Starting phenix.real_space_refine on Sun Jul 5 12:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uha_64160/07_2026/9uha_64160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uha_64160/07_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_64160/07_2026/9uha_64160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uha_64160/07_2026/9uha_64160.map" model { file = "/net/cci-nas-00/data/ceres_data/9uha_64160/07_2026/9uha_64160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uha_64160/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.87, per 1000 atoms: 0.21 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: 2.11 Conformation dependent library (CDL) restraints added in 886.1 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: 2.98 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: 5.35 Time building geometry restraints manager: 2.90 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: 4766 0.147 - 0.294: 13 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: 2.850 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.430 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.440 ------------------------------------------------------------------------------- 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= 0.139 Angle : 0.774 36.164 39937 Z= 0.443 Chirality : 0.041 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 0.00254 / 0.14 (28554) covalent geometry : angle 0.77324 / 0.44 (39931) hydrogen bonds : bond 0.15746 / 14.92 ( 1018) hydrogen bonds : angle 5.72178 / 6.80 ( 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 : 0.971 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: 0.7069 (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: 0.1765 time to fit residues: 100.3174 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 : 0.958 ------------------------------------------------------------------------------- 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: 10.0000 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: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 116 GLN F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3615 r_free = 0.3615 target = 0.072541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053551 restraints weight = 153841.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055066 restraints weight = 78297.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056055 restraints weight = 51726.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056685 restraints weight = 39937.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057023 restraints weight = 34030.556| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28558 Z= 0.123 Angle : 0.582 12.662 39937 Z= 0.294 Chirality : 0.038 0.181 4781 Planarity : 0.004 0.061 4056 Dihedral : 19.109 177.626 7260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.75 % Allowed : 25.38 % 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: 1.34 (0.16), residues: 1067 sheet: 0.63 (0.23), residues: 546 loop : -1.48 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 64 TYR 0.015 0.001 TYR K 45 PHE 0.019 0.001 PHE M 235 TRP 0.017 0.001 TRP C 104 HIS 0.005 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (28554) covalent geometry : angle 0.58085 / 0.29 (39931) hydrogen bonds : bond 0.04736 / 4.67 ( 1018) hydrogen bonds : angle 4.77103 / 5.75 ( 2895) metal coordination : bond 0.00485 / 0.27 ( 4) metal coordination : angle 2.31206 / 3.11 ( 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 374 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 0.809 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: B 130 LEU cc_start: 0.9365 (mt) cc_final: 0.9120 (mm) REVERT: B 133 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: B 144 MET cc_start: 0.9183 (mmm) cc_final: 0.8585 (mmm) REVERT: B 304 MET cc_start: 0.7821 (tmm) cc_final: 0.7609 (tmm) REVERT: B 628 MET cc_start: 0.9108 (mmm) cc_final: 0.8315 (mmm) REVERT: B 846 LEU cc_start: 0.9291 (tt) cc_final: 0.8994 (pp) REVERT: C 45 LEU cc_start: 0.9161 (mt) cc_final: 0.8911 (pp) REVERT: D 28 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9189 (mm-30) REVERT: D 109 TYR cc_start: 0.9161 (t80) cc_final: 0.8888 (t80) REVERT: D 134 ASP cc_start: 0.8619 (t0) cc_final: 0.8230 (p0) REVERT: D 160 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 88 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7977 (tp30) REVERT: E 144 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8269 (ttp80) REVERT: E 150 GLU cc_start: 0.7301 (mp0) cc_final: 0.6767 (tp30) REVERT: F 39 ARG cc_start: 0.8845 (ptm-80) cc_final: 0.8460 (ttp80) REVERT: F 67 PHE cc_start: 0.8900 (m-80) cc_final: 0.8566 (m-10) REVERT: G 39 VAL cc_start: 0.9546 (t) cc_final: 0.9132 (p) REVERT: H 69 LYS cc_start: 0.9004 (mppt) cc_final: 0.7829 (mmtm) REVERT: I 57 LEU cc_start: 0.9132 (tp) cc_final: 0.8399 (mt) REVERT: I 143 ASN cc_start: 0.9490 (m-40) cc_final: 0.9262 (m110) REVERT: I 177 MET cc_start: 0.8944 (tpp) cc_final: 0.8054 (tpp) REVERT: J 72 LYS cc_start: 0.8943 (tptm) cc_final: 0.8587 (tptm) REVERT: K 72 LEU cc_start: 0.7396 (pp) cc_final: 0.7082 (pp) REVERT: K 114 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7767 (m-70) REVERT: L 193 MET cc_start: 0.8335 (mmm) cc_final: 0.8133 (mmt) REVERT: L 226 GLU cc_start: 0.8330 (tp30) cc_final: 0.8021 (tt0) REVERT: M 14 ARG cc_start: 0.8561 (mmp80) cc_final: 0.8357 (mmp80) REVERT: M 16 ARG cc_start: 0.9251 (mmp80) cc_final: 0.9039 (mmp80) REVERT: M 53 LEU cc_start: 0.9122 (tt) cc_final: 0.8843 (mt) REVERT: M 76 MET cc_start: 0.8926 (mtm) cc_final: 0.8275 (mpp) REVERT: M 91 CYS cc_start: 0.9450 (m) cc_final: 0.8971 (t) REVERT: M 105 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9207 (pp30) REVERT: M 111 PHE cc_start: 0.9125 (m-80) cc_final: 0.8705 (m-80) REVERT: M 153 CYS cc_start: 0.9526 (m) cc_final: 0.9189 (m) REVERT: M 173 ASN cc_start: 0.9170 (m-40) cc_final: 0.8832 (m-40) REVERT: M 225 ASP cc_start: 0.9018 (t0) cc_final: 0.8628 (t0) outliers start: 66 outliers final: 31 residues processed: 357 average time/residue: 0.1780 time to fit residues: 101.8879 Evaluate side-chains 302 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 119 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 190 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 175 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.052234 restraints weight = 160799.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053784 restraints weight = 82560.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054779 restraints weight = 54818.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055382 restraints weight = 42716.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055769 restraints weight = 36839.917| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28558 Z= 0.127 Angle : 0.559 14.285 39937 Z= 0.284 Chirality : 0.038 0.192 4781 Planarity : 0.004 0.051 4056 Dihedral : 19.068 176.130 7260 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.29 % Allowed : 24.97 % Favored : 71.74 % 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: 0.25 (0.17), residues: 2699 helix: 1.50 (0.16), residues: 1074 sheet: 0.60 (0.23), residues: 527 loop : -1.44 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 147 TYR 0.017 0.001 TYR K 24 PHE 0.019 0.001 PHE M 157 TRP 0.023 0.001 TRP B 890 HIS 0.010 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (28554) covalent geometry : angle 0.55845 / 0.28 (39931) hydrogen bonds : bond 0.04228 / 4.23 ( 1018) hydrogen bonds : angle 4.58766 / 5.51 ( 2895) metal coordination : bond 0.00456 / 0.24 ( 4) metal coordination : angle 1.79189 / 2.51 ( 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 360 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 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: B 133 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: B 304 MET cc_start: 0.7890 (tmm) cc_final: 0.7657 (tmm) REVERT: B 628 MET cc_start: 0.9134 (mmm) cc_final: 0.8350 (mmm) REVERT: B 846 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8985 (pp) REVERT: C 45 LEU cc_start: 0.9103 (mt) cc_final: 0.8853 (pp) REVERT: D 109 TYR cc_start: 0.9169 (t80) cc_final: 0.8882 (t80) REVERT: D 134 ASP cc_start: 0.8652 (t0) cc_final: 0.8233 (p0) REVERT: D 160 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 71 LYS cc_start: 0.9616 (tppp) cc_final: 0.9123 (tppp) REVERT: E 144 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8388 (tmm160) REVERT: E 150 GLU cc_start: 0.7365 (mp0) cc_final: 0.6791 (tp30) REVERT: G 39 VAL cc_start: 0.9564 (t) cc_final: 0.9240 (p) REVERT: H 68 GLU cc_start: 0.8960 (pm20) cc_final: 0.8451 (pm20) REVERT: H 69 LYS cc_start: 0.9080 (mppt) cc_final: 0.8843 (mmtm) REVERT: I 41 PHE cc_start: 0.8826 (m-10) cc_final: 0.8557 (m-80) REVERT: I 63 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9001 (tp) REVERT: I 177 MET cc_start: 0.8902 (tpp) cc_final: 0.8077 (tpp) REVERT: J 72 LYS cc_start: 0.8961 (tptm) cc_final: 0.8598 (tptm) REVERT: J 177 MET cc_start: 0.8868 (tmm) cc_final: 0.8637 (mtm) REVERT: K 109 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8331 (mmm-85) REVERT: K 114 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7835 (m-70) REVERT: L 226 GLU cc_start: 0.8251 (tp30) cc_final: 0.7989 (tt0) REVERT: M 14 ARG cc_start: 0.8603 (mmp80) cc_final: 0.8380 (mmp80) REVERT: M 16 ARG cc_start: 0.9270 (mmp80) cc_final: 0.9043 (mmp80) REVERT: M 53 LEU cc_start: 0.9157 (tt) cc_final: 0.8890 (mt) REVERT: M 76 MET cc_start: 0.9027 (mtm) cc_final: 0.8383 (mpp) REVERT: M 91 CYS cc_start: 0.9451 (m) cc_final: 0.9011 (t) REVERT: M 105 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9204 (pp30) REVERT: M 111 PHE cc_start: 0.9114 (m-80) cc_final: 0.8675 (m-80) REVERT: M 153 CYS cc_start: 0.9523 (m) cc_final: 0.9111 (m) REVERT: M 169 PHE cc_start: 0.9086 (m-80) cc_final: 0.8752 (m-80) REVERT: M 173 ASN cc_start: 0.9226 (m-40) cc_final: 0.8953 (m-40) REVERT: M 193 ARG cc_start: 0.8563 (tpp80) cc_final: 0.7961 (mmm-85) REVERT: M 225 ASP cc_start: 0.9132 (t0) cc_final: 0.8805 (t0) outliers start: 79 outliers final: 49 residues processed: 334 average time/residue: 0.1849 time to fit residues: 99.3900 Evaluate side-chains 314 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 846 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 134 VAL Chi-restraints excluded: chain C residue 138 VAL 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 81 LEU 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 137 ILE Chi-restraints excluded: chain G residue 102 THR 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 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 39 PHE 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 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 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: 8.9990 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 18 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 602 GLN ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 GLN L 100 HIS L 315 GLN L 345 ASN M 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051250 restraints weight = 153313.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052697 restraints weight = 78308.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053640 restraints weight = 51829.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.054266 restraints weight = 40211.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054629 restraints weight = 34247.785| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28558 Z= 0.127 Angle : 0.561 12.914 39937 Z= 0.283 Chirality : 0.037 0.203 4781 Planarity : 0.004 0.051 4056 Dihedral : 19.041 175.391 7260 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.12 % Allowed : 25.63 % Favored : 70.25 % 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: 0.32 (0.17), residues: 2699 helix: 1.60 (0.16), residues: 1074 sheet: 0.55 (0.23), residues: 529 loop : -1.42 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 147 TYR 0.020 0.001 TYR K 24 PHE 0.020 0.001 PHE M 157 TRP 0.011 0.001 TRP L 324 HIS 0.006 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (28554) covalent geometry : angle 0.55952 / 0.28 (39931) hydrogen bonds : bond 0.03945 / 3.96 ( 1018) hydrogen bonds : angle 4.48361 / 5.35 ( 2895) metal coordination : bond 0.00476 / 0.27 ( 4) metal coordination : angle 2.93548 / 4.45 ( 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 377 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 278 time to evaluate : 1.048 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 126 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8748 (t) REVERT: B 130 LEU cc_start: 0.9314 (mm) cc_final: 0.9098 (mt) REVERT: B 133 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: B 144 MET cc_start: 0.9253 (mmm) cc_final: 0.8642 (mmm) REVERT: B 304 MET cc_start: 0.7901 (tmm) cc_final: 0.7672 (tmm) REVERT: B 628 MET cc_start: 0.9175 (mmm) cc_final: 0.8337 (mmm) REVERT: B 846 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9001 (pp) REVERT: C 45 LEU cc_start: 0.9078 (mt) cc_final: 0.8842 (pp) REVERT: D 28 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9214 (mm-30) REVERT: D 160 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8466 (tm-30) REVERT: E 71 LYS cc_start: 0.9601 (tppp) cc_final: 0.9088 (tppp) REVERT: E 92 HIS cc_start: 0.7742 (t-90) cc_final: 0.7458 (t-170) REVERT: E 144 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8199 (tmm160) REVERT: F 67 PHE cc_start: 0.9050 (m-10) cc_final: 0.8729 (m-10) REVERT: G 39 VAL cc_start: 0.9606 (t) cc_final: 0.9236 (p) REVERT: H 68 GLU cc_start: 0.8964 (pm20) cc_final: 0.8436 (pm20) REVERT: H 69 LYS cc_start: 0.9099 (mppt) cc_final: 0.8764 (mmtt) REVERT: I 41 PHE cc_start: 0.8859 (m-10) cc_final: 0.8615 (m-80) REVERT: I 63 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9043 (tp) REVERT: J 72 LYS cc_start: 0.8987 (tptm) cc_final: 0.8648 (tptm) REVERT: J 177 MET cc_start: 0.8927 (tmm) cc_final: 0.8633 (mtt) REVERT: K 114 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7750 (m-70) REVERT: L 226 GLU cc_start: 0.8320 (tp30) cc_final: 0.7871 (tt0) REVERT: M 53 LEU cc_start: 0.9194 (tt) cc_final: 0.8967 (mp) REVERT: M 76 MET cc_start: 0.9160 (mtm) cc_final: 0.8501 (mpp) REVERT: M 91 CYS cc_start: 0.9506 (m) cc_final: 0.9020 (t) REVERT: M 111 PHE cc_start: 0.9103 (m-80) cc_final: 0.8652 (m-80) REVERT: M 153 CYS cc_start: 0.9514 (m) cc_final: 0.9182 (m) REVERT: M 169 PHE cc_start: 0.9063 (m-80) cc_final: 0.8818 (m-80) REVERT: M 173 ASN cc_start: 0.9228 (m-40) cc_final: 0.9001 (m-40) REVERT: M 193 ARG cc_start: 0.8574 (tpp80) cc_final: 0.7923 (mmm-85) REVERT: M 225 ASP cc_start: 0.9154 (t0) cc_final: 0.8813 (t0) outliers start: 99 outliers final: 58 residues processed: 351 average time/residue: 0.1767 time to fit residues: 100.6070 Evaluate side-chains 322 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 557 ASP Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 846 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 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 161 THR Chi-restraints excluded: chain E residue 13 LEU 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 81 LEU 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 102 THR Chi-restraints excluded: chain H residue 12 VAL 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 88 ASN 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 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 26 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS 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 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 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: 8.9990 chunk 188 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS ** 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 ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN M 82 HIS M 206 GLN M 232 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.066494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047205 restraints weight = 156647.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048643 restraints weight = 82728.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049566 restraints weight = 56192.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050121 restraints weight = 44429.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050479 restraints weight = 38584.801| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 28558 Z= 0.234 Angle : 0.661 14.230 39937 Z= 0.338 Chirality : 0.040 0.237 4781 Planarity : 0.005 0.078 4056 Dihedral : 19.151 174.047 7260 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.87 % Allowed : 25.93 % Favored : 69.21 % 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: 0.14 (0.17), residues: 2699 helix: 1.46 (0.16), residues: 1087 sheet: 0.37 (0.23), residues: 532 loop : -1.50 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 147 TYR 0.043 0.002 TYR M 234 PHE 0.042 0.002 PHE M 235 TRP 0.012 0.002 TRP B 413 HIS 0.007 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (28554) covalent geometry : angle 0.65968 / 0.34 (39931) hydrogen bonds : bond 0.04722 / 4.71 ( 1018) hydrogen bonds : angle 4.81566 / 5.81 ( 2895) metal coordination : bond 0.00982 / 0.57 ( 4) metal coordination : angle 4.00507 / 5.97 ( 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 382 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 265 time to evaluate : 0.830 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 133 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: B 622 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9507 (pp) REVERT: B 628 MET cc_start: 0.9221 (mmm) cc_final: 0.8467 (mmm) REVERT: D 160 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8529 (tm-30) REVERT: E 11 CYS cc_start: 0.8768 (m) cc_final: 0.8492 (t) REVERT: E 71 LYS cc_start: 0.9603 (tppp) cc_final: 0.9087 (tppp) REVERT: E 92 HIS cc_start: 0.7799 (t-90) cc_final: 0.7516 (t-90) REVERT: E 94 TYR cc_start: 0.8840 (m-80) cc_final: 0.8277 (m-80) REVERT: F 39 ARG cc_start: 0.8830 (ptm-80) cc_final: 0.7723 (tmm160) REVERT: F 80 CYS cc_start: 0.9533 (m) cc_final: 0.9209 (t) REVERT: G 39 VAL cc_start: 0.9604 (t) cc_final: 0.9235 (p) REVERT: H 69 LYS cc_start: 0.9151 (mppt) cc_final: 0.8919 (mmtm) REVERT: H 102 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: I 63 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9088 (tp) REVERT: J 72 LYS cc_start: 0.8967 (tptm) cc_final: 0.8633 (tptm) REVERT: K 8 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8011 (tt0) REVERT: K 109 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: K 114 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7865 (m-70) REVERT: L 226 GLU cc_start: 0.8518 (tp30) cc_final: 0.7891 (tt0) REVERT: M 53 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9035 (mp) REVERT: M 78 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7497 (mtp180) REVERT: M 91 CYS cc_start: 0.9571 (m) cc_final: 0.9124 (t) REVERT: M 111 PHE cc_start: 0.9194 (m-80) cc_final: 0.8765 (m-80) REVERT: M 153 CYS cc_start: 0.9503 (m) cc_final: 0.9190 (m) REVERT: M 169 PHE cc_start: 0.9129 (m-80) cc_final: 0.8888 (m-80) REVERT: M 173 ASN cc_start: 0.9359 (m-40) cc_final: 0.9093 (m-40) REVERT: M 193 ARG cc_start: 0.8604 (tpp80) cc_final: 0.7976 (mmm-85) REVERT: M 225 ASP cc_start: 0.9208 (t0) cc_final: 0.8907 (t0) outliers start: 117 outliers final: 79 residues processed: 353 average time/residue: 0.1809 time to fit residues: 101.7598 Evaluate side-chains 332 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 247 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 414 ILE 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 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 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 962 THR 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 73 PHE Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 114 LEU 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 103 ARG Chi-restraints excluded: chain G residue 115 THR 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 98 LYS Chi-restraints excluded: chain H residue 102 PHE 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 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 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 80 TYR Chi-restraints excluded: chain K residue 98 SER 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 161 LYS Chi-restraints excluded: chain L residue 192 THR 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 100 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 219 ASP 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: 3.9990 chunk 139 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 205 optimal weight: 0.0980 chunk 118 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 15 ASN E 127 GLN F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 HIS J 175 ASN L 315 GLN M 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049192 restraints weight = 152860.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050676 restraints weight = 77911.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051621 restraints weight = 51484.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052218 restraints weight = 39930.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052556 restraints weight = 34200.234| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28558 Z= 0.107 Angle : 0.604 13.353 39937 Z= 0.295 Chirality : 0.038 0.209 4781 Planarity : 0.004 0.052 4056 Dihedral : 19.141 174.624 7260 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.00 % Allowed : 28.38 % Favored : 68.62 % 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: 0.30 (0.17), residues: 2699 helix: 1.64 (0.16), residues: 1075 sheet: 0.48 (0.23), residues: 517 loop : -1.44 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 147 TYR 0.021 0.001 TYR K 24 PHE 0.022 0.001 PHE M 157 TRP 0.019 0.001 TRP L 324 HIS 0.005 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (28554) covalent geometry : angle 0.60260 / 0.29 (39931) hydrogen bonds : bond 0.03827 / 3.85 ( 1018) hydrogen bonds : angle 4.47650 / 5.37 ( 2895) metal coordination : bond 0.00447 / 0.25 ( 4) metal coordination : angle 3.02457 / 4.17 ( 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 346 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 274 time to evaluate : 0.776 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 133 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: B 628 MET cc_start: 0.9124 (mmm) cc_final: 0.8192 (mmm) REVERT: B 846 LEU cc_start: 0.9337 (tt) cc_final: 0.8999 (pp) REVERT: D 28 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9197 (mm-30) REVERT: D 41 ARG cc_start: 0.9055 (mmp80) cc_final: 0.8815 (mmp80) REVERT: D 160 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8559 (tm-30) REVERT: E 11 CYS cc_start: 0.8712 (m) cc_final: 0.8472 (t) REVERT: E 34 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8522 (mtm-85) REVERT: E 39 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8787 (ttp80) REVERT: E 71 LYS cc_start: 0.9604 (tppp) cc_final: 0.9037 (tppp) REVERT: E 92 HIS cc_start: 0.7788 (t-90) cc_final: 0.7517 (t-90) REVERT: E 94 TYR cc_start: 0.8839 (m-80) cc_final: 0.8283 (m-80) REVERT: E 144 ARG cc_start: 0.8798 (ptm-80) cc_final: 0.8356 (ttp80) REVERT: G 39 VAL cc_start: 0.9553 (t) cc_final: 0.9184 (p) REVERT: H 68 GLU cc_start: 0.8989 (pm20) cc_final: 0.8424 (pm20) REVERT: H 69 LYS cc_start: 0.9225 (mppt) cc_final: 0.8857 (mmtm) REVERT: I 58 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8581 (t80) REVERT: I 177 MET cc_start: 0.9198 (ttt) cc_final: 0.8326 (tpp) REVERT: J 165 MET cc_start: 0.8853 (mmm) cc_final: 0.8619 (mmm) REVERT: J 175 ASN cc_start: 0.8692 (m110) cc_final: 0.8317 (m110) REVERT: J 177 MET cc_start: 0.9000 (tmm) cc_final: 0.8697 (mtt) REVERT: K 8 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8022 (tt0) REVERT: K 114 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7766 (m-70) REVERT: L 226 GLU cc_start: 0.8497 (tp30) cc_final: 0.7830 (tt0) REVERT: M 78 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7617 (mtp180) REVERT: M 91 CYS cc_start: 0.9542 (m) cc_final: 0.9076 (t) REVERT: M 111 PHE cc_start: 0.9198 (m-80) cc_final: 0.8730 (m-80) REVERT: M 169 PHE cc_start: 0.9070 (m-80) cc_final: 0.8799 (m-80) REVERT: M 173 ASN cc_start: 0.9268 (m-40) cc_final: 0.9048 (m-40) REVERT: M 176 MET cc_start: 0.9655 (mtp) cc_final: 0.9426 (mtp) REVERT: M 193 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8069 (mmm-85) REVERT: M 225 ASP cc_start: 0.9235 (t0) cc_final: 0.8915 (t0) outliers start: 72 outliers final: 46 residues processed: 331 average time/residue: 0.1744 time to fit residues: 92.9233 Evaluate side-chains 309 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN 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 557 ASP 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 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 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 115 ILE 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 124 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 221 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 119 HIS 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 80 TYR Chi-restraints excluded: chain K residue 114 HIS Chi-restraints excluded: chain L residue 74 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 100 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 64 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 217 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 206 optimal weight: 0.0970 chunk 6 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 overall best weight: 1.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 565 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN M 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.068137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048867 restraints weight = 156536.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050366 restraints weight = 81835.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051300 restraints weight = 55193.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051882 restraints weight = 43474.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052190 restraints weight = 37622.382| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28558 Z= 0.115 Angle : 0.591 13.512 39937 Z= 0.290 Chirality : 0.038 0.343 4781 Planarity : 0.004 0.054 4056 Dihedral : 19.103 175.053 7260 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.95 % Allowed : 29.05 % Favored : 68.00 % 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: 0.31 (0.17), residues: 2699 helix: 1.62 (0.16), residues: 1075 sheet: 0.51 (0.23), residues: 522 loop : -1.41 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG F 147 TYR 0.022 0.001 TYR K 24 PHE 0.023 0.001 PHE M 157 TRP 0.017 0.001 TRP L 324 HIS 0.008 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (28554) covalent geometry : angle 0.58951 / 0.29 (39931) hydrogen bonds : bond 0.03761 / 3.78 ( 1018) hydrogen bonds : angle 4.49985 / 5.38 ( 2895) metal coordination : bond 0.00440 / 0.25 ( 4) metal coordination : angle 2.87498 / 4.18 ( 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 339 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 1.023 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 133 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: B 144 MET cc_start: 0.9176 (mmm) cc_final: 0.8623 (mmm) REVERT: B 628 MET cc_start: 0.9126 (mmm) cc_final: 0.8257 (mmm) REVERT: B 846 LEU cc_start: 0.9303 (tt) cc_final: 0.8985 (pp) REVERT: D 83 GLU cc_start: 0.8849 (pm20) cc_final: 0.8621 (pm20) REVERT: D 160 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 34 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8513 (mtm-85) REVERT: E 71 LYS cc_start: 0.9590 (tppp) cc_final: 0.9053 (tppp) REVERT: E 92 HIS cc_start: 0.7870 (t-90) cc_final: 0.7577 (t-90) REVERT: E 94 TYR cc_start: 0.8764 (m-80) cc_final: 0.8151 (m-80) REVERT: E 99 ASN cc_start: 0.9433 (OUTLIER) cc_final: 0.9116 (t0) REVERT: E 144 ARG cc_start: 0.8743 (ptm-80) cc_final: 0.8247 (ttp80) REVERT: E 150 GLU cc_start: 0.7812 (mp0) cc_final: 0.6746 (tp30) REVERT: F 67 PHE cc_start: 0.9001 (m-10) cc_final: 0.8713 (m-10) REVERT: G 39 VAL cc_start: 0.9580 (t) cc_final: 0.9245 (p) REVERT: G 87 GLN cc_start: 0.9631 (tp40) cc_final: 0.9235 (mp10) REVERT: I 58 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8523 (t80) REVERT: I 177 MET cc_start: 0.9208 (ttt) cc_final: 0.8270 (tpp) REVERT: J 177 MET cc_start: 0.8917 (tmm) cc_final: 0.8665 (mtm) REVERT: K 8 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8001 (tt0) REVERT: K 109 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: K 114 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7793 (m-70) REVERT: L 217 LEU cc_start: 0.9321 (tt) cc_final: 0.9118 (mm) REVERT: L 226 GLU cc_start: 0.8372 (tp30) cc_final: 0.7867 (tt0) REVERT: M 78 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7602 (mtp180) REVERT: M 91 CYS cc_start: 0.9529 (m) cc_final: 0.9067 (t) REVERT: M 111 PHE cc_start: 0.9172 (m-80) cc_final: 0.8727 (m-80) REVERT: M 151 ASP cc_start: 0.9325 (t0) cc_final: 0.9095 (m-30) REVERT: M 169 PHE cc_start: 0.9072 (m-80) cc_final: 0.8799 (m-80) REVERT: M 173 ASN cc_start: 0.9300 (m-40) cc_final: 0.9065 (m-40) REVERT: M 176 MET cc_start: 0.9677 (mtp) cc_final: 0.9425 (mtp) REVERT: M 193 ARG cc_start: 0.8579 (tpp80) cc_final: 0.7993 (mmm-85) REVERT: M 225 ASP cc_start: 0.9305 (t0) cc_final: 0.9015 (t0) REVERT: M 234 TYR cc_start: 0.9046 (t80) cc_final: 0.8842 (t80) outliers start: 71 outliers final: 55 residues processed: 322 average time/residue: 0.1816 time to fit residues: 94.4137 Evaluate side-chains 315 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN 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 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 632 ILE 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 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 E residue 31 SER Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 ILE 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 124 ILE Chi-restraints excluded: chain H residue 18 GLU 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 102 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 196 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 268 optimal weight: 0.0060 chunk 217 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 282 optimal weight: 0.0050 chunk 283 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049571 restraints weight = 150395.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051079 restraints weight = 76353.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052057 restraints weight = 50467.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052682 restraints weight = 39139.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053011 restraints weight = 33360.638| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28558 Z= 0.104 Angle : 0.611 14.042 39937 Z= 0.297 Chirality : 0.038 0.235 4781 Planarity : 0.004 0.051 4056 Dihedral : 19.059 175.302 7260 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.58 % Allowed : 29.17 % Favored : 68.25 % 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: 0.32 (0.17), residues: 2699 helix: 1.63 (0.16), residues: 1068 sheet: 0.53 (0.23), residues: 517 loop : -1.39 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 32 TYR 0.025 0.001 TYR K 24 PHE 0.021 0.001 PHE M 157 TRP 0.022 0.001 TRP L 324 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (28554) covalent geometry : angle 0.61036 / 0.30 (39931) hydrogen bonds : bond 0.03521 / 3.57 ( 1018) hydrogen bonds : angle 4.39193 / 5.22 ( 2895) metal coordination : bond 0.00540 / 0.29 ( 4) metal coordination : angle 2.65755 / 3.74 ( 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 339 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.161 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: 0.8404 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 304 MET cc_start: 0.7439 (tmm) cc_final: 0.7051 (tmm) REVERT: B 628 MET cc_start: 0.9111 (mmm) cc_final: 0.8204 (mmm) REVERT: B 846 LEU cc_start: 0.9329 (tt) cc_final: 0.9012 (pp) REVERT: D 41 ARG cc_start: 0.8996 (mmp80) cc_final: 0.8714 (mmp80) REVERT: D 83 GLU cc_start: 0.8858 (pm20) cc_final: 0.8565 (pm20) REVERT: D 160 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8570 (tm-30) REVERT: E 34 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8501 (mtm-85) REVERT: E 39 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8809 (ttp80) REVERT: E 71 LYS cc_start: 0.9582 (tppp) cc_final: 0.9018 (tppp) REVERT: E 92 HIS cc_start: 0.7867 (t-90) cc_final: 0.7553 (t-90) REVERT: E 94 TYR cc_start: 0.8822 (m-80) cc_final: 0.8222 (m-80) REVERT: E 144 ARG cc_start: 0.8769 (ptm-80) cc_final: 0.8285 (ttp80) REVERT: E 150 GLU cc_start: 0.7768 (mp0) cc_final: 0.6796 (tp30) REVERT: F 57 MET cc_start: 0.9391 (tpp) cc_final: 0.9150 (tpt) REVERT: F 67 PHE cc_start: 0.9002 (m-10) cc_final: 0.8699 (m-10) REVERT: G 39 VAL cc_start: 0.9437 (t) cc_final: 0.9139 (p) REVERT: G 87 GLN cc_start: 0.9599 (tp40) cc_final: 0.9184 (mp10) REVERT: H 68 GLU cc_start: 0.9030 (pm20) cc_final: 0.8368 (pm20) REVERT: I 57 LEU cc_start: 0.9097 (tp) cc_final: 0.8308 (mt) REVERT: I 58 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8496 (t80) REVERT: I 177 MET cc_start: 0.9297 (ttt) cc_final: 0.8259 (tpp) REVERT: J 177 MET cc_start: 0.8922 (tmm) cc_final: 0.8616 (mtt) REVERT: K 8 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8008 (tt0) REVERT: K 109 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8327 (mmm-85) REVERT: K 114 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.7723 (m-70) REVERT: L 226 GLU cc_start: 0.8433 (tp30) cc_final: 0.7836 (tt0) REVERT: M 78 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7542 (mtp180) REVERT: M 91 CYS cc_start: 0.9498 (m) cc_final: 0.9067 (t) REVERT: M 94 ARG cc_start: 0.9074 (mmt90) cc_final: 0.8325 (mmm-85) REVERT: M 111 PHE cc_start: 0.9150 (m-80) cc_final: 0.8736 (m-80) REVERT: M 151 ASP cc_start: 0.9359 (t0) cc_final: 0.9114 (m-30) REVERT: M 169 PHE cc_start: 0.9036 (m-80) cc_final: 0.8757 (m-80) REVERT: M 173 ASN cc_start: 0.9255 (m-40) cc_final: 0.9031 (m-40) REVERT: M 176 MET cc_start: 0.9658 (mtp) cc_final: 0.9414 (mtp) REVERT: M 193 ARG cc_start: 0.8580 (tpp80) cc_final: 0.7956 (mmm-85) REVERT: M 225 ASP cc_start: 0.9352 (t0) cc_final: 0.8842 (t0) outliers start: 62 outliers final: 49 residues processed: 329 average time/residue: 0.1811 time to fit residues: 95.5456 Evaluate side-chains 317 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 308 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 557 ASP Chi-restraints excluded: chain B residue 632 ILE 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 E residue 34 ARG 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 107 ILE 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 66 CYS Chi-restraints excluded: chain G residue 124 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 221 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 98 SER 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 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: 0.7980 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 206 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 172 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.068249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049208 restraints weight = 151337.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050698 restraints weight = 77118.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051660 restraints weight = 51193.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052245 restraints weight = 39680.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052629 restraints weight = 33979.295| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28558 Z= 0.108 Angle : 0.606 14.602 39937 Z= 0.295 Chirality : 0.038 0.221 4781 Planarity : 0.004 0.049 4056 Dihedral : 19.029 175.383 7260 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.33 % Allowed : 29.75 % Favored : 67.92 % 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: 0.35 (0.17), residues: 2699 helix: 1.65 (0.16), residues: 1069 sheet: 0.55 (0.23), residues: 522 loop : -1.38 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 147 TYR 0.026 0.001 TYR K 24 PHE 0.023 0.001 PHE M 108 TRP 0.015 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (28554) covalent geometry : angle 0.60502 / 0.30 (39931) hydrogen bonds : bond 0.03515 / 3.55 ( 1018) hydrogen bonds : angle 4.41694 / 5.25 ( 2895) metal coordination : bond 0.00468 / 0.26 ( 4) metal coordination : angle 2.91095 / 4.21 ( 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 327 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 0.934 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: 0.8372 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 144 MET cc_start: 0.9171 (mmm) cc_final: 0.8440 (mmm) REVERT: B 304 MET cc_start: 0.7508 (tmm) cc_final: 0.7099 (tmm) REVERT: B 628 MET cc_start: 0.9149 (mmm) cc_final: 0.8254 (mmm) REVERT: B 846 LEU cc_start: 0.9329 (tt) cc_final: 0.9004 (pp) REVERT: D 83 GLU cc_start: 0.8899 (pm20) cc_final: 0.8602 (pm20) REVERT: D 160 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8603 (tm-30) REVERT: E 71 LYS cc_start: 0.9583 (tppp) cc_final: 0.8998 (tppp) REVERT: E 92 HIS cc_start: 0.7882 (t-90) cc_final: 0.7560 (t-90) REVERT: E 94 TYR cc_start: 0.8810 (m-80) cc_final: 0.8146 (m-80) REVERT: E 144 ARG cc_start: 0.8781 (ptm-80) cc_final: 0.8302 (ttp80) REVERT: E 150 GLU cc_start: 0.7772 (mp0) cc_final: 0.6806 (tp30) REVERT: F 67 PHE cc_start: 0.8993 (m-10) cc_final: 0.8690 (m-10) REVERT: G 39 VAL cc_start: 0.9462 (t) cc_final: 0.9139 (p) REVERT: G 87 GLN cc_start: 0.9633 (tp40) cc_final: 0.9215 (mp10) REVERT: I 57 LEU cc_start: 0.9101 (tp) cc_final: 0.8313 (mt) REVERT: I 58 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8509 (t80) REVERT: I 177 MET cc_start: 0.9297 (ttt) cc_final: 0.8298 (tpp) REVERT: J 177 MET cc_start: 0.8939 (tmm) cc_final: 0.8606 (mtt) REVERT: K 8 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8022 (tt0) REVERT: K 109 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: K 114 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7741 (m-70) REVERT: L 226 GLU cc_start: 0.8436 (tp30) cc_final: 0.7930 (tt0) REVERT: M 78 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7592 (mtp180) REVERT: M 91 CYS cc_start: 0.9496 (m) cc_final: 0.9078 (t) REVERT: M 94 ARG cc_start: 0.9057 (mmt90) cc_final: 0.8318 (mmm-85) REVERT: M 111 PHE cc_start: 0.9176 (m-80) cc_final: 0.8748 (m-80) REVERT: M 151 ASP cc_start: 0.9373 (t0) cc_final: 0.9138 (m-30) REVERT: M 169 PHE cc_start: 0.9052 (m-80) cc_final: 0.8792 (m-80) REVERT: M 176 MET cc_start: 0.9664 (mtp) cc_final: 0.9416 (mtp) REVERT: M 193 ARG cc_start: 0.8586 (tpp80) cc_final: 0.7988 (mmm-85) REVERT: M 225 ASP cc_start: 0.9261 (t0) cc_final: 0.8911 (t0) outliers start: 56 outliers final: 49 residues processed: 318 average time/residue: 0.1633 time to fit residues: 84.2416 Evaluate side-chains 310 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 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 308 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 464 HIS 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 557 ASP 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 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 E residue 31 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 12 VAL 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 221 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 98 SER 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 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 282 optimal weight: 0.2980 chunk 139 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047557 restraints weight = 153250.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048997 restraints weight = 79192.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049932 restraints weight = 53210.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050518 restraints weight = 41588.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050844 restraints weight = 35808.383| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28558 Z= 0.149 Angle : 0.625 15.187 39937 Z= 0.310 Chirality : 0.039 0.218 4781 Planarity : 0.004 0.051 4056 Dihedral : 19.057 174.437 7260 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.25 % Allowed : 30.05 % 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: 0.32 (0.17), residues: 2699 helix: 1.70 (0.16), residues: 1059 sheet: 0.46 (0.23), residues: 522 loop : -1.42 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 147 TYR 0.027 0.001 TYR K 24 PHE 0.020 0.001 PHE M 157 TRP 0.010 0.001 TRP L 183 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (28554) covalent geometry : angle 0.62330 / 0.31 (39931) hydrogen bonds : bond 0.03791 / 3.79 ( 1018) hydrogen bonds : angle 4.54997 / 5.41 ( 2895) metal coordination : bond 0.00547 / 0.32 ( 4) metal coordination : angle 3.58681 / 5.42 ( 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 312 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 0.934 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: B 130 LEU cc_start: 0.9226 (mp) cc_final: 0.9000 (pt) REVERT: B 144 MET cc_start: 0.9184 (mmm) cc_final: 0.8495 (mmm) REVERT: B 304 MET cc_start: 0.7624 (tmm) cc_final: 0.7184 (tmm) REVERT: B 628 MET cc_start: 0.9187 (mmm) cc_final: 0.8312 (mmm) REVERT: B 646 GLU cc_start: 0.9381 (mp0) cc_final: 0.8951 (mp0) REVERT: B 846 LEU cc_start: 0.9347 (tt) cc_final: 0.9010 (pp) REVERT: D 83 GLU cc_start: 0.8940 (pm20) cc_final: 0.8647 (pm20) REVERT: D 160 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8639 (tm-30) REVERT: E 39 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8810 (ttp80) REVERT: E 71 LYS cc_start: 0.9598 (tppp) cc_final: 0.9015 (tppp) REVERT: E 92 HIS cc_start: 0.7948 (t-90) cc_final: 0.7610 (t-90) REVERT: E 94 TYR cc_start: 0.8860 (m-80) cc_final: 0.8229 (m-80) REVERT: E 144 ARG cc_start: 0.8813 (ptm-80) cc_final: 0.8352 (ttp80) REVERT: E 150 GLU cc_start: 0.7787 (mp0) cc_final: 0.6836 (tp30) REVERT: F 57 MET cc_start: 0.9424 (tpp) cc_final: 0.9147 (tpt) REVERT: F 67 PHE cc_start: 0.9004 (m-10) cc_final: 0.8719 (m-10) REVERT: G 39 VAL cc_start: 0.9566 (t) cc_final: 0.9285 (p) REVERT: G 87 GLN cc_start: 0.9652 (tp40) cc_final: 0.9184 (mp10) REVERT: I 58 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8570 (t80) REVERT: I 177 MET cc_start: 0.9339 (ttt) cc_final: 0.8364 (tpp) REVERT: J 177 MET cc_start: 0.8952 (tmm) cc_final: 0.8681 (mtm) REVERT: K 8 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7990 (tt0) REVERT: K 109 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8408 (mmm-85) REVERT: K 114 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7844 (m-70) REVERT: M 14 ARG cc_start: 0.8643 (mmp80) cc_final: 0.8283 (mmp80) REVERT: M 78 ARG cc_start: 0.7976 (ptm160) cc_final: 0.7685 (mtp180) REVERT: M 91 CYS cc_start: 0.9522 (m) cc_final: 0.9099 (t) REVERT: M 94 ARG cc_start: 0.9113 (mmt90) cc_final: 0.8389 (mmm-85) REVERT: M 111 PHE cc_start: 0.9188 (m-80) cc_final: 0.8757 (m-80) REVERT: M 173 ASN cc_start: 0.9301 (m-40) cc_final: 0.9045 (m-40) REVERT: M 176 MET cc_start: 0.9680 (mtp) cc_final: 0.9444 (mtp) REVERT: M 193 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8067 (mmm-85) REVERT: M 225 ASP cc_start: 0.9184 (t0) cc_final: 0.8812 (t0) REVERT: M 234 TYR cc_start: 0.9280 (t80) cc_final: 0.8770 (t80) outliers start: 54 outliers final: 49 residues processed: 303 average time/residue: 0.1711 time to fit residues: 83.7330 Evaluate side-chains 301 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 HIS 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 557 ASP 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 56 VAL Chi-restraints excluded: chain D residue 135 LEU 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 122 LEU Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 12 VAL 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 119 HIS 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 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 98 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 144 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 273 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 83 optimal weight: 0.0970 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.064647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045596 restraints weight = 159345.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047011 restraints weight = 83655.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047913 restraints weight = 57038.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048472 restraints weight = 45164.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048770 restraints weight = 39224.078| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28558 Z= 0.201 Angle : 0.672 14.192 39937 Z= 0.338 Chirality : 0.040 0.214 4781 Planarity : 0.005 0.046 4056 Dihedral : 19.252 173.772 7260 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.62 % Allowed : 29.80 % Favored : 67.58 % 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: 0.11 (0.17), residues: 2699 helix: 1.51 (0.16), residues: 1066 sheet: 0.22 (0.23), residues: 519 loop : -1.46 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 64 TYR 0.025 0.002 TYR K 24 PHE 0.020 0.002 PHE C 189 TRP 0.017 0.002 TRP L 183 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (28554) covalent geometry : angle 0.66987 / 0.34 (39931) hydrogen bonds : bond 0.04456 / 4.47 ( 1018) hydrogen bonds : angle 4.78649 / 5.72 ( 2895) metal coordination : bond 0.00820 / 0.50 ( 4) metal coordination : angle 4.49514 / 6.83 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.88 seconds wall clock time: 87 minutes 54.37 seconds (5274.37 seconds total)