836 Planarity : 0.004 0.049 7603 Dihedral : 12.766 74.118 6790 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.41 % Allowed : 12.46 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5187 helix: 1.31 (0.12), residues: 1944 sheet: 0.53 (0.18), residues: 851 loop : 0.06 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 60 TYR 0.022 0.001 TYR I 54 PHE 0.028 0.001 PHE G 77 TRP 0.019 0.001 TRP B 453 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (45083) covalent geometry : angle 0.54467 / 0.29 (61281) hydrogen bonds : bond 0.04487 / 3.03 ( 1164) hydrogen bonds : angle 3.78586 / 2.74 ( 3285) metal coordination : bond 0.00944 / 0.56 ( 40) metal coordination : angle 3.91316 / 2.56 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 638 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7821 (ttp) cc_final: 0.6944 (tmm) REVERT: A 104 MET cc_start: 0.8347 (mtm) cc_final: 0.8143 (ptp) REVERT: A 244 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8084 (mmm-85) REVERT: A 248 MET cc_start: 0.8230 (mtm) cc_final: 0.7848 (ttm) REVERT: A 266 MET cc_start: 0.3538 (ppp) cc_final: 0.3005 (pmt) REVERT: A 329 MET cc_start: 0.7456 (mmm) cc_final: 0.7179 (mmm) REVERT: A 762 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: A 951 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8610 (mm-30) REVERT: A 1015 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 1224 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6991 (mtt180) REVERT: A 1279 MET cc_start: 0.4033 (tmt) cc_final: 0.3027 (mpt) REVERT: A 1303 GLN cc_start: 0.8471 (mp10) cc_final: 0.8198 (mp10) REVERT: A 1411 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (mt) REVERT: A 1437 ASP cc_start: 0.8158 (m-30) cc_final: 0.7835 (p0) REVERT: A 1441 GLU cc_start: 0.7582 (tp30) cc_final: 0.7335 (tp30) REVERT: B 332 LYS cc_start: 0.8047 (tmmt) cc_final: 0.7718 (tmmt) REVERT: B 358 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: B 673 VAL cc_start: 0.9172 (t) cc_final: 0.8894 (m) REVERT: B 764 MET cc_start: 0.9135 (mtm) cc_final: 0.8882 (mtp) REVERT: B 851 ASP cc_start: 0.8035 (p0) cc_final: 0.7689 (p0) REVERT: B 1072 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8462 (mpt-90) REVERT: C 100 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: C 217 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: E 103 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8115 (mp) REVERT: G 1 MET cc_start: 0.6389 (pp-130) cc_final: 0.5792 (pp-130) REVERT: G 104 MET cc_start: 0.5909 (ptp) cc_final: 0.5204 (mpt) REVERT: I 18 GLN cc_start: 0.8131 (mm110) cc_final: 0.7898 (mm110) REVERT: K 22 ASN cc_start: 0.8675 (m-40) cc_final: 0.8263 (m-40) REVERT: K 97 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: L 27 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6031 (tt0) REVERT: M 44 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7274 (mtt180) REVERT: M 227 GLN cc_start: 0.8200 (mp10) cc_final: 0.7163 (tp40) REVERT: M 263 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7490 (mm110) REVERT: M 277 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8328 (mm) REVERT: O 166 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8192 (mm-40) REVERT: O 193 ASN cc_start: 0.9019 (t0) cc_final: 0.8710 (t0) REVERT: O 320 GLU cc_start: 0.8590 (tp30) cc_final: 0.8270 (tp30) REVERT: Q 169 LYS cc_start: 0.3656 (tppt) cc_final: 0.2507 (mmmt) REVERT: R 43 LEU cc_start: 0.7950 (pt) cc_final: 0.7693 (tm) REVERT: U 51 MET cc_start: 0.5136 (mmp) cc_final: 0.3299 (mpp) REVERT: U 323 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4863 (pp20) REVERT: W 76 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4443 (mmm) REVERT: X 167 LEU cc_start: 0.4930 (OUTLIER) cc_final: 0.4569 (tm) outliers start: 112 outliers final: 28 residues processed: 690 average time/residue: 0.7141 time to fit residues: 602.3303 Evaluate side-chains 639 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 596 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain O residue 202 MET Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 295 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain W residue 76 MET Chi-restraints excluded: chain X residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 120 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 338 optimal weight: 0.0870 chunk 280 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 182 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 465 HIS A 673 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS B1115 GLN C 217 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 ASN R 152 ASN R 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.219887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161915 restraints weight = 50179.633| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.24 r_work: 0.3085 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 45123 Z= 0.184 Angle : 0.576 17.221 61335 Z= 0.295 Chirality : 0.043 0.221 6836 Planarity : 0.004 0.060 7603 Dihedral : 12.859 74.732 6790 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.69 % Allowed : 13.28 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5187 helix: 1.20 (0.12), residues: 1946 sheet: 0.46 (0.18), residues: 842 loop : -0.00 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1085 TYR 0.024 0.002 TYR I 54 PHE 0.020 0.002 PHE G 77 TRP 0.025 0.002 TRP B 453 HIS 0.018 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (45083) covalent geometry : angle 0.56151 / 0.29 (61281) hydrogen bonds : bond 0.04349 / 2.94 ( 1164) hydrogen bonds : angle 3.70531 / 2.68 ( 3285) metal coordination : bond 0.02010 / 1.53 ( 40) metal coordination : angle 4.34354 / 2.78 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 628 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7532 (mmtt) REVERT: A 104 MET cc_start: 0.8248 (mtm) cc_final: 0.7913 (ptp) REVERT: A 244 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8076 (mmm-85) REVERT: A 248 MET cc_start: 0.8177 (mtm) cc_final: 0.7860 (ttm) REVERT: A 266 MET cc_start: 0.3835 (ppp) cc_final: 0.3281 (pmt) REVERT: A 388 MET cc_start: 0.8997 (mtm) cc_final: 0.8722 (mtm) REVERT: A 762 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 845 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8523 (mm-30) REVERT: A 1015 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: A 1184 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 1224 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6918 (mtt180) REVERT: A 1258 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7821 (mtp-110) REVERT: A 1279 MET cc_start: 0.3657 (tmt) cc_final: 0.2746 (mpt) REVERT: A 1303 GLN cc_start: 0.8435 (mp10) cc_final: 0.8130 (mp10) REVERT: A 1411 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 358 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: B 579 ASP cc_start: 0.8623 (t0) cc_final: 0.8099 (t0) REVERT: B 581 GLU cc_start: 0.8197 (pm20) cc_final: 0.7874 (pm20) REVERT: B 582 GLN cc_start: 0.7885 (pp30) cc_final: 0.7377 (tm-30) REVERT: B 851 ASP cc_start: 0.7998 (p0) cc_final: 0.7748 (p0) REVERT: B 918 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8675 (p90) REVERT: C 91 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6934 (mm-30) REVERT: C 210 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: E 103 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7973 (mp) REVERT: E 116 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8258 (tp-100) REVERT: G 10 GLU cc_start: 0.7932 (mp0) cc_final: 0.7666 (mm-30) REVERT: G 104 MET cc_start: 0.6208 (ptp) cc_final: 0.5772 (mpt) REVERT: I 18 GLN cc_start: 0.8283 (mm110) cc_final: 0.8000 (mm110) REVERT: K 22 ASN cc_start: 0.8540 (m-40) cc_final: 0.8155 (m-40) REVERT: L 58 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7503 (mmm-85) REVERT: M 44 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7254 (mtt180) REVERT: M 263 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7425 (mm110) REVERT: M 273 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7493 (pt0) REVERT: M 277 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8244 (mm) REVERT: O 167 ASN cc_start: 0.6454 (t0) cc_final: 0.6070 (t160) REVERT: O 193 ASN cc_start: 0.9029 (t0) cc_final: 0.8745 (t0) REVERT: O 282 SER cc_start: 0.8686 (t) cc_final: 0.8109 (p) REVERT: Q 169 LYS cc_start: 0.3685 (tppt) cc_final: 0.2860 (mmmt) REVERT: R 22 LYS cc_start: 0.6994 (ttpt) cc_final: 0.6657 (ptmm) REVERT: U 51 MET cc_start: 0.4893 (mmp) cc_final: 0.3035 (mpp) REVERT: W 76 MET cc_start: 0.4513 (mmp) cc_final: 0.4163 (mmm) REVERT: X 167 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.4254 (tm) outliers start: 125 outliers final: 54 residues processed: 696 average time/residue: 0.7149 time to fit residues: 610.5744 Evaluate side-chains 663 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 594 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain X residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 419 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 187 optimal weight: 0.5980 chunk 363 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 397 optimal weight: 2.9990 chunk 288 optimal weight: 40.0000 chunk 341 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 465 HIS ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1071 ASN B1115 GLN C 51 GLN C 217 GLN I 60 HIS ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.220363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162174 restraints weight = 50362.238| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.24 r_work: 0.3092 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 45123 Z= 0.161 Angle : 0.582 16.522 61335 Z= 0.294 Chirality : 0.043 0.284 6836 Planarity : 0.004 0.088 7603 Dihedral : 12.906 75.320 6790 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.80 % Allowed : 14.33 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.12), residues: 5187 helix: 1.12 (0.12), residues: 1947 sheet: 0.37 (0.18), residues: 840 loop : -0.04 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1085 TYR 0.023 0.001 TYR I 54 PHE 0.020 0.001 PHE G 77 TRP 0.023 0.001 TRP B 453 HIS 0.020 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (45083) covalent geometry : angle 0.56743 / 0.29 (61281) hydrogen bonds : bond 0.04106 / 2.79 ( 1164) hydrogen bonds : angle 3.66059 / 2.65 ( 3285) metal coordination : bond 0.02266 / 1.73 ( 40) metal coordination : angle 4.39159 / 2.78 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 612 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 19 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7524 (mmtt) REVERT: A 33 ARG cc_start: 0.8864 (ttp-110) cc_final: 0.8637 (ttp-110) REVERT: A 58 MET cc_start: 0.7751 (ttp) cc_final: 0.6774 (tmm) REVERT: A 244 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: A 248 MET cc_start: 0.8192 (mtm) cc_final: 0.7842 (ttm) REVERT: A 266 MET cc_start: 0.3907 (ppp) cc_final: 0.3347 (pmt) REVERT: A 388 MET cc_start: 0.9009 (mtm) cc_final: 0.8751 (mtm) REVERT: A 701 ASP cc_start: 0.8124 (m-30) cc_final: 0.7914 (m-30) REVERT: A 762 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: A 845 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 951 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 1015 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 1184 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8111 (t) REVERT: A 1217 ASP cc_start: 0.7130 (t0) cc_final: 0.6926 (t0) REVERT: A 1224 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6916 (mtt180) REVERT: A 1258 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7995 (mtp-110) REVERT: A 1279 MET cc_start: 0.3737 (tmt) cc_final: 0.2782 (mpt) REVERT: A 1303 GLN cc_start: 0.8430 (mp10) cc_final: 0.8076 (mp10) REVERT: A 1337 GLU cc_start: 0.7555 (tt0) cc_final: 0.7140 (tp30) REVERT: B 255 ARG cc_start: 0.8073 (ptm-80) cc_final: 0.7694 (ptt-90) REVERT: B 358 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: B 579 ASP cc_start: 0.8586 (t0) cc_final: 0.8150 (t0) REVERT: B 581 GLU cc_start: 0.8144 (pm20) cc_final: 0.7899 (pm20) REVERT: B 673 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8845 (m) REVERT: B 851 ASP cc_start: 0.7973 (p0) cc_final: 0.7726 (p0) REVERT: B 918 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8659 (p90) REVERT: C 91 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: C 210 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: E 103 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7788 (mp) REVERT: E 115 LYS cc_start: 0.9054 (tttt) cc_final: 0.8743 (mmmm) REVERT: G 1 MET cc_start: 0.5722 (ppp) cc_final: 0.5284 (pp-130) REVERT: G 10 GLU cc_start: 0.8006 (mp0) cc_final: 0.7705 (mm-30) REVERT: G 104 MET cc_start: 0.6547 (ptp) cc_final: 0.5983 (mpt) REVERT: I 18 GLN cc_start: 0.8296 (mm110) cc_final: 0.7983 (mm110) REVERT: I 45 GLN cc_start: 0.9097 (mt0) cc_final: 0.8750 (mt0) REVERT: K 22 ASN cc_start: 0.8573 (m-40) cc_final: 0.8203 (m-40) REVERT: M 44 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: M 227 GLN cc_start: 0.7913 (mp10) cc_final: 0.7031 (tp40) REVERT: M 277 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (mm) REVERT: O 193 ASN cc_start: 0.9111 (t0) cc_final: 0.8839 (t0) REVERT: O 282 SER cc_start: 0.8566 (t) cc_final: 0.8026 (p) REVERT: O 293 TYR cc_start: 0.8196 (t80) cc_final: 0.6785 (t80) REVERT: Q 29 MET cc_start: 0.7088 (ttm) cc_final: 0.6456 (tpp) REVERT: Q 169 LYS cc_start: 0.3685 (tppt) cc_final: 0.2948 (mmmt) REVERT: R 22 LYS cc_start: 0.7021 (ttpt) cc_final: 0.6651 (ptmm) REVERT: U 51 MET cc_start: 0.4852 (mmp) cc_final: 0.3070 (mpp) outliers start: 130 outliers final: 56 residues processed: 684 average time/residue: 0.7261 time to fit residues: 609.4002 Evaluate side-chains 666 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 597 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 54 optimal weight: 0.6980 chunk 359 optimal weight: 0.4980 chunk 402 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 280 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 313 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 465 HIS A 904 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 649 ASN B1049 GLN B1071 ASN B1115 GLN C 51 GLN E 116 GLN J 26 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.220233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160786 restraints weight = 50365.154| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 45123 Z= 0.161 Angle : 0.575 16.400 61335 Z= 0.291 Chirality : 0.043 0.203 6836 Planarity : 0.004 0.087 7603 Dihedral : 12.943 75.579 6790 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 15.28 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 5187 helix: 1.11 (0.12), residues: 1947 sheet: 0.34 (0.18), residues: 840 loop : -0.06 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1085 TYR 0.025 0.001 TYR I 54 PHE 0.015 0.001 PHE B 918 TRP 0.023 0.001 TRP B 453 HIS 0.013 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (45083) covalent geometry : angle 0.56099 / 0.29 (61281) hydrogen bonds : bond 0.03983 / 2.70 ( 1164) hydrogen bonds : angle 3.62687 / 2.63 ( 3285) metal coordination : bond 0.02251 / 1.72 ( 40) metal coordination : angle 4.35308 / 2.76 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 609 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7576 (mmtt) REVERT: A 58 MET cc_start: 0.7751 (ttp) cc_final: 0.6923 (tmm) REVERT: A 244 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: A 248 MET cc_start: 0.8160 (mtm) cc_final: 0.7836 (ttm) REVERT: A 266 MET cc_start: 0.3951 (ppp) cc_final: 0.3366 (pmt) REVERT: A 388 MET cc_start: 0.8996 (mtm) cc_final: 0.8733 (mtm) REVERT: A 701 ASP cc_start: 0.8135 (m-30) cc_final: 0.7921 (m-30) REVERT: A 762 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: A 845 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8531 (mm-30) REVERT: A 951 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8367 (mm-30) REVERT: A 1015 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 1184 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8084 (t) REVERT: A 1224 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6892 (mtt180) REVERT: A 1258 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7833 (mtp-110) REVERT: A 1279 MET cc_start: 0.3767 (tmt) cc_final: 0.2854 (mpt) REVERT: A 1303 GLN cc_start: 0.8383 (mp10) cc_final: 0.8045 (mp10) REVERT: A 1337 GLU cc_start: 0.7511 (tt0) cc_final: 0.6938 (tp30) REVERT: B 143 GLN cc_start: 0.7289 (pt0) cc_final: 0.6902 (tp40) REVERT: B 358 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: B 579 ASP cc_start: 0.8564 (t0) cc_final: 0.8135 (t0) REVERT: B 581 GLU cc_start: 0.8222 (pm20) cc_final: 0.7964 (pm20) REVERT: B 673 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8817 (m) REVERT: B 918 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8651 (p90) REVERT: C 91 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: C 210 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: D 86 LEU cc_start: 0.7680 (tp) cc_final: 0.7350 (pt) REVERT: E 103 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7825 (mp) REVERT: G 10 GLU cc_start: 0.8037 (mp0) cc_final: 0.7738 (mm-30) REVERT: G 104 MET cc_start: 0.6611 (ptp) cc_final: 0.5724 (mpt) REVERT: I 18 GLN cc_start: 0.8360 (mm110) cc_final: 0.8076 (mm110) REVERT: I 25 TYR cc_start: 0.7825 (m-80) cc_final: 0.7300 (m-80) REVERT: I 40 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8016 (mtt180) REVERT: K 22 ASN cc_start: 0.8532 (m-40) cc_final: 0.8175 (m-40) REVERT: K 97 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: L 58 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7328 (mmm-85) REVERT: M 44 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7281 (mtt180) REVERT: M 263 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7304 (mm110) REVERT: M 273 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7440 (pt0) REVERT: M 277 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8304 (mm) REVERT: O 193 ASN cc_start: 0.9095 (t0) cc_final: 0.8821 (t0) REVERT: O 282 SER cc_start: 0.8641 (t) cc_final: 0.8155 (p) REVERT: O 293 TYR cc_start: 0.8035 (t80) cc_final: 0.7768 (t80) REVERT: O 295 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: Q 20 LYS cc_start: 0.5082 (mppt) cc_final: 0.4736 (mppt) REVERT: Q 29 MET cc_start: 0.7002 (ttm) cc_final: 0.6489 (tpp) REVERT: Q 111 LYS cc_start: 0.8467 (tppp) cc_final: 0.7643 (tptt) REVERT: Q 169 LYS cc_start: 0.3424 (tppt) cc_final: 0.2823 (mmmt) REVERT: R 22 LYS cc_start: 0.6983 (ttpt) cc_final: 0.6623 (ptmm) REVERT: R 43 LEU cc_start: 0.7513 (pt) cc_final: 0.7162 (tp) REVERT: U 51 MET cc_start: 0.4782 (mmp) cc_final: 0.2971 (mpp) outliers start: 122 outliers final: 59 residues processed: 674 average time/residue: 0.7488 time to fit residues: 622.0499 Evaluate side-chains 668 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 593 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 295 MET Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 464 optimal weight: 50.0000 chunk 69 optimal weight: 2.9990 chunk 506 optimal weight: 4.9990 chunk 496 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 235 optimal weight: 0.4980 chunk 290 optimal weight: 10.0000 chunk 263 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1115 GLN C 217 GLN ** O 166 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.220434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161488 restraints weight = 49836.796| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.25 r_work: 0.3114 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 45123 Z= 0.149 Angle : 0.575 15.984 61335 Z= 0.290 Chirality : 0.043 0.208 6836 Planarity : 0.004 0.061 7603 Dihedral : 12.976 75.685 6790 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.43 % Allowed : 15.99 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.12), residues: 5187 helix: 1.13 (0.12), residues: 1948 sheet: 0.29 (0.18), residues: 831 loop : -0.12 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 33 TYR 0.026 0.001 TYR I 54 PHE 0.015 0.001 PHE B 918 TRP 0.022 0.001 TRP B 453 HIS 0.013 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (45083) covalent geometry : angle 0.56075 / 0.29 (61281) hydrogen bonds : bond 0.03840 / 2.60 ( 1164) hydrogen bonds : angle 3.56665 / 2.58 ( 3285) metal coordination : bond 0.01606 / 1.20 ( 40) metal coordination : angle 4.33933 / 2.76 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 612 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7768 (mmtt) REVERT: A 58 MET cc_start: 0.7719 (ttp) cc_final: 0.7040 (tmm) REVERT: A 242 TYR cc_start: 0.7993 (m-80) cc_final: 0.7773 (m-80) REVERT: A 248 MET cc_start: 0.8200 (mtm) cc_final: 0.7908 (ttm) REVERT: A 266 MET cc_start: 0.3946 (ppp) cc_final: 0.3344 (pmt) REVERT: A 762 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 845 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8804 (mm-30) REVERT: A 951 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 1015 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: A 1184 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8011 (t) REVERT: A 1220 HIS cc_start: 0.8161 (m90) cc_final: 0.7957 (m90) REVERT: A 1224 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7076 (mtt180) REVERT: A 1258 ARG cc_start: 0.8406 (mtm180) cc_final: 0.8145 (mtp-110) REVERT: A 1279 MET cc_start: 0.3849 (tmt) cc_final: 0.2906 (mpt) REVERT: A 1303 GLN cc_start: 0.8436 (mp10) cc_final: 0.8147 (mp10) REVERT: B 93 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 143 GLN cc_start: 0.7513 (pt0) cc_final: 0.6962 (tp40) REVERT: B 255 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.8049 (ptt-90) REVERT: B 358 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: B 429 PHE cc_start: 0.8991 (p90) cc_final: 0.8742 (p90) REVERT: B 579 ASP cc_start: 0.8750 (t0) cc_final: 0.8349 (t0) REVERT: B 581 GLU cc_start: 0.8446 (pm20) cc_final: 0.8189 (pm20) REVERT: B 673 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8860 (m) REVERT: B 851 ASP cc_start: 0.8162 (p0) cc_final: 0.7754 (p0) REVERT: B 918 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8730 (p90) REVERT: C 91 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: C 210 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: D 30 GLU cc_start: 0.6238 (pt0) cc_final: 0.6031 (pt0) REVERT: D 86 LEU cc_start: 0.7632 (tp) cc_final: 0.7338 (pt) REVERT: E 103 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7897 (mp) REVERT: G 10 GLU cc_start: 0.8200 (mp0) cc_final: 0.7915 (mm-30) REVERT: G 104 MET cc_start: 0.6719 (ptp) cc_final: 0.5846 (mpt) REVERT: I 18 GLN cc_start: 0.8342 (mm110) cc_final: 0.8086 (mm110) REVERT: K 22 ASN cc_start: 0.8737 (m-40) cc_final: 0.8406 (m-40) REVERT: M 44 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7532 (mtt180) REVERT: M 227 GLN cc_start: 0.8128 (mp10) cc_final: 0.7385 (tp40) REVERT: M 273 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7511 (pt0) REVERT: M 277 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8421 (mm) REVERT: O 193 ASN cc_start: 0.9091 (t0) cc_final: 0.8816 (t0) REVERT: O 219 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7974 (tpp) REVERT: O 282 SER cc_start: 0.8801 (t) cc_final: 0.8376 (p) REVERT: Q 29 MET cc_start: 0.7021 (ttm) cc_final: 0.6420 (tpp) REVERT: Q 111 LYS cc_start: 0.8490 (tppp) cc_final: 0.7619 (tptt) REVERT: Q 146 PHE cc_start: 0.5994 (m-80) cc_final: 0.5680 (m-80) REVERT: Q 169 LYS cc_start: 0.3219 (tppt) cc_final: 0.2721 (mmmt) REVERT: R 22 LYS cc_start: 0.6952 (ttpt) cc_final: 0.6649 (ptmm) REVERT: R 43 LEU cc_start: 0.7562 (pt) cc_final: 0.7207 (tp) REVERT: U 51 MET cc_start: 0.5011 (mmp) cc_final: 0.3145 (mpp) REVERT: W 48 MET cc_start: 0.5619 (mmt) cc_final: 0.5299 (mpm) REVERT: W 76 MET cc_start: 0.3554 (mmm) cc_final: -0.1900 (mtm) REVERT: X 228 MET cc_start: 0.3217 (tmm) cc_final: 0.2934 (tmm) outliers start: 113 outliers final: 60 residues processed: 673 average time/residue: 0.7363 time to fit residues: 604.1374 Evaluate side-chains 672 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 597 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 219 MET Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 55 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 464 optimal weight: 40.0000 chunk 518 optimal weight: 40.0000 chunk 130 optimal weight: 0.8980 chunk 390 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 905 ASN A1129 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1115 GLN C 217 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.220441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162981 restraints weight = 50168.753| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.25 r_work: 0.3099 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 45123 Z= 0.160 Angle : 0.591 15.981 61335 Z= 0.297 Chirality : 0.043 0.211 6836 Planarity : 0.004 0.061 7603 Dihedral : 13.019 75.639 6790 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.32 % Allowed : 16.66 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5187 helix: 1.11 (0.12), residues: 1949 sheet: 0.26 (0.18), residues: 845 loop : -0.11 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 40 TYR 0.028 0.001 TYR I 54 PHE 0.017 0.001 PHE K 13 TRP 0.023 0.001 TRP B 453 HIS 0.012 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (45083) covalent geometry : angle 0.57675 / 0.30 (61281) hydrogen bonds : bond 0.03831 / 2.59 ( 1164) hydrogen bonds : angle 3.57559 / 2.59 ( 3285) metal coordination : bond 0.02378 / 1.82 ( 40) metal coordination : angle 4.32088 / 2.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 606 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7611 (mmtt) REVERT: A 58 MET cc_start: 0.7721 (ttp) cc_final: 0.6903 (tmm) REVERT: A 244 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: A 248 MET cc_start: 0.8165 (mtm) cc_final: 0.7877 (ttm) REVERT: A 762 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 845 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8528 (mm-30) REVERT: A 951 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8291 (mm-30) REVERT: A 1015 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 1184 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8092 (t) REVERT: A 1224 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6962 (mtt180) REVERT: A 1258 ARG cc_start: 0.8254 (mtm180) cc_final: 0.7962 (mtp-110) REVERT: A 1259 ILE cc_start: 0.9294 (mt) cc_final: 0.9089 (mp) REVERT: A 1279 MET cc_start: 0.3730 (tmt) cc_final: 0.2877 (mpt) REVERT: A 1302 GLU cc_start: 0.8102 (mp0) cc_final: 0.7694 (mp0) REVERT: A 1303 GLN cc_start: 0.8398 (mp10) cc_final: 0.8053 (mp10) REVERT: B 89 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: B 93 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8650 (tp) REVERT: B 143 GLN cc_start: 0.7364 (pt0) cc_final: 0.6916 (tp40) REVERT: B 358 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: B 429 PHE cc_start: 0.8945 (p90) cc_final: 0.8727 (p90) REVERT: B 673 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 851 ASP cc_start: 0.7882 (p0) cc_final: 0.7513 (p0) REVERT: B 918 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8694 (p90) REVERT: B 1054 MET cc_start: 0.9023 (mpp) cc_final: 0.8534 (mtm) REVERT: B 1165 MET cc_start: 0.7755 (mtp) cc_final: 0.7479 (ttm) REVERT: C 91 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: C 210 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: D 86 LEU cc_start: 0.7665 (tp) cc_final: 0.7329 (pt) REVERT: D 88 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7601 (mm) REVERT: E 103 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7841 (mp) REVERT: G 1 MET cc_start: 0.4798 (pp-130) cc_final: 0.4144 (pmm) REVERT: G 10 GLU cc_start: 0.8095 (mp0) cc_final: 0.7765 (mm-30) REVERT: G 104 MET cc_start: 0.6643 (ptp) cc_final: 0.5814 (mpt) REVERT: H 146 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8240 (ptpt) REVERT: I 18 GLN cc_start: 0.8409 (mm110) cc_final: 0.8111 (mm110) REVERT: I 25 TYR cc_start: 0.7682 (m-80) cc_final: 0.7286 (m-80) REVERT: K 22 ASN cc_start: 0.8525 (m-40) cc_final: 0.8186 (m-40) REVERT: M 44 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7285 (mtt180) REVERT: M 107 MET cc_start: 0.6174 (ttt) cc_final: 0.5682 (ptp) REVERT: M 273 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7429 (pt0) REVERT: M 277 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (mm) REVERT: O 193 ASN cc_start: 0.9143 (t0) cc_final: 0.8840 (t0) REVERT: O 219 MET cc_start: 0.8625 (tpt) cc_final: 0.8027 (tpp) REVERT: O 282 SER cc_start: 0.8597 (t) cc_final: 0.8184 (p) REVERT: O 293 TYR cc_start: 0.8139 (t80) cc_final: 0.7521 (t80) REVERT: O 295 MET cc_start: 0.8278 (mmm) cc_final: 0.7952 (mmp) REVERT: Q 29 MET cc_start: 0.7043 (ttm) cc_final: 0.6440 (tpp) REVERT: Q 111 LYS cc_start: 0.8509 (tppp) cc_final: 0.7718 (tptt) REVERT: Q 163 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7525 (mm-30) REVERT: Q 169 LYS cc_start: 0.3355 (tppt) cc_final: 0.2904 (mmmt) REVERT: R 22 LYS cc_start: 0.6956 (ttpt) cc_final: 0.6687 (ptmm) REVERT: R 140 ARG cc_start: 0.5807 (ttp-170) cc_final: 0.5506 (ttp-170) REVERT: U 51 MET cc_start: 0.4732 (mmp) cc_final: 0.2996 (mpp) REVERT: W 76 MET cc_start: 0.3172 (mmm) cc_final: -0.2233 (mtm) REVERT: X 228 MET cc_start: 0.3277 (tmm) cc_final: 0.3047 (tmm) outliers start: 108 outliers final: 64 residues processed: 668 average time/residue: 0.7230 time to fit residues: 590.6223 Evaluate side-chains 677 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 597 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 942 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 11 optimal weight: 0.9980 chunk 374 optimal weight: 0.6980 chunk 313 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 chunk 446 optimal weight: 30.0000 chunk 233 optimal weight: 0.7980 chunk 68 optimal weight: 0.0010 chunk 125 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 470 optimal weight: 7.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A1129 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1115 GLN C 217 GLN E 107 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.220645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161466 restraints weight = 50278.908| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.19 r_work: 0.3116 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 45123 Z= 0.146 Angle : 0.589 15.635 61335 Z= 0.297 Chirality : 0.043 0.215 6836 Planarity : 0.004 0.070 7603 Dihedral : 13.036 75.574 6790 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.17 % Allowed : 17.11 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5187 helix: 1.13 (0.12), residues: 1949 sheet: 0.26 (0.18), residues: 840 loop : -0.12 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 40 TYR 0.027 0.001 TYR I 54 PHE 0.032 0.001 PHE O 280 TRP 0.021 0.001 TRP B 453 HIS 0.012 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (45083) covalent geometry : angle 0.57543 / 0.30 (61281) hydrogen bonds : bond 0.03746 / 2.53 ( 1164) hydrogen bonds : angle 3.55314 / 2.57 ( 3285) metal coordination : bond 0.02106 / 1.61 ( 40) metal coordination : angle 4.28580 / 2.70 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 606 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7777 (mmtt) REVERT: A 58 MET cc_start: 0.7743 (ttp) cc_final: 0.7027 (tmm) REVERT: A 238 MET cc_start: 0.7834 (mtm) cc_final: 0.7391 (mtt) REVERT: A 244 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8057 (mmm-85) REVERT: A 248 MET cc_start: 0.8225 (mtm) cc_final: 0.7918 (ttm) REVERT: A 611 ASP cc_start: 0.6980 (p0) cc_final: 0.6661 (t0) REVERT: A 762 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: A 845 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8769 (mm-30) REVERT: A 951 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8447 (mm-30) REVERT: A 1015 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 1184 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.7996 (t) REVERT: A 1224 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7053 (mtt180) REVERT: A 1279 MET cc_start: 0.3873 (tmt) cc_final: 0.2975 (mpt) REVERT: A 1302 GLU cc_start: 0.8150 (mp0) cc_final: 0.7809 (mp0) REVERT: A 1303 GLN cc_start: 0.8417 (mp10) cc_final: 0.8140 (mp10) REVERT: B 93 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 143 GLN cc_start: 0.7623 (pt0) cc_final: 0.7053 (tp40) REVERT: B 358 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7931 (pt0) REVERT: B 673 VAL cc_start: 0.9129 (t) cc_final: 0.8863 (m) REVERT: B 851 ASP cc_start: 0.7996 (p0) cc_final: 0.7615 (p0) REVERT: B 918 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8719 (p90) REVERT: C 91 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: C 210 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: D 86 LEU cc_start: 0.7677 (tp) cc_final: 0.7352 (pt) REVERT: D 88 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7756 (mm) REVERT: E 103 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7934 (mp) REVERT: E 107 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8009 (mm-40) REVERT: G 1 MET cc_start: 0.5520 (pp-130) cc_final: 0.4902 (pmm) REVERT: G 10 GLU cc_start: 0.8219 (mp0) cc_final: 0.7931 (mm-30) REVERT: G 73 LYS cc_start: 0.7522 (mmmm) cc_final: 0.6918 (mmmt) REVERT: G 104 MET cc_start: 0.6802 (ptp) cc_final: 0.5885 (mpt) REVERT: H 146 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8305 (ptpt) REVERT: I 18 GLN cc_start: 0.8403 (mm110) cc_final: 0.8149 (mm110) REVERT: I 57 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7817 (pptt) REVERT: K 22 ASN cc_start: 0.8686 (m-40) cc_final: 0.8380 (m-40) REVERT: M 44 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7369 (mtt180) REVERT: M 107 MET cc_start: 0.6437 (ttt) cc_final: 0.5857 (ptp) REVERT: M 120 GLU cc_start: 0.8575 (tp30) cc_final: 0.7970 (mp0) REVERT: M 227 GLN cc_start: 0.8170 (mp10) cc_final: 0.7331 (tp40) REVERT: M 277 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8434 (mm) REVERT: O 193 ASN cc_start: 0.9148 (t0) cc_final: 0.8865 (t0) REVERT: O 219 MET cc_start: 0.8645 (tpt) cc_final: 0.8169 (tpp) REVERT: O 282 SER cc_start: 0.8762 (t) cc_final: 0.8402 (p) REVERT: O 293 TYR cc_start: 0.8333 (t80) cc_final: 0.7703 (t80) REVERT: O 295 MET cc_start: 0.8474 (mmm) cc_final: 0.8139 (mmp) REVERT: Q 20 LYS cc_start: 0.5375 (mppt) cc_final: 0.4842 (mppt) REVERT: Q 111 LYS cc_start: 0.8512 (tppp) cc_final: 0.7645 (tptt) REVERT: Q 163 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7564 (mm-30) REVERT: Q 169 LYS cc_start: 0.3283 (tppt) cc_final: 0.2993 (mmtt) REVERT: R 22 LYS cc_start: 0.6939 (ttpt) cc_final: 0.6668 (ptmm) REVERT: R 140 ARG cc_start: 0.5804 (ttp-170) cc_final: 0.5471 (ttp-170) REVERT: U 51 MET cc_start: 0.5000 (mmp) cc_final: 0.3115 (mpp) REVERT: W 48 MET cc_start: 0.5820 (mmt) cc_final: 0.5562 (mpm) REVERT: W 76 MET cc_start: 0.3369 (mmm) cc_final: -0.2256 (mtm) REVERT: X 228 MET cc_start: 0.3413 (tmm) cc_final: 0.3130 (tmm) outliers start: 101 outliers final: 63 residues processed: 666 average time/residue: 0.7198 time to fit residues: 587.1700 Evaluate side-chains 675 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 596 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 296 optimal weight: 0.0870 chunk 172 optimal weight: 0.0060 chunk 442 optimal weight: 0.0270 chunk 454 optimal weight: 0.3980 chunk 521 optimal weight: 8.9990 chunk 395 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 509 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 437 optimal weight: 10.0000 overall best weight: 0.1210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 731 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1115 GLN C 217 GLN E 107 GLN I 41 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.221843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163119 restraints weight = 50453.741| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.27 r_work: 0.3136 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 45123 Z= 0.114 Angle : 0.585 14.487 61335 Z= 0.294 Chirality : 0.042 0.227 6836 Planarity : 0.004 0.069 7603 Dihedral : 13.022 75.448 6790 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.68 % Allowed : 17.86 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 5187 helix: 1.18 (0.12), residues: 1950 sheet: 0.24 (0.18), residues: 842 loop : -0.11 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 33 TYR 0.033 0.001 TYR R 197 PHE 0.025 0.001 PHE Q 146 TRP 0.019 0.001 TRP B 453 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (45083) covalent geometry : angle 0.57379 / 0.29 (61281) hydrogen bonds : bond 0.03545 / 2.39 ( 1164) hydrogen bonds : angle 3.52886 / 2.56 ( 3285) metal coordination : bond 0.01877 / 1.43 ( 40) metal coordination : angle 3.91959 / 2.50 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 605 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7575 (mmtt) REVERT: A 58 MET cc_start: 0.7617 (ttp) cc_final: 0.6882 (tmm) REVERT: A 238 MET cc_start: 0.7746 (mtm) cc_final: 0.7297 (mtt) REVERT: A 244 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: A 248 MET cc_start: 0.8141 (mtm) cc_final: 0.7832 (ttm) REVERT: A 266 MET cc_start: 0.3642 (ppp) cc_final: 0.3104 (pmt) REVERT: A 388 MET cc_start: 0.8924 (mtm) cc_final: 0.8655 (mtm) REVERT: A 762 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 845 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8532 (mm-30) REVERT: A 859 TYR cc_start: 0.8041 (t80) cc_final: 0.7789 (t80) REVERT: A 951 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 1015 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: A 1224 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7072 (mtt180) REVERT: A 1279 MET cc_start: 0.3545 (tmt) cc_final: 0.2849 (mpt) REVERT: A 1302 GLU cc_start: 0.8012 (mp0) cc_final: 0.7595 (mp0) REVERT: A 1303 GLN cc_start: 0.8365 (mp10) cc_final: 0.8045 (mp10) REVERT: B 93 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 143 GLN cc_start: 0.7369 (pt0) cc_final: 0.6935 (tp40) REVERT: B 358 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: B 673 VAL cc_start: 0.9045 (t) cc_final: 0.8826 (m) REVERT: B 851 ASP cc_start: 0.7654 (p0) cc_final: 0.7318 (p0) REVERT: C 210 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: D 86 LEU cc_start: 0.7656 (tp) cc_final: 0.7332 (pt) REVERT: D 88 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7695 (mm) REVERT: E 103 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7711 (mp) REVERT: E 107 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8061 (mm110) REVERT: E 115 LYS cc_start: 0.9012 (tttt) cc_final: 0.8755 (mmmm) REVERT: G 1 MET cc_start: 0.4817 (pp-130) cc_final: 0.4288 (pmm) REVERT: G 10 GLU cc_start: 0.8105 (mp0) cc_final: 0.7777 (mm-30) REVERT: G 73 LYS cc_start: 0.7486 (mmmm) cc_final: 0.6882 (mmmt) REVERT: G 104 MET cc_start: 0.6559 (ptp) cc_final: 0.5691 (mpt) REVERT: H 146 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8239 (ptpt) REVERT: I 18 GLN cc_start: 0.8414 (mm110) cc_final: 0.8116 (mm110) REVERT: I 23 MET cc_start: 0.7512 (mmm) cc_final: 0.7039 (ttt) REVERT: I 25 TYR cc_start: 0.7104 (m-80) cc_final: 0.6524 (m-80) REVERT: I 57 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7656 (pptt) REVERT: K 22 ASN cc_start: 0.8523 (m-40) cc_final: 0.8028 (m110) REVERT: L 46 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8837 (mtmt) REVERT: M 107 MET cc_start: 0.6269 (ttt) cc_final: 0.5668 (ptp) REVERT: M 120 GLU cc_start: 0.8380 (tp30) cc_final: 0.7812 (mp0) REVERT: M 227 GLN cc_start: 0.8032 (mp10) cc_final: 0.7017 (tp40) REVERT: M 273 GLU cc_start: 0.7586 (pt0) cc_final: 0.7252 (pt0) REVERT: O 193 ASN cc_start: 0.9152 (t0) cc_final: 0.8849 (t0) REVERT: O 219 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7856 (tpp) REVERT: O 279 GLN cc_start: 0.8071 (pm20) cc_final: 0.7717 (pm20) REVERT: O 282 SER cc_start: 0.8582 (t) cc_final: 0.8250 (p) REVERT: O 293 TYR cc_start: 0.8258 (t80) cc_final: 0.7891 (t80) REVERT: Q 20 LYS cc_start: 0.5218 (mppt) cc_final: 0.4745 (mppt) REVERT: Q 29 MET cc_start: 0.7048 (ttm) cc_final: 0.6079 (tpp) REVERT: Q 111 LYS cc_start: 0.8557 (tppp) cc_final: 0.7739 (tptt) REVERT: Q 163 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7498 (mm-30) REVERT: R 22 LYS cc_start: 0.6987 (ttpt) cc_final: 0.6706 (ptmm) REVERT: R 43 LEU cc_start: 0.7323 (pt) cc_final: 0.6919 (tp) REVERT: R 140 ARG cc_start: 0.5970 (ttp-170) cc_final: 0.5745 (ttp-170) REVERT: U 51 MET cc_start: 0.4769 (mmp) cc_final: 0.2960 (mpp) REVERT: W 48 MET cc_start: 0.5571 (mmt) cc_final: 0.5316 (mpm) REVERT: W 76 MET cc_start: 0.3048 (mmm) cc_final: -0.2321 (mtm) outliers start: 78 outliers final: 44 residues processed: 650 average time/residue: 0.7431 time to fit residues: 587.8911 Evaluate side-chains 644 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 588 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 219 MET Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 170 optimal weight: 0.4980 chunk 446 optimal weight: 0.6980 chunk 239 optimal weight: 0.0980 chunk 432 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 398 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 481 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 731 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B1115 GLN C 217 GLN E 107 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN M 140 ASN ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.220051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162233 restraints weight = 50295.248| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.24 r_work: 0.3112 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 45123 Z= 0.166 Angle : 0.611 15.501 61335 Z= 0.307 Chirality : 0.043 0.220 6836 Planarity : 0.004 0.078 7603 Dihedral : 13.067 75.154 6790 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.72 % Allowed : 18.04 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5187 helix: 1.13 (0.12), residues: 1939 sheet: 0.29 (0.18), residues: 842 loop : -0.12 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1153 TYR 0.027 0.001 TYR I 54 PHE 0.019 0.001 PHE Q 146 TRP 0.021 0.001 TRP B 453 HIS 0.011 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (45083) covalent geometry : angle 0.59837 / 0.31 (61281) hydrogen bonds : bond 0.03740 / 2.51 ( 1164) hydrogen bonds : angle 3.57638 / 2.58 ( 3285) metal coordination : bond 0.02045 / 1.56 ( 40) metal coordination : angle 4.22690 / 2.66 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16532.58 seconds wall clock time: 281 minutes 39.39 seconds (16899.39 seconds total)