Starting phenix.real_space_refine on Sat Aug 8 12:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.map" model { file = "/net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uha_64160/08_2026/9uha_64160.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 270 5.49 5 S 121 5.16 5 C 16439 2.51 5 N 4837 2.21 5 O 5774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27442 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 5722 Classifications: {'RNA': 270} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 19, 'rna3p_pur': 105, 'rna3p_pyr': 128} Link IDs: {'rna2p': 37, 'rna3p': 232} Chain: "B" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5689 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 47, 'TRANS': 670} Chain breaks: 6 Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1078 Classifications: {'peptide': 137} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1502 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "E" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1215 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain breaks: 1 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1829 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "J" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1916 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain: "K" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 963 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 341} Chain: "M" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1828 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "K" 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 22051 SG CYS K 43 73.225 91.101 50.250 1.00137.97 S ATOM 22076 SG CYS K 46 73.247 87.267 50.959 1.00138.36 S ATOM 22554 SG CYS K 104 70.917 88.628 48.370 1.00156.89 S ATOM 22576 SG CYS K 107 70.379 89.339 52.069 1.00158.23 S Time building chain proxies: 5.12, per 1000 atoms: 0.19 Number of scatterers: 27442 At special positions: 0 Unit cell: (147.4, 165, 192.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 121 16.00 P 270 15.00 O 5774 8.00 N 4837 7.00 C 16439 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: 1.54 Conformation dependent library (CDL) restraints added in 629.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 107 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 46 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 104 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " Number of angles added : 6 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5196 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 18 sheets defined 44.1% alpha, 17.6% beta 19 base pairs and 129 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.599A pdb=" N ARG B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.675A pdb=" N ARG B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 4.065A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.645A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.737A pdb=" N ILE B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 removed outlier: 4.362A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.678A pdb=" N GLU B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.634A pdb=" N ARG B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.863A pdb=" N TRP B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 632 " --> pdb=" O MET B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 643 through 654 Processing helix chain 'B' and resid 666 through 686 removed outlier: 3.538A pdb=" N ARG B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 808 through 820 removed outlier: 3.638A pdb=" N GLN B 814 " --> pdb=" O LYS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.931A pdb=" N ASP B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 905 through 919 removed outlier: 3.901A pdb=" N LEU B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 910 " --> pdb=" O SER B 906 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 removed outlier: 4.430A pdb=" N CYS B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 removed outlier: 4.383A pdb=" N ASP B 992 " --> pdb=" O THR B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 56 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.862A pdb=" N ARG C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 141 through 154 removed outlier: 4.297A pdb=" N HIS C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 173 Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 10 through 17 removed outlier: 4.024A pdb=" N ALA D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 44 through 53 removed outlier: 4.213A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP D 49 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 removed outlier: 3.589A pdb=" N LEU D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.549A pdb=" N LEU D 98 " --> pdb=" O ARG D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 114 removed outlier: 3.602A pdb=" N CYS D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 removed outlier: 3.888A pdb=" N ILE D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 74 through 81 removed outlier: 3.860A pdb=" N ALA E 80 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 126 removed outlier: 3.608A pdb=" N CYS E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 4.111A pdb=" N GLN E 139 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 4.143A pdb=" N GLN F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 88 removed outlier: 4.331A pdb=" N LYS F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 58 Processing helix chain 'G' and resid 75 through 92 removed outlier: 3.995A pdb=" N ASN G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 53 removed outlier: 4.006A pdb=" N LEU H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.793A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'I' and resid 14 through 29 removed outlier: 3.627A pdb=" N LEU I 28 " --> pdb=" O THR I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.507A pdb=" N LEU I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 58 " --> pdb=" O VAL I 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 53 through 58' Processing helix chain 'I' and resid 83 through 92 removed outlier: 3.841A pdb=" N CYS I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN I 88 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 100 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 156 through 162 removed outlier: 3.768A pdb=" N LYS I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 162 " --> pdb=" O PRO I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 178 removed outlier: 3.747A pdb=" N TYR I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 211 removed outlier: 3.521A pdb=" N ASN I 205 " --> pdb=" O TYR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 222 through 238 removed outlier: 3.886A pdb=" N ARG I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.624A pdb=" N LEU J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 removed outlier: 4.003A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.615A pdb=" N CYS J 117 " --> pdb=" O PHE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.625A pdb=" N ILE J 142 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 162 removed outlier: 4.009A pdb=" N LYS J 161 " --> pdb=" O SER J 157 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP J 162 " --> pdb=" O PRO J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 157 through 162' Processing helix chain 'J' and resid 163 through 180 removed outlier: 3.901A pdb=" N ARG J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 197 removed outlier: 3.580A pdb=" N ILE J 197 " --> pdb=" O PRO J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 211 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 222 through 238 removed outlier: 3.569A pdb=" N ARG J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA J 238 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.815A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.852A pdb=" N ALA K 22 " --> pdb=" O CYS K 18 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS K 33 " --> pdb=" O TYR K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 79 removed outlier: 4.218A pdb=" N ARG K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 95 Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 53 through 62 Processing helix chain 'L' and resid 75 through 78 Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.765A pdb=" N LEU L 155 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 192 through 197 Processing helix chain 'L' and resid 236 through 249 removed outlier: 3.844A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP L 242 " --> pdb=" O LEU L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'L' and resid 300 through 303 removed outlier: 4.078A pdb=" N GLU L 303 " --> pdb=" O TYR L 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 300 through 303' Processing helix chain 'M' and resid 10 through 14 Processing helix chain 'M' and resid 32 through 54 Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.667A pdb=" N ASP M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 98 removed outlier: 3.667A pdb=" N MET M 98 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 113 removed outlier: 3.917A pdb=" N SER M 103 " --> pdb=" O ASN M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 165 removed outlier: 3.599A pdb=" N VAL M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY M 165 " --> pdb=" O VAL M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 195 Processing helix chain 'M' and resid 197 through 212 Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.621A pdb=" N GLY M 231 " --> pdb=" O THR M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 239 removed outlier: 3.770A pdb=" N PHE M 235 " --> pdb=" O GLY M 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 509 removed outlier: 5.299A pdb=" N THR B 503 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN B 601 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B 246 " --> pdb=" O GLY B 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 294 removed outlier: 3.561A pdb=" N GLY B 290 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 306 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 804 through 805 removed outlier: 7.232A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 873 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 965 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER B 986 " --> pdb=" O GLY B 965 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 967 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 984 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.588A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 132 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL C 161 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL C 134 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 178 removed outlier: 6.946A pdb=" N ILE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU D 160 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS D 166 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 140 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU D 187 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL D 142 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR D 185 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.620A pdb=" N ALA E 54 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU E 12 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR E 100 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 14 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE E 98 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AB1, first strand: chain 'F' and resid 36 through 39 removed outlier: 5.971A pdb=" N VAL F 36 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER F 68 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET F 38 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N CYS F 70 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 93 " --> pdb=" O GLN F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 20 through 24 removed outlier: 3.580A pdb=" N ARG G 123 " --> pdb=" O ASP G 109 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU G 74 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 14 removed outlier: 3.571A pdb=" N VAL H 11 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU L 15 " --> pdb=" O TYR H 13 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU L 14 " --> pdb=" O VAL L 355 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR L 311 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR L 40 " --> pdb=" O GLY L 283 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 62 through 64 removed outlier: 6.960A pdb=" N TYR H 21 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL H 107 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS H 23 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 5 through 10 removed outlier: 4.740A pdb=" N ALA I 5 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA I 34 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU I 7 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASN I 36 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU I 9 " --> pdb=" O ASN I 36 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE I 38 " --> pdb=" O LEU I 9 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR I 78 " --> pdb=" O HIS I 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 81 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 103 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N CYS I 126 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL I 105 " --> pdb=" O CYS I 126 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL I 125 " --> pdb=" O GLU I 153 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL I 155 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE I 152 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER I 188 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU I 154 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 5 through 10 removed outlier: 4.757A pdb=" N ALA J 5 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA J 34 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU J 7 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN J 36 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU J 9 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE J 38 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL J 33 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG J 76 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE J 35 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR J 78 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS J 37 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE J 80 " --> pdb=" O HIS J 37 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL J 102 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 103 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N CYS J 126 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 105 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE J 152 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER J 188 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU J 154 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 55 through 60 removed outlier: 6.218A pdb=" N SER K 98 " --> pdb=" O GLY K 115 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY K 115 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 132 through 133 removed outlier: 6.247A pdb=" N VAL L 107 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE L 179 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS L 70 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU L 181 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE L 68 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N TRP L 183 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR L 66 " --> pdb=" O TRP L 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 26 through 29 971 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 129 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.18 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: 7844 1.34 - 1.46: 7078 1.46 - 1.58: 12932 1.58 - 1.70: 539 1.70 - 1.82: 161 Bond restraints: 28554 Sorted by residual: bond pdb=" N9 A A 154 " pdb=" C4 A A 154 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.55e+01 bond pdb=" N9 A A 191 " pdb=" C4 A A 191 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.91e+00 bond pdb=" N9 A A 36 " pdb=" C4 A A 36 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.46e+00 bond pdb=" N3 A A 154 " pdb=" C4 A A 154 " ideal model delta sigma weight residual 1.344 1.332 0.012 6.00e-03 2.78e+04 4.32e+00 bond pdb=" N1 C A 202 " pdb=" C2 C A 202 " ideal model delta sigma weight residual 1.397 1.417 -0.020 1.00e-02 1.00e+04 4.04e+00 ... (remaining 28549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.23: 39879 7.23 - 14.47: 43 14.47 - 21.70: 6 21.70 - 28.93: 2 28.93 - 36.16: 1 Bond angle restraints: 39931 Sorted by residual: angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" C ALA B 999 " ideal model delta sigma weight residual 112.23 148.39 -36.16 1.26e+00 6.30e-01 8.24e+02 angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta sigma weight residual 110.30 85.89 24.41 1.54e+00 4.22e-01 2.51e+02 angle pdb=" N PRO B 998 " pdb=" CA PRO B 998 " pdb=" C PRO B 998 " ideal model delta sigma weight residual 112.47 84.28 28.19 2.06e+00 2.36e-01 1.87e+02 angle pdb=" N ALA B1000 " pdb=" CA ALA B1000 " pdb=" C ALA B1000 " ideal model delta sigma weight residual 113.12 99.46 13.66 1.25e+00 6.40e-01 1.19e+02 angle pdb=" C LYS B 299 " pdb=" CA LYS B 299 " pdb=" CB LYS B 299 " ideal model delta sigma weight residual 111.23 96.30 14.93 1.68e+00 3.54e-01 7.90e+01 ... (remaining 39926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16741 35.58 - 71.16: 947 71.16 - 106.74: 136 106.74 - 142.32: 0 142.32 - 177.90: 3 Dihedral angle restraints: 17827 sinusoidal: 9833 harmonic: 7994 Sorted by residual: dihedral pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta harmonic sigma weight residual 122.90 97.12 25.78 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" C ALA B 999 " pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta harmonic sigma weight residual -122.60 -100.85 -21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" O4' C A 243 " pdb=" C1' C A 243 " pdb=" N1 C A 243 " pdb=" C2 C A 243 " ideal model delta sinusoidal sigma weight residual 232.00 54.10 177.90 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4764 0.147 - 0.294: 15 0.294 - 0.441: 0 0.441 - 0.588: 1 0.588 - 0.734: 1 Chirality restraints: 4781 Sorted by residual: chirality pdb=" CA ALA B 999 " pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CB ALA B 999 " both_signs ideal model delta sigma weight residual False 2.48 1.75 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA PRO B 998 " pdb=" N PRO B 998 " pdb=" C PRO B 998 " pdb=" CB PRO B 998 " both_signs ideal model delta sigma weight residual False 2.72 3.24 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CG LEU K 26 " pdb=" CB LEU K 26 " pdb=" CD1 LEU K 26 " pdb=" CD2 LEU K 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4778 not shown) Planarity restraints: 4056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 300 " 0.043 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO B 301 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 328 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" CD GLU L 328 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU L 328 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU L 328 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 997 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 998 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 998 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 998 " -0.029 5.00e-02 4.00e+02 ... (remaining 4053 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 119 2.61 - 3.18: 22312 3.18 - 3.75: 45005 3.75 - 4.33: 57771 4.33 - 4.90: 88738 Nonbonded interactions: 213945 Sorted by model distance: nonbonded pdb=" N PRO B 998 " pdb=" O PRO B 998 " model vdw 2.033 2.496 nonbonded pdb=" OD1 ASP K 53 " pdb=" N ASN K 54 " model vdw 2.250 3.120 nonbonded pdb=" C GLN B 997 " pdb=" O PRO B 998 " model vdw 2.339 3.270 nonbonded pdb=" O HIS B 146 " pdb=" ND1 HIS B 146 " model vdw 2.372 3.120 nonbonded pdb=" O GLN M 232 " pdb=" OE1 GLN M 232 " model vdw 2.421 3.040 ... (remaining 213940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 238) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.003 0.046 28558 Z= 0.146 Angle : 0.838 36.164 39937 Z= 0.507 Chirality : 0.051 0.734 4781 Planarity : 0.004 0.063 4056 Dihedral : 19.808 177.896 12631 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.12 % Allowed : 29.38 % Favored : 70.50 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.13 % 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: -0.10 (0.16), residues: 2699 helix: 1.11 (0.16), residues: 1028 sheet: 0.61 (0.23), residues: 539 loop : -1.54 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 210 TYR 0.024 0.001 TYR B 295 PHE 0.028 0.001 PHE M 157 TRP 0.026 0.001 TRP L 324 HIS 0.010 0.001 HIS L 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (28554) covalent geometry : angle 0.83734 / 0.51 (39931) hydrogen bonds : bond 0.15746 / 16.47 ( 1018) hydrogen bonds : angle 5.72178 / 7.08 ( 2895) metal coordination : bond 0.00402 / 0.21 ( 4) metal coordination : angle 2.71172 / 4.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 1.095 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: B 144 MET cc_start: 0.8417 (mmm) cc_final: 0.7928 (mmm) REVERT: B 846 LEU cc_start: 0.9371 (tt) cc_final: 0.9041 (pp) REVERT: C 39 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8597 (pp20) REVERT: C 45 LEU cc_start: 0.8985 (mt) cc_final: 0.8733 (pp) REVERT: D 109 TYR cc_start: 0.9202 (t80) cc_final: 0.8928 (t80) REVERT: D 134 ASP cc_start: 0.8744 (t0) cc_final: 0.8248 (p0) REVERT: D 160 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8437 (tm-30) REVERT: D 171 GLU cc_start: 0.8901 (pm20) cc_final: 0.8545 (pm20) REVERT: D 172 ASP cc_start: 0.8834 (p0) cc_final: 0.8522 (p0) REVERT: E 88 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7769 (tp30) REVERT: E 98 PHE cc_start: 0.9428 (m-10) cc_final: 0.9220 (m-80) REVERT: E 150 GLU cc_start: 0.7254 (mp0) cc_final: 0.6841 (tp30) REVERT: F 142 ASP cc_start: 0.9010 (m-30) cc_final: 0.8800 (p0) REVERT: G 39 VAL cc_start: 0.9297 (t) cc_final: 0.9044 (p) REVERT: I 57 LEU cc_start: 0.9194 (tp) cc_final: 0.8410 (mt) REVERT: I 143 ASN cc_start: 0.9506 (m-40) cc_final: 0.9289 (m110) REVERT: I 177 MET cc_start: 0.9036 (tpp) cc_final: 0.8076 (tpp) REVERT: J 72 LYS cc_start: 0.8912 (tptm) cc_final: 0.8548 (tptm) REVERT: J 165 MET cc_start: 0.8861 (mmm) cc_final: 0.8625 (mmm) REVERT: J 168 TYR cc_start: 0.9021 (m-80) cc_final: 0.8782 (m-80) REVERT: J 177 MET cc_start: 0.8874 (tmm) cc_final: 0.8501 (mtt) REVERT: K 80 TYR cc_start: 0.7302 (p90) cc_final: 0.7050 (p90) REVERT: L 193 MET cc_start: 0.8592 (mmm) cc_final: 0.8252 (mmt) REVERT: L 226 GLU cc_start: 0.8721 (tp30) cc_final: 0.8143 (tt0) REVERT: M 16 ARG cc_start: 0.9257 (mmp80) cc_final: 0.9036 (mmp80) REVERT: M 51 LEU cc_start: 0.9472 (mt) cc_final: 0.9043 (pp) REVERT: M 53 LEU cc_start: 0.9146 (tt) cc_final: 0.8855 (mt) REVERT: M 76 MET cc_start: 0.8472 (mtm) cc_final: 0.8116 (mpp) REVERT: M 91 CYS cc_start: 0.9427 (m) cc_final: 0.8931 (t) REVERT: M 111 PHE cc_start: 0.9208 (m-80) cc_final: 0.8811 (m-80) REVERT: M 153 CYS cc_start: 0.9502 (m) cc_final: 0.9174 (m) REVERT: M 176 MET cc_start: 0.9674 (mtp) cc_final: 0.9384 (mtp) REVERT: M 193 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7833 (mmm-85) outliers start: 3 outliers final: 2 residues processed: 355 average time/residue: 0.1886 time to fit residues: 107.6151 Evaluate side-chains 294 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain E residue 73 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 0.0040 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN M 82 HIS M 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053201 restraints weight = 154662.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054748 restraints weight = 78786.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055742 restraints weight = 51990.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.056373 restraints weight = 40084.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056690 restraints weight = 34212.904| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28558 Z= 0.134 Angle : 0.588 12.514 39937 Z= 0.298 Chirality : 0.038 0.191 4781 Planarity : 0.004 0.054 4056 Dihedral : 19.064 178.159 7260 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.91 % Allowed : 25.22 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.15 (0.17), residues: 2699 helix: 1.37 (0.16), residues: 1065 sheet: 0.60 (0.23), residues: 546 loop : -1.49 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 64 TYR 0.015 0.001 TYR K 45 PHE 0.018 0.001 PHE M 235 TRP 0.018 0.001 TRP C 104 HIS 0.005 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (28554) covalent geometry : angle 0.58744 / 0.30 (39931) hydrogen bonds : bond 0.04850 / 5.18 ( 1018) hydrogen bonds : angle 4.80961 / 6.02 ( 2895) metal coordination : bond 0.00508 / 0.34 ( 4) metal coordination : angle 2.38418 / 3.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 0.997 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: B 126 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8669 (t) REVERT: B 130 LEU cc_start: 0.9352 (mt) cc_final: 0.9101 (mm) REVERT: B 133 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: B 144 MET cc_start: 0.9180 (mmm) cc_final: 0.8646 (mmm) REVERT: B 304 MET cc_start: 0.7852 (tmm) cc_final: 0.7640 (tmm) REVERT: B 628 MET cc_start: 0.9123 (mmm) cc_final: 0.8340 (mmm) REVERT: B 846 LEU cc_start: 0.9299 (tt) cc_final: 0.8986 (pp) REVERT: C 45 LEU cc_start: 0.9161 (mt) cc_final: 0.8914 (pp) REVERT: D 28 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9191 (mm-30) REVERT: D 109 TYR cc_start: 0.9168 (t80) cc_final: 0.8908 (t80) REVERT: D 134 ASP cc_start: 0.8635 (t0) cc_final: 0.8232 (p0) REVERT: D 160 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8294 (tm-30) REVERT: E 144 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8279 (ttp80) REVERT: E 150 GLU cc_start: 0.7311 (mp0) cc_final: 0.6776 (tp30) REVERT: F 39 ARG cc_start: 0.8838 (ptm-80) cc_final: 0.8455 (ttp80) REVERT: F 67 PHE cc_start: 0.8901 (m-80) cc_final: 0.8575 (m-10) REVERT: G 39 VAL cc_start: 0.9550 (t) cc_final: 0.9133 (p) REVERT: H 69 LYS cc_start: 0.9104 (mppt) cc_final: 0.7989 (mmtm) REVERT: I 143 ASN cc_start: 0.9492 (m-40) cc_final: 0.9253 (m-40) REVERT: I 177 MET cc_start: 0.8957 (tpp) cc_final: 0.8078 (tpp) REVERT: J 72 LYS cc_start: 0.8948 (tptm) cc_final: 0.8593 (tptm) REVERT: K 72 LEU cc_start: 0.7389 (pp) cc_final: 0.7098 (pp) REVERT: K 114 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7796 (m-70) REVERT: L 193 MET cc_start: 0.8351 (mmm) cc_final: 0.8141 (mmt) REVERT: L 226 GLU cc_start: 0.8365 (tp30) cc_final: 0.8032 (tt0) REVERT: M 14 ARG cc_start: 0.8578 (mmp80) cc_final: 0.8378 (mmp80) REVERT: M 16 ARG cc_start: 0.9236 (mmp80) cc_final: 0.9007 (mmp80) REVERT: M 53 LEU cc_start: 0.9125 (tt) cc_final: 0.8844 (mt) REVERT: M 76 MET cc_start: 0.8950 (mtm) cc_final: 0.8288 (mpp) REVERT: M 91 CYS cc_start: 0.9454 (m) cc_final: 0.8973 (t) REVERT: M 97 ASN cc_start: 0.9191 (p0) cc_final: 0.8990 (p0) REVERT: M 105 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9216 (pp30) REVERT: M 111 PHE cc_start: 0.9139 (m-80) cc_final: 0.8712 (m-80) REVERT: M 153 CYS cc_start: 0.9529 (m) cc_final: 0.9193 (m) REVERT: M 173 ASN cc_start: 0.9178 (m-40) cc_final: 0.8846 (m-40) REVERT: M 225 ASP cc_start: 0.9027 (t0) cc_final: 0.8676 (t0) outliers start: 70 outliers final: 33 residues processed: 354 average time/residue: 0.1834 time to fit residues: 104.4055 Evaluate side-chains 308 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 119 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 190 optimal weight: 0.0050 chunk 93 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 37 HIS I 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN L 315 GLN L 345 ASN ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.068242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049084 restraints weight = 163032.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050530 restraints weight = 84742.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.051501 restraints weight = 57182.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.052089 restraints weight = 44843.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052374 restraints weight = 38757.428| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28558 Z= 0.220 Angle : 0.629 15.117 39937 Z= 0.322 Chirality : 0.040 0.205 4781 Planarity : 0.005 0.065 4056 Dihedral : 19.066 174.670 7260 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.49 % Allowed : 25.09 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.09 (0.16), residues: 2699 helix: 1.41 (0.16), residues: 1080 sheet: 0.45 (0.23), residues: 528 loop : -1.56 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 64 TYR 0.021 0.002 TYR M 234 PHE 0.020 0.002 PHE M 157 TRP 0.027 0.002 TRP B 890 HIS 0.011 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (28554) covalent geometry : angle 0.62814 / 0.32 (39931) hydrogen bonds : bond 0.04754 / 5.15 ( 1018) hydrogen bonds : angle 4.82349 / 6.05 ( 2895) metal coordination : bond 0.00928 / 0.51 ( 4) metal coordination : angle 2.14967 / 2.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 270 time to evaluate : 0.976 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: B 130 LEU cc_start: 0.9364 (mt) cc_final: 0.9129 (mm) REVERT: B 133 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: B 144 MET cc_start: 0.9190 (mmm) cc_final: 0.8661 (mmm) REVERT: B 304 MET cc_start: 0.8085 (tmm) cc_final: 0.7824 (tmm) REVERT: B 628 MET cc_start: 0.9231 (mmm) cc_final: 0.8491 (mmm) REVERT: B 1001 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8961 (pm20) REVERT: C 45 LEU cc_start: 0.9107 (mt) cc_final: 0.8866 (pp) REVERT: D 160 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 71 LYS cc_start: 0.9597 (tppp) cc_final: 0.9160 (tppp) REVERT: E 144 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8199 (tmm160) REVERT: G 39 VAL cc_start: 0.9597 (t) cc_final: 0.9195 (p) REVERT: H 51 LEU cc_start: 0.9287 (tp) cc_final: 0.9072 (tt) REVERT: H 68 GLU cc_start: 0.8988 (pm20) cc_final: 0.8544 (pm20) REVERT: H 69 LYS cc_start: 0.9204 (mppt) cc_final: 0.8876 (mmtm) REVERT: I 41 PHE cc_start: 0.8864 (m-10) cc_final: 0.8619 (m-80) REVERT: I 63 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8991 (tp) REVERT: I 177 MET cc_start: 0.8976 (tpp) cc_final: 0.8144 (tpp) REVERT: I 212 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9245 (mm) REVERT: J 72 LYS cc_start: 0.8962 (tptm) cc_final: 0.8661 (tptm) REVERT: J 177 MET cc_start: 0.8878 (tmm) cc_final: 0.8663 (mtm) REVERT: K 8 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8023 (tt0) REVERT: K 109 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8539 (mmm-85) REVERT: K 114 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7807 (m-70) REVERT: L 226 GLU cc_start: 0.8411 (tp30) cc_final: 0.8021 (tt0) REVERT: M 14 ARG cc_start: 0.8649 (mmp80) cc_final: 0.8422 (mmp80) REVERT: M 16 ARG cc_start: 0.9247 (mmp80) cc_final: 0.9027 (mmp80) REVERT: M 53 LEU cc_start: 0.9189 (tt) cc_final: 0.8941 (mt) REVERT: M 76 MET cc_start: 0.9133 (mtm) cc_final: 0.8412 (mpp) REVERT: M 91 CYS cc_start: 0.9521 (m) cc_final: 0.9117 (t) REVERT: M 111 PHE cc_start: 0.9189 (m-80) cc_final: 0.8748 (m-80) REVERT: M 153 CYS cc_start: 0.9514 (m) cc_final: 0.9155 (m) REVERT: M 173 ASN cc_start: 0.9320 (m-40) cc_final: 0.9095 (m-40) REVERT: M 193 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8012 (mmm-85) REVERT: M 225 ASP cc_start: 0.9194 (t0) cc_final: 0.8872 (t0) outliers start: 108 outliers final: 64 residues processed: 351 average time/residue: 0.1854 time to fit residues: 105.0122 Evaluate side-chains 317 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 109 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 chunk 81 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 602 GLN ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN J 175 ASN K 21 GLN L 315 GLN M 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.068920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049754 restraints weight = 159927.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051252 restraints weight = 82443.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052262 restraints weight = 55237.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052837 restraints weight = 42994.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053123 restraints weight = 37244.547| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28558 Z= 0.121 Angle : 0.567 12.789 39937 Z= 0.284 Chirality : 0.038 0.203 4781 Planarity : 0.004 0.050 4056 Dihedral : 19.074 175.329 7260 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.87 % Allowed : 26.80 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.26 (0.17), residues: 2699 helix: 1.59 (0.16), residues: 1081 sheet: 0.46 (0.23), residues: 528 loop : -1.47 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 147 TYR 0.018 0.001 TYR K 24 PHE 0.021 0.001 PHE M 169 TRP 0.022 0.001 TRP B 890 HIS 0.005 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (28554) covalent geometry : angle 0.56612 / 0.28 (39931) hydrogen bonds : bond 0.04037 / 4.36 ( 1018) hydrogen bonds : angle 4.60546 / 5.74 ( 2895) metal coordination : bond 0.00415 / 0.30 ( 4) metal coordination : angle 2.79287 / 3.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 280 time to evaluate : 0.714 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: B 133 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: B 144 MET cc_start: 0.9172 (mmm) cc_final: 0.8578 (mmm) REVERT: B 304 MET cc_start: 0.7919 (tmm) cc_final: 0.7705 (tmm) REVERT: B 628 MET cc_start: 0.9155 (mmm) cc_final: 0.8391 (mmm) REVERT: B 846 LEU cc_start: 0.9301 (tt) cc_final: 0.8979 (pp) REVERT: C 45 LEU cc_start: 0.9063 (mt) cc_final: 0.8856 (pp) REVERT: C 119 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6698 (mp0) REVERT: D 28 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9153 (mm-30) REVERT: D 160 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8436 (tm-30) REVERT: E 71 LYS cc_start: 0.9616 (tppp) cc_final: 0.9098 (tppp) REVERT: F 39 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.7493 (tmm160) REVERT: F 80 CYS cc_start: 0.9508 (m) cc_final: 0.9155 (t) REVERT: G 39 VAL cc_start: 0.9547 (t) cc_final: 0.9208 (p) REVERT: H 45 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9292 (pt) REVERT: H 51 LEU cc_start: 0.9231 (tp) cc_final: 0.9017 (tt) REVERT: H 68 GLU cc_start: 0.8941 (pm20) cc_final: 0.8401 (pm20) REVERT: H 69 LYS cc_start: 0.9224 (mppt) cc_final: 0.8944 (mmtm) REVERT: I 41 PHE cc_start: 0.8862 (m-10) cc_final: 0.8623 (m-80) REVERT: I 63 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9134 (tp) REVERT: J 72 LYS cc_start: 0.8984 (tptm) cc_final: 0.8675 (tptm) REVERT: J 175 ASN cc_start: 0.8719 (m110) cc_final: 0.8333 (m110) REVERT: K 8 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7975 (tt0) REVERT: K 109 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: K 114 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7869 (m-70) REVERT: L 226 GLU cc_start: 0.8361 (tp30) cc_final: 0.7881 (tt0) REVERT: M 14 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8424 (mmp80) REVERT: M 16 ARG cc_start: 0.9249 (mmp80) cc_final: 0.9030 (mmp80) REVERT: M 53 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9011 (mp) REVERT: M 76 MET cc_start: 0.9112 (mtm) cc_final: 0.8457 (mpp) REVERT: M 91 CYS cc_start: 0.9528 (m) cc_final: 0.9072 (t) REVERT: M 97 ASN cc_start: 0.9284 (p0) cc_final: 0.8960 (p0) REVERT: M 111 PHE cc_start: 0.9181 (m-80) cc_final: 0.8715 (m-80) REVERT: M 169 PHE cc_start: 0.9125 (m-80) cc_final: 0.8818 (m-80) REVERT: M 173 ASN cc_start: 0.9303 (m-40) cc_final: 0.9087 (m-40) REVERT: M 176 MET cc_start: 0.9673 (mtp) cc_final: 0.9415 (mtp) REVERT: M 193 ARG cc_start: 0.8520 (tpp80) cc_final: 0.7890 (mmm-85) REVERT: M 225 ASP cc_start: 0.9189 (t0) cc_final: 0.8849 (t0) outliers start: 93 outliers final: 58 residues processed: 349 average time/residue: 0.1522 time to fit residues: 84.8334 Evaluate side-chains 319 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 133 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN L 315 GLN ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 GLN M 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046050 restraints weight = 160705.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047457 restraints weight = 85339.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048357 restraints weight = 58382.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048887 restraints weight = 46509.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049217 restraints weight = 40594.389| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 28558 Z= 0.269 Angle : 0.686 14.768 39937 Z= 0.349 Chirality : 0.042 0.258 4781 Planarity : 0.005 0.049 4056 Dihedral : 19.198 174.263 7260 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.29 % Allowed : 26.55 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.04 (0.17), residues: 2699 helix: 1.28 (0.16), residues: 1089 sheet: 0.24 (0.23), residues: 530 loop : -1.55 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 147 TYR 0.021 0.002 TYR K 24 PHE 0.032 0.002 PHE M 235 TRP 0.015 0.002 TRP B 413 HIS 0.007 0.001 HIS L 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (28554) covalent geometry : angle 0.68350 / 0.35 (39931) hydrogen bonds : bond 0.04933 / 5.33 ( 1018) hydrogen bonds : angle 5.02512 / 6.33 ( 2895) metal coordination : bond 0.01012 / 0.57 ( 4) metal coordination : angle 4.96933 / 7.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 259 time to evaluate : 1.323 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: B 130 LEU cc_start: 0.9361 (mt) cc_final: 0.9138 (mm) REVERT: B 133 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: B 141 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7245 (tpp-160) REVERT: B 144 MET cc_start: 0.9150 (mmm) cc_final: 0.8633 (mmm) REVERT: B 622 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9499 (pp) REVERT: B 628 MET cc_start: 0.9247 (mmm) cc_final: 0.8592 (mmm) REVERT: B 700 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9104 (p) REVERT: B 846 LEU cc_start: 0.9357 (tt) cc_final: 0.9027 (pp) REVERT: C 191 ASP cc_start: 0.9171 (t0) cc_final: 0.8966 (t0) REVERT: C 194 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6339 (ttp-170) REVERT: D 158 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 160 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8560 (tm-30) REVERT: E 34 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8572 (mtm-85) REVERT: E 71 LYS cc_start: 0.9613 (tppp) cc_final: 0.9087 (tppp) REVERT: E 92 HIS cc_start: 0.7808 (t-90) cc_final: 0.7599 (t-90) REVERT: E 146 CYS cc_start: 0.8409 (m) cc_final: 0.8152 (m) REVERT: H 45 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9361 (pt) REVERT: H 102 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8325 (m-10) REVERT: I 44 LYS cc_start: 0.9532 (mttt) cc_final: 0.9075 (mmmt) REVERT: I 177 MET cc_start: 0.8895 (ttm) cc_final: 0.8254 (tpp) REVERT: I 212 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9177 (mm) REVERT: J 6 ASP cc_start: 0.7986 (t0) cc_final: 0.7735 (t0) REVERT: J 72 LYS cc_start: 0.9000 (tptm) cc_final: 0.8669 (tptm) REVERT: J 175 ASN cc_start: 0.8833 (m110) cc_final: 0.8401 (m110) REVERT: J 177 MET cc_start: 0.8989 (tmm) cc_final: 0.8722 (mtm) REVERT: K 8 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8019 (tt0) REVERT: K 86 GLU cc_start: 0.4662 (tp30) cc_final: 0.4454 (tp30) REVERT: K 109 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8565 (mmm-85) REVERT: K 114 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.7938 (m-70) REVERT: L 226 GLU cc_start: 0.8569 (tp30) cc_final: 0.7916 (tt0) REVERT: M 16 ARG cc_start: 0.9251 (mmp80) cc_final: 0.9020 (mmp80) REVERT: M 53 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9012 (mp) REVERT: M 78 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7577 (tmt170) REVERT: M 91 CYS cc_start: 0.9588 (m) cc_final: 0.9157 (t) REVERT: M 111 PHE cc_start: 0.9225 (m-80) cc_final: 0.8744 (m-80) REVERT: M 176 MET cc_start: 0.9718 (mtp) cc_final: 0.9473 (mtp) REVERT: M 182 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8830 (mmt90) REVERT: M 193 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8044 (mmm-85) REVERT: M 225 ASP cc_start: 0.9204 (t0) cc_final: 0.8883 (t0) outliers start: 127 outliers final: 85 residues processed: 353 average time/residue: 0.1842 time to fit residues: 105.2849 Evaluate side-chains 338 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 239 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 166 optimal weight: 0.0270 chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 ASN E 127 GLN F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047766 restraints weight = 152733.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049201 restraints weight = 78759.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050133 restraints weight = 52841.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050724 restraints weight = 41267.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051039 restraints weight = 35534.097| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28558 Z= 0.117 Angle : 0.595 15.463 39937 Z= 0.296 Chirality : 0.039 0.219 4781 Planarity : 0.004 0.050 4056 Dihedral : 19.213 174.816 7260 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.75 % Allowed : 28.55 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.19 (0.17), residues: 2699 helix: 1.53 (0.16), residues: 1074 sheet: 0.33 (0.23), residues: 523 loop : -1.43 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 64 TYR 0.020 0.001 TYR H 95 PHE 0.022 0.001 PHE M 157 TRP 0.019 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (28554) covalent geometry : angle 0.59377 / 0.30 (39931) hydrogen bonds : bond 0.04069 / 4.42 ( 1018) hydrogen bonds : angle 4.66312 / 5.83 ( 2895) metal coordination : bond 0.00354 / 0.24 ( 4) metal coordination : angle 3.57518 / 4.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 269 time to evaluate : 1.003 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: B 111 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8958 (mpt-90) REVERT: B 133 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: B 141 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7892 (tpp-160) REVERT: B 144 MET cc_start: 0.9131 (mmm) cc_final: 0.8821 (mmm) REVERT: B 628 MET cc_start: 0.9131 (mmm) cc_final: 0.8243 (mmm) REVERT: B 846 LEU cc_start: 0.9319 (tt) cc_final: 0.9020 (pp) REVERT: D 28 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9158 (mm-30) REVERT: D 41 ARG cc_start: 0.9084 (mmp80) cc_final: 0.8849 (mmp80) REVERT: D 160 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8502 (tm-30) REVERT: E 39 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8778 (ttp80) REVERT: E 71 LYS cc_start: 0.9613 (tppp) cc_final: 0.9069 (tppp) REVERT: E 144 ARG cc_start: 0.8774 (ptm-80) cc_final: 0.8334 (ttp80) REVERT: E 149 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: E 150 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: G 39 VAL cc_start: 0.9565 (t) cc_final: 0.9183 (p) REVERT: H 45 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9314 (pt) REVERT: I 58 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8552 (t80) REVERT: J 175 ASN cc_start: 0.8806 (m110) cc_final: 0.8600 (m-40) REVERT: J 177 MET cc_start: 0.8886 (tmm) cc_final: 0.8652 (mtt) REVERT: K 8 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7966 (tt0) REVERT: K 109 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8528 (mmm-85) REVERT: K 114 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: M 16 ARG cc_start: 0.9261 (mmp80) cc_final: 0.9042 (mmp80) REVERT: M 91 CYS cc_start: 0.9541 (m) cc_final: 0.9075 (t) REVERT: M 111 PHE cc_start: 0.9162 (m-80) cc_final: 0.8646 (m-80) REVERT: M 173 ASN cc_start: 0.9320 (m-40) cc_final: 0.9067 (m-40) REVERT: M 182 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8651 (tpp-160) REVERT: M 193 ARG cc_start: 0.8617 (tpp80) cc_final: 0.7959 (mmm-85) REVERT: M 225 ASP cc_start: 0.9248 (t0) cc_final: 0.8931 (t0) outliers start: 90 outliers final: 62 residues processed: 334 average time/residue: 0.1882 time to fit residues: 100.8391 Evaluate side-chains 322 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 722 TYR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 64 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 217 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN ** M 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046259 restraints weight = 159056.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047668 restraints weight = 83908.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048582 restraints weight = 57256.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049123 restraints weight = 45376.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049484 restraints weight = 39472.146| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28558 Z= 0.184 Angle : 0.625 15.074 39937 Z= 0.314 Chirality : 0.040 0.241 4781 Planarity : 0.004 0.053 4056 Dihedral : 19.224 174.944 7260 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.12 % Allowed : 29.01 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.12 (0.17), residues: 2699 helix: 1.48 (0.16), residues: 1078 sheet: 0.29 (0.23), residues: 523 loop : -1.47 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 147 TYR 0.023 0.001 TYR K 24 PHE 0.024 0.002 PHE M 157 TRP 0.010 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (28554) covalent geometry : angle 0.62248 / 0.31 (39931) hydrogen bonds : bond 0.04259 / 4.61 ( 1018) hydrogen bonds : angle 4.79818 / 6.04 ( 2895) metal coordination : bond 0.00586 / 0.35 ( 4) metal coordination : angle 4.31288 / 6.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 252 time to evaluate : 0.964 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: B 111 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.9002 (mpt-90) REVERT: B 133 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: B 141 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7951 (tpp-160) REVERT: B 144 MET cc_start: 0.9112 (mmm) cc_final: 0.8805 (mmm) REVERT: B 304 MET cc_start: 0.7716 (tmm) cc_final: 0.7299 (tmm) REVERT: B 628 MET cc_start: 0.9198 (mmm) cc_final: 0.8343 (mmm) REVERT: B 846 LEU cc_start: 0.9333 (tt) cc_final: 0.9011 (pp) REVERT: D 158 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9273 (mm) REVERT: D 160 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8567 (tm-30) REVERT: E 34 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8552 (mtm-85) REVERT: E 39 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8797 (ttp80) REVERT: E 71 LYS cc_start: 0.9618 (tppp) cc_final: 0.9069 (tppp) REVERT: E 149 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: E 150 GLU cc_start: 0.7978 (mp0) cc_final: 0.6656 (tp30) REVERT: G 39 VAL cc_start: 0.9579 (t) cc_final: 0.9223 (p) REVERT: H 45 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9341 (pt) REVERT: H 69 LYS cc_start: 0.9306 (mppt) cc_final: 0.9024 (mmtm) REVERT: I 46 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8840 (pm20) REVERT: J 175 ASN cc_start: 0.8929 (m110) cc_final: 0.8425 (m110) REVERT: J 177 MET cc_start: 0.8901 (tmm) cc_final: 0.8553 (mtm) REVERT: K 8 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7984 (tt0) REVERT: K 27 TRP cc_start: 0.9446 (OUTLIER) cc_final: 0.9144 (t-100) REVERT: K 109 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8571 (mmm-85) REVERT: K 114 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8010 (m-70) REVERT: L 226 GLU cc_start: 0.8350 (tp30) cc_final: 0.8088 (tm-30) REVERT: M 91 CYS cc_start: 0.9526 (m) cc_final: 0.9090 (t) REVERT: M 111 PHE cc_start: 0.9242 (m-80) cc_final: 0.8726 (m-80) REVERT: M 176 MET cc_start: 0.9699 (mtp) cc_final: 0.9470 (mtp) REVERT: M 182 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8715 (tpp-160) REVERT: M 193 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8307 (mmm160) REVERT: M 225 ASP cc_start: 0.9260 (t0) cc_final: 0.8954 (t0) outliers start: 99 outliers final: 71 residues processed: 330 average time/residue: 0.1943 time to fit residues: 102.1854 Evaluate side-chains 328 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 245 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 268 optimal weight: 0.2980 chunk 217 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 282 optimal weight: 0.0020 chunk 283 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 12 optimal weight: 50.0000 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 HIS B 565 ASN B 602 GLN E 127 GLN F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN I 46 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN L 315 GLN M 232 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048152 restraints weight = 157920.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049661 restraints weight = 82223.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050600 restraints weight = 55227.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051178 restraints weight = 43468.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051530 restraints weight = 37639.809| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28558 Z= 0.110 Angle : 0.622 14.028 39937 Z= 0.303 Chirality : 0.039 0.233 4781 Planarity : 0.004 0.059 4056 Dihedral : 19.197 175.397 7260 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.16 % Allowed : 29.92 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.26 (0.17), residues: 2699 helix: 1.59 (0.16), residues: 1071 sheet: 0.37 (0.23), residues: 524 loop : -1.39 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 147 TYR 0.027 0.001 TYR H 95 PHE 0.021 0.001 PHE M 157 TRP 0.022 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (28554) covalent geometry : angle 0.62071 / 0.30 (39931) hydrogen bonds : bond 0.03653 / 3.95 ( 1018) hydrogen bonds : angle 4.50552 / 5.63 ( 2895) metal coordination : bond 0.00393 / 0.27 ( 4) metal coordination : angle 3.22741 / 4.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 277 time to evaluate : 0.986 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: B 111 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8908 (mtt180) REVERT: B 133 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: B 141 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8687 (mmm160) REVERT: B 304 MET cc_start: 0.7415 (tmm) cc_final: 0.7014 (tmm) REVERT: B 628 MET cc_start: 0.9131 (mmm) cc_final: 0.8257 (mmm) REVERT: B 846 LEU cc_start: 0.9352 (tt) cc_final: 0.9036 (pp) REVERT: C 29 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: D 41 ARG cc_start: 0.9070 (mmp80) cc_final: 0.8785 (mmp80) REVERT: D 158 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9238 (mm) REVERT: D 160 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8559 (tm-30) REVERT: E 39 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8802 (ttp80) REVERT: E 71 LYS cc_start: 0.9596 (tppp) cc_final: 0.9038 (tppp) REVERT: E 144 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8306 (ttp80) REVERT: E 149 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: E 150 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: G 39 VAL cc_start: 0.9459 (t) cc_final: 0.9094 (p) REVERT: G 87 GLN cc_start: 0.9657 (tp40) cc_final: 0.9248 (mp10) REVERT: H 69 LYS cc_start: 0.9295 (mppt) cc_final: 0.9028 (mmtm) REVERT: I 58 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8573 (t80) REVERT: J 175 ASN cc_start: 0.8860 (m110) cc_final: 0.8608 (m-40) REVERT: J 177 MET cc_start: 0.8902 (tmm) cc_final: 0.8614 (mtm) REVERT: K 8 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7935 (tt0) REVERT: K 114 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.7885 (m-70) REVERT: M 91 CYS cc_start: 0.9506 (m) cc_final: 0.9081 (t) REVERT: M 94 ARG cc_start: 0.9078 (mmt90) cc_final: 0.8356 (mmm-85) REVERT: M 111 PHE cc_start: 0.9241 (m-80) cc_final: 0.8722 (m-80) REVERT: M 151 ASP cc_start: 0.9354 (t0) cc_final: 0.9112 (m-30) REVERT: M 173 ASN cc_start: 0.9290 (m-40) cc_final: 0.9064 (m-40) REVERT: M 186 LEU cc_start: 0.9709 (mm) cc_final: 0.9505 (mp) REVERT: M 193 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8019 (mmm-85) REVERT: M 225 ASP cc_start: 0.9304 (t0) cc_final: 0.9020 (t0) outliers start: 76 outliers final: 48 residues processed: 332 average time/residue: 0.1859 time to fit residues: 99.3856 Evaluate side-chains 316 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 722 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.066802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047847 restraints weight = 153404.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049287 restraints weight = 79092.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050238 restraints weight = 52922.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050823 restraints weight = 41101.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051146 restraints weight = 35279.826| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28558 Z= 0.114 Angle : 0.622 13.652 39937 Z= 0.302 Chirality : 0.038 0.228 4781 Planarity : 0.004 0.056 4056 Dihedral : 19.139 175.637 7260 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.62 % Allowed : 30.88 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.24 (0.17), residues: 2699 helix: 1.55 (0.16), residues: 1081 sheet: 0.41 (0.23), residues: 522 loop : -1.43 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 147 TYR 0.032 0.001 TYR M 234 PHE 0.021 0.001 PHE M 108 TRP 0.016 0.001 TRP L 324 HIS 0.009 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (28554) covalent geometry : angle 0.62069 / 0.30 (39931) hydrogen bonds : bond 0.03682 / 3.96 ( 1018) hydrogen bonds : angle 4.52957 / 5.65 ( 2895) metal coordination : bond 0.00407 / 0.25 ( 4) metal coordination : angle 3.36113 / 4.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 0.902 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: B 133 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: B 304 MET cc_start: 0.7490 (tmm) cc_final: 0.7046 (tmm) REVERT: B 628 MET cc_start: 0.9166 (mmm) cc_final: 0.8308 (mmm) REVERT: B 846 LEU cc_start: 0.9358 (tt) cc_final: 0.9042 (pp) REVERT: C 29 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: D 158 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9244 (mm) REVERT: D 160 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8581 (tm-30) REVERT: E 39 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8785 (ttp80) REVERT: E 71 LYS cc_start: 0.9602 (tppp) cc_final: 0.9056 (tppp) REVERT: E 144 ARG cc_start: 0.8824 (ptm-80) cc_final: 0.8343 (ttp80) REVERT: E 149 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: E 150 GLU cc_start: 0.7899 (mp0) cc_final: 0.6650 (tp30) REVERT: G 39 VAL cc_start: 0.9461 (t) cc_final: 0.9182 (p) REVERT: G 87 GLN cc_start: 0.9616 (tp40) cc_final: 0.9217 (mp10) REVERT: H 69 LYS cc_start: 0.9288 (mppt) cc_final: 0.8981 (mmtm) REVERT: I 57 LEU cc_start: 0.9089 (tp) cc_final: 0.8319 (mt) REVERT: I 58 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8526 (t80) REVERT: J 175 ASN cc_start: 0.8924 (m110) cc_final: 0.8666 (m-40) REVERT: J 177 MET cc_start: 0.8936 (tmm) cc_final: 0.8614 (mtm) REVERT: K 8 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7949 (tt0) REVERT: K 114 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7819 (m-70) REVERT: M 91 CYS cc_start: 0.9497 (m) cc_final: 0.9084 (t) REVERT: M 94 ARG cc_start: 0.9100 (mmt90) cc_final: 0.8395 (mmm-85) REVERT: M 111 PHE cc_start: 0.9131 (m-80) cc_final: 0.8662 (m-80) REVERT: M 151 ASP cc_start: 0.9361 (t0) cc_final: 0.9123 (m-30) REVERT: M 173 ASN cc_start: 0.9306 (m-40) cc_final: 0.9096 (m-40) REVERT: M 176 MET cc_start: 0.9658 (mtp) cc_final: 0.9446 (mtp) REVERT: M 193 ARG cc_start: 0.8647 (tpp80) cc_final: 0.8045 (mmm-85) REVERT: M 225 ASP cc_start: 0.9296 (t0) cc_final: 0.8775 (t0) REVERT: M 234 TYR cc_start: 0.9061 (t80) cc_final: 0.8705 (t80) outliers start: 63 outliers final: 49 residues processed: 311 average time/residue: 0.1912 time to fit residues: 95.3470 Evaluate side-chains 307 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 282 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 260 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 453 HIS E 127 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN L 315 GLN M 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044357 restraints weight = 163615.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045730 restraints weight = 86563.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046609 restraints weight = 59125.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047156 restraints weight = 46943.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047467 restraints weight = 40854.099| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 28558 Z= 0.295 Angle : 0.748 16.029 39937 Z= 0.376 Chirality : 0.043 0.232 4781 Planarity : 0.005 0.061 4056 Dihedral : 19.318 173.063 7260 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.62 % Allowed : 31.00 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.20 (0.16), residues: 2699 helix: 1.17 (0.16), residues: 1077 sheet: 0.14 (0.23), residues: 523 loop : -1.61 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 51 TYR 0.025 0.002 TYR H 95 PHE 0.024 0.002 PHE C 189 TRP 0.020 0.002 TRP B 948 HIS 0.008 0.002 HIS L 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.29 (28554) covalent geometry : angle 0.74489 / 0.38 (39931) hydrogen bonds : bond 0.05007 / 5.40 ( 1018) hydrogen bonds : angle 5.12559 / 6.48 ( 2895) metal coordination : bond 0.01252 / 0.72 ( 4) metal coordination : angle 5.60215 / 8.59 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 0.982 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: B 144 MET cc_start: 0.9050 (mmm) cc_final: 0.8747 (mmm) REVERT: B 304 MET cc_start: 0.7873 (tmm) cc_final: 0.7414 (tmm) REVERT: B 575 MET cc_start: 0.9517 (mpp) cc_final: 0.9196 (mpp) REVERT: B 628 MET cc_start: 0.9258 (mmm) cc_final: 0.8499 (mmm) REVERT: D 41 ARG cc_start: 0.9187 (mmp80) cc_final: 0.8900 (mmp80) REVERT: D 160 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8607 (tm-30) REVERT: E 71 LYS cc_start: 0.9617 (tppp) cc_final: 0.9092 (tppp) REVERT: E 149 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: E 150 GLU cc_start: 0.7977 (mp0) cc_final: 0.6596 (tp30) REVERT: F 67 PHE cc_start: 0.9078 (m-10) cc_final: 0.8737 (m-10) REVERT: F 80 CYS cc_start: 0.9590 (m) cc_final: 0.9387 (t) REVERT: G 39 VAL cc_start: 0.9480 (t) cc_final: 0.9127 (p) REVERT: G 87 GLN cc_start: 0.9650 (tp40) cc_final: 0.9226 (mp10) REVERT: H 69 LYS cc_start: 0.9327 (mppt) cc_final: 0.9048 (mmtm) REVERT: H 102 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: K 8 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7992 (tt0) REVERT: K 109 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8369 (mmm-85) REVERT: M 91 CYS cc_start: 0.9564 (m) cc_final: 0.9159 (t) REVERT: M 111 PHE cc_start: 0.9221 (m-80) cc_final: 0.8757 (m-80) REVERT: M 176 MET cc_start: 0.9712 (mtp) cc_final: 0.9491 (mtp) REVERT: M 182 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8762 (mmt90) REVERT: M 225 ASP cc_start: 0.9213 (t0) cc_final: 0.8840 (t0) REVERT: M 234 TYR cc_start: 0.9100 (t80) cc_final: 0.8737 (t80) outliers start: 63 outliers final: 51 residues processed: 281 average time/residue: 0.1788 time to fit residues: 81.9555 Evaluate side-chains 286 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 144 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 HIS ** L 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044173 restraints weight = 161184.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045567 restraints weight = 85119.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046450 restraints weight = 58063.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046984 restraints weight = 45953.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047308 restraints weight = 40126.433| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28558 Z= 0.250 Angle : 0.704 16.426 39937 Z= 0.355 Chirality : 0.042 0.228 4781 Planarity : 0.005 0.054 4056 Dihedral : 19.483 175.196 7260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.75 % Allowed : 31.04 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.27 (0.16), residues: 2699 helix: 1.19 (0.16), residues: 1064 sheet: 0.05 (0.23), residues: 522 loop : -1.68 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 64 TYR 0.027 0.002 TYR M 234 PHE 0.024 0.002 PHE H 102 TRP 0.013 0.002 TRP B 858 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (28554) covalent geometry : angle 0.70216 / 0.36 (39931) hydrogen bonds : bond 0.04703 / 5.05 ( 1018) hydrogen bonds : angle 5.08266 / 6.43 ( 2895) metal coordination : bond 0.01065 / 0.61 ( 4) metal coordination : angle 4.63600 / 7.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.25 seconds wall clock time: 93 minutes 9.10 seconds (5589.10 seconds total)