Starting phenix.real_space_refine on Tue May 5 07:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uha_64160/05_2026/9uha_64160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uha_64160/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uha_64160/05_2026/9uha_64160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uha_64160/05_2026/9uha_64160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uha_64160/05_2026/9uha_64160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uha_64160/05_2026/9uha_64160.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 6.18, per 1000 atoms: 0.23 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: 2.60 Conformation dependent library (CDL) restraints added in 984.1 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: 3.13 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: 5.21 Time building geometry restraints manager: 3.42 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=" N PRO B 998 " pdb=" CD PRO B 998 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.62e+00 bond pdb=" N PRO B 301 " pdb=" CD PRO B 301 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.97e+00 bond pdb=" N GLY B 643 " pdb=" CA GLY B 643 " ideal model delta sigma weight residual 1.445 1.458 -0.013 8.30e-03 1.45e+04 2.45e+00 bond pdb=" CB GLU H 68 " pdb=" CG GLU H 68 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" CB GLU D 171 " pdb=" CG GLU D 171 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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= 0.126 Angle : 0.774 36.164 39937 Z= 0.400 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 covalent geometry : bond 0.00253 (28554) covalent geometry : angle 0.77314 (39931) hydrogen bonds : bond 0.15746 ( 1018) hydrogen bonds : angle 5.72178 ( 2895) metal coordination : bond 0.00402 ( 4) metal coordination : angle 2.71172 ( 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 : 0.835 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: 0.1689 time to fit residues: 96.6450 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 : 0.889 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN M 82 HIS M 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.072500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053189 restraints weight = 160780.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.054747 restraints weight = 82506.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055760 restraints weight = 55016.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056394 restraints weight = 42853.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056709 restraints weight = 36757.951| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28558 Z= 0.118 Angle : 0.583 12.534 39937 Z= 0.285 Chirality : 0.037 0.178 4781 Planarity : 0.004 0.050 4056 Dihedral : 19.069 176.420 7260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.91 % Allowed : 25.47 % Favored : 71.62 % 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: 0.15 (0.17), residues: 2699 helix: 1.35 (0.16), residues: 1068 sheet: 0.65 (0.23), residues: 546 loop : -1.50 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 147 TYR 0.014 0.001 TYR K 45 PHE 0.020 0.001 PHE M 235 TRP 0.020 0.001 TRP C 104 HIS 0.005 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00253 (28554) covalent geometry : angle 0.58250 (39931) hydrogen bonds : bond 0.04411 ( 1018) hydrogen bonds : angle 4.68966 ( 2895) metal coordination : bond 0.00436 ( 4) metal coordination : angle 2.33580 ( 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 377 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 LEU cc_start: 0.9350 (mt) cc_final: 0.9087 (mm) REVERT: B 133 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: B 144 MET cc_start: 0.9238 (mmm) cc_final: 0.8648 (mmm) REVERT: B 846 LEU cc_start: 0.9286 (tt) cc_final: 0.8990 (pp) REVERT: C 45 LEU cc_start: 0.9137 (mt) cc_final: 0.8888 (pp) REVERT: D 28 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9166 (mm-30) REVERT: D 109 TYR cc_start: 0.9159 (t80) cc_final: 0.8881 (t80) REVERT: D 134 ASP cc_start: 0.8595 (t0) cc_final: 0.8202 (p0) REVERT: D 160 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8320 (tm-30) REVERT: E 71 LYS cc_start: 0.9624 (tppp) cc_final: 0.9207 (tppp) REVERT: E 144 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8390 (tmm160) REVERT: E 150 GLU cc_start: 0.7300 (mp0) cc_final: 0.6772 (tp30) REVERT: F 67 PHE cc_start: 0.8896 (m-80) cc_final: 0.8544 (m-10) REVERT: G 39 VAL cc_start: 0.9554 (t) cc_final: 0.9226 (p) REVERT: H 69 LYS cc_start: 0.8986 (mppt) cc_final: 0.7739 (mmtm) REVERT: I 46 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8928 (pm20) REVERT: I 63 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9065 (tp) REVERT: I 177 MET cc_start: 0.8880 (tpp) cc_final: 0.7981 (tpp) REVERT: J 72 LYS cc_start: 0.8953 (tptm) cc_final: 0.8602 (tptm) REVERT: J 178 GLN cc_start: 0.9302 (tp40) cc_final: 0.9044 (tp40) REVERT: K 8 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8076 (tt0) REVERT: K 54 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8228 (p0) REVERT: K 72 LEU cc_start: 0.7388 (pp) cc_final: 0.7103 (pp) REVERT: K 114 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7815 (m-70) REVERT: L 226 GLU cc_start: 0.8276 (tp30) cc_final: 0.7962 (tt0) REVERT: M 14 ARG cc_start: 0.8620 (mmp80) cc_final: 0.8047 (mmp80) REVERT: M 16 ARG cc_start: 0.9267 (mmp80) cc_final: 0.9036 (mmp80) REVERT: M 53 LEU cc_start: 0.9132 (tt) cc_final: 0.8865 (mt) REVERT: M 76 MET cc_start: 0.8945 (mtm) cc_final: 0.8299 (mpp) REVERT: M 91 CYS cc_start: 0.9443 (m) cc_final: 0.8960 (t) REVERT: M 111 PHE cc_start: 0.9143 (m-80) cc_final: 0.8710 (m-80) REVERT: M 153 CYS cc_start: 0.9521 (m) cc_final: 0.9187 (m) REVERT: M 169 PHE cc_start: 0.9072 (m-80) cc_final: 0.8753 (m-80) REVERT: M 173 ASN cc_start: 0.9204 (m-40) cc_final: 0.8952 (m-40) REVERT: M 225 ASP cc_start: 0.9055 (t0) cc_final: 0.8684 (t0) outliers start: 70 outliers final: 33 residues processed: 361 average time/residue: 0.1797 time to fit residues: 104.1659 Evaluate side-chains 307 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 ILE 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 G residue 102 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 46 GLN 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 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 54 ASN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 114 HIS 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 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 119 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 190 optimal weight: 0.0000 chunk 93 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN J 175 ASN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.071345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.052134 restraints weight = 160817.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053676 restraints weight = 82452.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.054658 restraints weight = 54998.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055241 restraints weight = 42957.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055647 restraints weight = 37074.951| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28558 Z= 0.117 Angle : 0.567 12.735 39937 Z= 0.276 Chirality : 0.037 0.172 4781 Planarity : 0.004 0.048 4056 Dihedral : 19.029 174.666 7260 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.20 % Allowed : 25.63 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2699 helix: 1.54 (0.16), residues: 1076 sheet: 0.63 (0.23), residues: 545 loop : -1.41 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 147 TYR 0.015 0.001 TYR K 24 PHE 0.017 0.001 PHE M 157 TRP 0.012 0.001 TRP L 324 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00252 (28554) covalent geometry : angle 0.56619 (39931) hydrogen bonds : bond 0.03870 ( 1018) hydrogen bonds : angle 4.49368 ( 2895) metal coordination : bond 0.00458 ( 4) metal coordination : angle 2.47774 ( 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 363 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: B 304 MET cc_start: 0.7479 (tmm) cc_final: 0.7086 (tmm) REVERT: B 628 MET cc_start: 0.9113 (mmm) cc_final: 0.8364 (mmm) REVERT: B 846 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8987 (pp) REVERT: C 45 LEU cc_start: 0.9083 (mt) cc_final: 0.8853 (pp) REVERT: D 109 TYR cc_start: 0.9182 (t80) cc_final: 0.8892 (t80) REVERT: D 134 ASP cc_start: 0.8665 (t0) cc_final: 0.8247 (p0) REVERT: D 160 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 171 GLU cc_start: 0.8885 (pm20) cc_final: 0.8515 (pm20) REVERT: E 71 LYS cc_start: 0.9616 (tppp) cc_final: 0.9140 (tppp) REVERT: E 144 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8378 (tmm160) REVERT: E 150 GLU cc_start: 0.7373 (mp0) cc_final: 0.6835 (tp30) REVERT: F 67 PHE cc_start: 0.8994 (m-80) cc_final: 0.8578 (m-10) REVERT: G 39 VAL cc_start: 0.9607 (t) cc_final: 0.9242 (p) REVERT: H 68 GLU cc_start: 0.8940 (pm20) cc_final: 0.8585 (pm20) REVERT: H 69 LYS cc_start: 0.8964 (mppt) cc_final: 0.8391 (mmtm) REVERT: I 63 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9003 (tp) REVERT: I 177 MET cc_start: 0.8914 (tpp) cc_final: 0.8054 (tpp) REVERT: J 72 LYS cc_start: 0.8959 (tptm) cc_final: 0.8584 (tptm) REVERT: K 8 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8022 (tt0) REVERT: K 114 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7824 (m-70) REVERT: L 226 GLU cc_start: 0.8245 (tp30) cc_final: 0.7850 (tt0) REVERT: M 14 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8423 (mmp80) REVERT: M 16 ARG cc_start: 0.9263 (mmp80) cc_final: 0.9057 (mmp80) REVERT: M 53 LEU cc_start: 0.9180 (tt) cc_final: 0.8908 (mt) REVERT: M 76 MET cc_start: 0.9014 (mtm) cc_final: 0.8368 (mpp) REVERT: M 91 CYS cc_start: 0.9445 (m) cc_final: 0.9013 (t) REVERT: M 111 PHE cc_start: 0.9128 (m-80) cc_final: 0.8690 (m-80) REVERT: M 149 LEU cc_start: 0.9334 (tp) cc_final: 0.9128 (tt) REVERT: M 153 CYS cc_start: 0.9520 (m) cc_final: 0.9112 (m) REVERT: M 169 PHE cc_start: 0.9075 (m-80) cc_final: 0.8741 (m-80) REVERT: M 173 ASN cc_start: 0.9192 (m-40) cc_final: 0.8919 (m-40) REVERT: M 193 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8385 (tpp80) REVERT: M 225 ASP cc_start: 0.9151 (t0) cc_final: 0.8830 (t0) REVERT: M 238 PHE cc_start: 0.9150 (m-80) cc_final: 0.8946 (m-80) outliers start: 77 outliers final: 46 residues processed: 338 average time/residue: 0.1811 time to fit residues: 98.4282 Evaluate side-chains 311 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain B residue 568 SER 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 891 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU 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 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 145 SER Chi-restraints excluded: chain F residue 77 THR 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 209 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 106 THR 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 161 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 109 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 GLN D 15 ASN F 37 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN L 315 GLN L 345 ASN M 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.069717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050613 restraints weight = 150747.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.052077 restraints weight = 77358.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053029 restraints weight = 51468.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053649 restraints weight = 40028.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054020 restraints weight = 34175.744| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1891 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= 0.121 Angle : 0.570 13.097 39937 Z= 0.277 Chirality : 0.037 0.172 4781 Planarity : 0.004 0.050 4056 Dihedral : 19.012 173.400 7260 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.95 % Allowed : 24.89 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2699 helix: 1.59 (0.16), residues: 1084 sheet: 0.59 (0.23), residues: 528 loop : -1.39 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 147 TYR 0.017 0.001 TYR K 24 PHE 0.019 0.001 PHE M 157 TRP 0.011 0.001 TRP L 324 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00264 (28554) covalent geometry : angle 0.56912 (39931) hydrogen bonds : bond 0.03682 ( 1018) hydrogen bonds : angle 4.36589 ( 2895) metal coordination : bond 0.00566 ( 4) metal coordination : angle 3.11880 ( 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 379 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 284 time to evaluate : 0.895 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: 0.8308 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: B 144 MET cc_start: 0.9278 (mmm) cc_final: 0.8702 (mmm) REVERT: B 304 MET cc_start: 0.7651 (tmm) cc_final: 0.7256 (tmm) REVERT: B 628 MET cc_start: 0.9141 (mmm) cc_final: 0.8336 (mmm) REVERT: B 846 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9001 (pp) REVERT: C 45 LEU cc_start: 0.9092 (mt) cc_final: 0.8837 (pp) REVERT: C 119 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7263 (mp0) REVERT: D 28 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9196 (mm-30) REVERT: D 160 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8508 (tm-30) REVERT: D 171 GLU cc_start: 0.8783 (pm20) cc_final: 0.8517 (pm20) REVERT: E 71 LYS cc_start: 0.9614 (tppp) cc_final: 0.9079 (tppp) REVERT: E 134 GLU cc_start: 0.8673 (pt0) cc_final: 0.8384 (pt0) REVERT: E 136 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8689 (pp20) REVERT: E 144 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8397 (tmm160) REVERT: E 149 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: E 150 GLU cc_start: 0.7481 (mp0) cc_final: 0.6809 (tp30) REVERT: F 39 ARG cc_start: 0.8906 (ptm-80) cc_final: 0.8548 (ttp80) REVERT: F 67 PHE cc_start: 0.9000 (m-80) cc_final: 0.8565 (m-10) REVERT: G 39 VAL cc_start: 0.9581 (t) cc_final: 0.9191 (p) REVERT: I 58 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8525 (t80) REVERT: I 63 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9047 (tp) REVERT: I 177 MET cc_start: 0.9000 (tpp) cc_final: 0.8140 (tpp) REVERT: I 212 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9117 (mm) REVERT: J 72 LYS cc_start: 0.8986 (tptm) cc_final: 0.8655 (tptm) REVERT: J 177 MET cc_start: 0.8945 (tmm) cc_final: 0.8689 (mtm) REVERT: K 21 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9215 (mm-40) REVERT: K 109 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8394 (mmm-85) REVERT: K 113 HIS cc_start: 0.8966 (m-70) cc_final: 0.8629 (m-70) REVERT: K 114 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7711 (m-70) REVERT: L 226 GLU cc_start: 0.8329 (tp30) cc_final: 0.7890 (tt0) REVERT: M 53 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8971 (mp) REVERT: M 76 MET cc_start: 0.9104 (mtm) cc_final: 0.8382 (mpp) REVERT: M 78 ARG cc_start: 0.7729 (ptm160) cc_final: 0.7517 (ptm160) REVERT: M 91 CYS cc_start: 0.9459 (m) cc_final: 0.9028 (t) REVERT: M 111 PHE cc_start: 0.9114 (m-80) cc_final: 0.8660 (m-80) REVERT: M 149 LEU cc_start: 0.9365 (tp) cc_final: 0.9145 (tt) REVERT: M 153 CYS cc_start: 0.9526 (m) cc_final: 0.9122 (m) REVERT: M 169 PHE cc_start: 0.9030 (m-80) cc_final: 0.8775 (m-80) REVERT: M 173 ASN cc_start: 0.9223 (m-40) cc_final: 0.8989 (m-40) REVERT: M 193 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8048 (mmm-85) REVERT: M 225 ASP cc_start: 0.9247 (t0) cc_final: 0.8815 (t0) REVERT: M 238 PHE cc_start: 0.9143 (m-80) cc_final: 0.8876 (m-80) outliers start: 95 outliers final: 51 residues processed: 352 average time/residue: 0.1782 time to fit residues: 100.1060 Evaluate side-chains 317 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 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 172 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 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 145 SER Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 12 VAL 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 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 I residue 212 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU 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 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 53 LEU Chi-restraints excluded: chain M residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 133 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 15 optimal weight: 11.9990 chunk 124 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 141 optimal weight: 0.0770 chunk 107 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS F 37 HIS I 46 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN J 46 GLN J 114 HIS ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS M 97 ASN M 206 GLN M 232 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.066789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047873 restraints weight = 153174.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049277 restraints weight = 79415.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050201 restraints weight = 53222.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050786 restraints weight = 41686.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051075 restraints weight = 35842.898| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28558 Z= 0.188 Angle : 0.614 13.698 39937 Z= 0.303 Chirality : 0.038 0.191 4781 Planarity : 0.004 0.049 4056 Dihedral : 19.103 172.970 7258 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.20 % Allowed : 26.34 % Favored : 69.45 % 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: 0.33 (0.17), residues: 2699 helix: 1.65 (0.16), residues: 1074 sheet: 0.47 (0.23), residues: 534 loop : -1.41 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG F 147 TYR 0.020 0.001 TYR K 24 PHE 0.022 0.002 PHE M 157 TRP 0.010 0.001 TRP K 27 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00401 (28554) covalent geometry : angle 0.61280 (39931) hydrogen bonds : bond 0.04104 ( 1018) hydrogen bonds : angle 4.58203 ( 2895) metal coordination : bond 0.00659 ( 4) metal coordination : angle 3.58321 ( 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 374 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 273 time to evaluate : 0.910 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: 0.8255 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: B 141 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.7981 (tpp-160) REVERT: B 304 MET cc_start: 0.7846 (tmm) cc_final: 0.7538 (tmm) REVERT: B 622 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9459 (pp) REVERT: B 628 MET cc_start: 0.9204 (mmm) cc_final: 0.8412 (mmm) REVERT: B 846 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9027 (pp) REVERT: D 160 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8571 (tm-30) REVERT: E 39 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8777 (ttp80) REVERT: E 71 LYS cc_start: 0.9618 (tppp) cc_final: 0.9092 (tppp) REVERT: E 136 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8744 (pp20) REVERT: E 144 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8456 (tmm160) REVERT: E 150 GLU cc_start: 0.7597 (mp0) cc_final: 0.6982 (tp30) REVERT: F 38 MET cc_start: 0.8590 (mmm) cc_final: 0.8225 (mmm) REVERT: G 39 VAL cc_start: 0.9576 (t) cc_final: 0.9227 (p) REVERT: H 68 GLU cc_start: 0.9077 (pm20) cc_final: 0.8454 (pm20) REVERT: H 69 LYS cc_start: 0.9312 (mppt) cc_final: 0.8984 (mmtm) REVERT: I 58 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8587 (t80) REVERT: J 72 LYS cc_start: 0.8966 (tptm) cc_final: 0.8612 (tptm) REVERT: K 8 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8040 (tt0) REVERT: K 109 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: K 113 HIS cc_start: 0.8978 (m-70) cc_final: 0.8730 (m-70) REVERT: K 114 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7820 (m-70) REVERT: L 114 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8924 (ptpp) REVERT: L 226 GLU cc_start: 0.8521 (tp30) cc_final: 0.7870 (tt0) REVERT: M 14 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8490 (mmp80) REVERT: M 76 MET cc_start: 0.9202 (mtm) cc_final: 0.8476 (mpp) REVERT: M 91 CYS cc_start: 0.9509 (m) cc_final: 0.9036 (t) REVERT: M 111 PHE cc_start: 0.9208 (m-80) cc_final: 0.8754 (m-80) REVERT: M 153 CYS cc_start: 0.9515 (m) cc_final: 0.9218 (m) REVERT: M 169 PHE cc_start: 0.9107 (m-80) cc_final: 0.8861 (m-80) REVERT: M 173 ASN cc_start: 0.9302 (m-40) cc_final: 0.9080 (m-40) REVERT: M 176 MET cc_start: 0.9678 (mtp) cc_final: 0.9455 (mtp) REVERT: M 193 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8067 (mmm-85) REVERT: M 225 ASP cc_start: 0.9359 (t0) cc_final: 0.9059 (t0) REVERT: M 238 PHE cc_start: 0.9206 (m-80) cc_final: 0.8896 (m-80) outliers start: 101 outliers final: 63 residues processed: 348 average time/residue: 0.1855 time to fit residues: 102.1728 Evaluate side-chains 323 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 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 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 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 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 58 PHE 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 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 239 PHE Chi-restraints excluded: chain K residue 5 HIS 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 114 LYS 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 L residue 338 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 166 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN L 315 GLN M 56 GLN ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.067760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048668 restraints weight = 151888.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050132 restraints weight = 77928.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051073 restraints weight = 52012.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051679 restraints weight = 40595.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052057 restraints weight = 34723.908| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28558 Z= 0.105 Angle : 0.596 13.877 39937 Z= 0.285 Chirality : 0.037 0.228 4781 Planarity : 0.004 0.053 4056 Dihedral : 19.125 172.863 7258 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.37 % Allowed : 27.51 % Favored : 69.12 % 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: 0.42 (0.17), residues: 2699 helix: 1.71 (0.16), residues: 1080 sheet: 0.55 (0.23), residues: 527 loop : -1.38 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 147 TYR 0.021 0.001 TYR K 24 PHE 0.022 0.001 PHE M 157 TRP 0.014 0.001 TRP L 324 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00231 (28554) covalent geometry : angle 0.59524 (39931) hydrogen bonds : bond 0.03579 ( 1018) hydrogen bonds : angle 4.35753 ( 2895) metal coordination : bond 0.00361 ( 4) metal coordination : angle 2.81664 ( 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 349 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 0.877 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: 0.8361 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: B 304 MET cc_start: 0.7718 (tmm) cc_final: 0.7402 (tmm) REVERT: B 628 MET cc_start: 0.9164 (mmm) cc_final: 0.8313 (mmm) REVERT: B 846 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9014 (pp) REVERT: D 28 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9167 (mm-30) REVERT: D 160 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8577 (tm-30) REVERT: E 39 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8804 (ttp80) REVERT: E 71 LYS cc_start: 0.9603 (tppp) cc_final: 0.9065 (tppp) REVERT: E 136 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8733 (pp20) REVERT: E 150 GLU cc_start: 0.7595 (mp0) cc_final: 0.6986 (tp30) REVERT: G 39 VAL cc_start: 0.9567 (t) cc_final: 0.9212 (p) REVERT: G 86 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8654 (tt) REVERT: G 87 GLN cc_start: 0.9635 (tp40) cc_final: 0.9225 (mp10) REVERT: H 69 LYS cc_start: 0.9265 (mppt) cc_final: 0.9031 (mmtm) REVERT: I 58 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8552 (t80) REVERT: J 165 MET cc_start: 0.8824 (mmm) cc_final: 0.8613 (mmm) REVERT: J 175 ASN cc_start: 0.8764 (m110) cc_final: 0.8408 (m110) REVERT: K 8 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7986 (tt0) REVERT: K 109 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: K 113 HIS cc_start: 0.8966 (m-70) cc_final: 0.8708 (m-70) REVERT: K 114 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7816 (m-70) REVERT: L 114 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8881 (ptpp) REVERT: L 226 GLU cc_start: 0.8467 (tp30) cc_final: 0.7812 (tt0) REVERT: M 78 ARG cc_start: 0.7907 (ptm160) cc_final: 0.7616 (mtp180) REVERT: M 91 CYS cc_start: 0.9487 (m) cc_final: 0.9076 (t) REVERT: M 111 PHE cc_start: 0.9167 (m-80) cc_final: 0.8735 (m-80) REVERT: M 169 PHE cc_start: 0.9074 (m-80) cc_final: 0.8823 (m-80) REVERT: M 173 ASN cc_start: 0.9273 (m-40) cc_final: 0.9052 (m-40) REVERT: M 176 MET cc_start: 0.9686 (mtp) cc_final: 0.9441 (mtp) REVERT: M 193 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8007 (mmm-85) REVERT: M 225 ASP cc_start: 0.9353 (t0) cc_final: 0.9048 (t0) REVERT: M 238 PHE cc_start: 0.9184 (m-80) cc_final: 0.8849 (m-80) outliers start: 81 outliers final: 53 residues processed: 326 average time/residue: 0.1797 time to fit residues: 92.8692 Evaluate side-chains 313 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 632 ILE 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 C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 86 LEU 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 189 SER Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 206 LEU 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 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 114 LYS 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 171 ILE Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 891 HIS E 127 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN L 315 GLN M 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.063487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044518 restraints weight = 160609.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045910 restraints weight = 85013.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046794 restraints weight = 58106.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047337 restraints weight = 46142.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047670 restraints weight = 40153.423| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 28558 Z= 0.301 Angle : 0.727 13.654 39937 Z= 0.362 Chirality : 0.041 0.269 4781 Planarity : 0.005 0.046 4056 Dihedral : 19.357 171.883 7258 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.20 % Allowed : 28.17 % Favored : 67.62 % 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: -0.01 (0.16), residues: 2699 helix: 1.34 (0.16), residues: 1081 sheet: 0.28 (0.23), residues: 518 loop : -1.54 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 147 TYR 0.019 0.002 TYR K 24 PHE 0.023 0.002 PHE M 157 TRP 0.016 0.002 TRP L 183 HIS 0.006 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00635 (28554) covalent geometry : angle 0.72377 (39931) hydrogen bonds : bond 0.04825 ( 1018) hydrogen bonds : angle 4.97804 ( 2895) metal coordination : bond 0.01265 ( 4) metal coordination : angle 5.48892 ( 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 350 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 249 time to evaluate : 0.967 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 144 MET cc_start: 0.9194 (mmm) cc_final: 0.8558 (mmm) REVERT: B 304 MET cc_start: 0.8015 (tmm) cc_final: 0.7774 (tmm) REVERT: B 622 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9453 (pp) REVERT: B 628 MET cc_start: 0.9242 (mmm) cc_final: 0.8439 (mmm) REVERT: C 194 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6677 (ttp-170) REVERT: D 160 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 71 LYS cc_start: 0.9625 (tppp) cc_final: 0.9139 (tppp) REVERT: E 144 ARG cc_start: 0.8728 (ptm-80) cc_final: 0.8312 (tmm160) REVERT: E 146 CYS cc_start: 0.8232 (m) cc_final: 0.7832 (m) REVERT: E 150 GLU cc_start: 0.7678 (mp0) cc_final: 0.6895 (tp30) REVERT: H 69 LYS cc_start: 0.9233 (mppt) cc_final: 0.8939 (mmtm) REVERT: H 102 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: I 177 MET cc_start: 0.9206 (ttt) cc_final: 0.8148 (tpp) REVERT: J 6 ASP cc_start: 0.7976 (t0) cc_final: 0.7649 (t0) REVERT: J 175 ASN cc_start: 0.8920 (m110) cc_final: 0.8540 (m110) REVERT: K 8 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8097 (tt0) REVERT: K 109 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8329 (mmm-85) REVERT: K 113 HIS cc_start: 0.9017 (m-70) cc_final: 0.8741 (m-70) REVERT: M 91 CYS cc_start: 0.9577 (m) cc_final: 0.9150 (t) REVERT: M 111 PHE cc_start: 0.9284 (m-80) cc_final: 0.8777 (m-80) REVERT: M 193 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8473 (tpp80) REVERT: M 225 ASP cc_start: 0.9389 (t0) cc_final: 0.9102 (t0) REVERT: M 238 PHE cc_start: 0.9273 (m-80) cc_final: 0.8915 (m-80) outliers start: 101 outliers final: 78 residues processed: 321 average time/residue: 0.1773 time to fit residues: 91.3385 Evaluate side-chains 317 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 236 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 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 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 B residue 962 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain 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 102 PHE Chi-restraints excluded: chain I residue 58 PHE 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 212 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 80 TYR 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 114 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 268 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 565 ASN E 127 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN L 315 GLN M 56 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 = 0.3488 r_free = 0.3488 target = 0.066122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047255 restraints weight = 154921.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048727 restraints weight = 78812.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049665 restraints weight = 52376.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050166 restraints weight = 40719.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050607 restraints weight = 35336.743| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3216 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= 0.109 Angle : 0.637 16.859 39937 Z= 0.305 Chirality : 0.038 0.208 4781 Planarity : 0.004 0.048 4056 Dihedral : 19.330 172.313 7258 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.46 % Allowed : 30.09 % Favored : 67.46 % 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: 1.61 (0.16), residues: 1081 sheet: 0.44 (0.24), residues: 520 loop : -1.40 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 147 TYR 0.033 0.001 TYR B 892 PHE 0.023 0.001 PHE M 169 TRP 0.022 0.001 TRP L 324 HIS 0.010 0.001 HIS B 891 Details of bonding type rmsd covalent geometry : bond 0.00235 (28554) covalent geometry : angle 0.63586 (39931) hydrogen bonds : bond 0.03597 ( 1018) hydrogen bonds : angle 4.45149 ( 2895) metal coordination : bond 0.00291 ( 4) metal coordination : angle 3.13342 ( 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 331 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 0.903 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 144 MET cc_start: 0.9197 (mmm) cc_final: 0.8652 (mmm) REVERT: B 628 MET cc_start: 0.9131 (mmm) cc_final: 0.8317 (mmm) REVERT: B 846 LEU cc_start: 0.9357 (tt) cc_final: 0.9015 (pp) REVERT: D 41 ARG cc_start: 0.9184 (mmp80) cc_final: 0.8866 (mmp80) REVERT: D 160 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8596 (tm-30) REVERT: E 39 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8822 (ttp80) REVERT: E 71 LYS cc_start: 0.9599 (tppp) cc_final: 0.9100 (tppp) REVERT: E 144 ARG cc_start: 0.8726 (ptm-80) cc_final: 0.8373 (ttp80) REVERT: E 146 CYS cc_start: 0.8081 (m) cc_final: 0.7777 (m) REVERT: E 150 GLU cc_start: 0.7674 (mp0) cc_final: 0.6942 (tp30) REVERT: G 39 VAL cc_start: 0.9563 (t) cc_final: 0.9228 (p) REVERT: G 87 GLN cc_start: 0.9621 (tp40) cc_final: 0.9173 (mp10) REVERT: I 57 LEU cc_start: 0.9149 (tp) cc_final: 0.8341 (mt) REVERT: I 58 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8533 (t80) REVERT: J 165 MET cc_start: 0.8925 (mmm) cc_final: 0.8724 (mmm) REVERT: J 168 TYR cc_start: 0.8946 (m-80) cc_final: 0.8733 (m-80) REVERT: J 177 MET cc_start: 0.8924 (tmm) cc_final: 0.8681 (ttm) REVERT: K 8 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7967 (tt0) REVERT: K 109 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8467 (mmm-85) REVERT: K 113 HIS cc_start: 0.8992 (m-70) cc_final: 0.8749 (m-70) REVERT: M 91 CYS cc_start: 0.9496 (m) cc_final: 0.9006 (t) REVERT: M 94 ARG cc_start: 0.9050 (mmt90) cc_final: 0.8328 (mmm-85) REVERT: M 111 PHE cc_start: 0.9231 (m-80) cc_final: 0.8721 (m-80) REVERT: M 176 MET cc_start: 0.9670 (mtp) cc_final: 0.9460 (mtp) REVERT: M 193 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8079 (mmm-85) REVERT: M 225 ASP cc_start: 0.9392 (t0) cc_final: 0.9114 (t0) REVERT: M 238 PHE cc_start: 0.9223 (m-80) cc_final: 0.8865 (m-80) outliers start: 59 outliers final: 49 residues processed: 314 average time/residue: 0.1811 time to fit residues: 91.1695 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 : 0.830 ------------------------------------------------------------------------------- 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 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 606 VAL Chi-restraints excluded: chain B residue 722 TYR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 891 HIS Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU 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 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 84 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 J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 153 CYS 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: 0.8980 chunk 136 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 206 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN J 46 GLN J 175 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.066324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047383 restraints weight = 153999.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048835 restraints weight = 79281.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049775 restraints weight = 52889.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050343 restraints weight = 41248.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050722 restraints weight = 35513.068| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28558 Z= 0.109 Angle : 0.627 16.684 39937 Z= 0.300 Chirality : 0.038 0.186 4781 Planarity : 0.004 0.048 4056 Dihedral : 19.228 173.116 7258 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.37 % Allowed : 30.05 % 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: 0.35 (0.17), residues: 2699 helix: 1.63 (0.16), residues: 1078 sheet: 0.51 (0.23), residues: 527 loop : -1.36 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 147 TYR 0.021 0.001 TYR H 95 PHE 0.024 0.001 PHE M 169 TRP 0.018 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00239 (28554) covalent geometry : angle 0.62555 (39931) hydrogen bonds : bond 0.03490 ( 1018) hydrogen bonds : angle 4.41204 ( 2895) metal coordination : bond 0.00358 ( 4) metal coordination : angle 3.16667 ( 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 326 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 1.131 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: B 144 MET cc_start: 0.9170 (mmm) cc_final: 0.8651 (mmm) REVERT: B 628 MET cc_start: 0.9158 (mmm) cc_final: 0.8350 (mmm) REVERT: B 846 LEU cc_start: 0.9367 (tt) cc_final: 0.9026 (pp) REVERT: C 119 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6871 (mp0) REVERT: D 160 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8584 (tm-30) REVERT: D 172 ASP cc_start: 0.8969 (p0) cc_final: 0.8436 (p0) REVERT: E 39 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8808 (ttp80) REVERT: E 71 LYS cc_start: 0.9596 (tppp) cc_final: 0.9085 (tppp) REVERT: E 144 ARG cc_start: 0.8777 (ptm-80) cc_final: 0.8366 (ttp80) REVERT: E 146 CYS cc_start: 0.8198 (m) cc_final: 0.7882 (m) REVERT: E 150 GLU cc_start: 0.7755 (mp0) cc_final: 0.7067 (tp30) REVERT: G 39 VAL cc_start: 0.9558 (t) cc_final: 0.9250 (p) REVERT: G 87 GLN cc_start: 0.9582 (tp40) cc_final: 0.9196 (mp10) REVERT: I 57 LEU cc_start: 0.9142 (tp) cc_final: 0.8347 (mt) REVERT: I 58 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8546 (t80) REVERT: I 177 MET cc_start: 0.9297 (ttp) cc_final: 0.8438 (tpp) REVERT: J 165 MET cc_start: 0.8872 (mmm) cc_final: 0.8662 (mmm) REVERT: J 175 ASN cc_start: 0.8796 (m110) cc_final: 0.8502 (m110) REVERT: J 177 MET cc_start: 0.8946 (tmm) cc_final: 0.8635 (mtm) REVERT: K 8 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7996 (tt0) REVERT: K 109 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8485 (mmm-85) REVERT: K 113 HIS cc_start: 0.9000 (m-70) cc_final: 0.8753 (m-70) REVERT: L 114 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8914 (ptpp) REVERT: M 45 GLU cc_start: 0.9133 (tp30) cc_final: 0.8735 (tp30) REVERT: M 76 MET cc_start: 0.9169 (mtm) cc_final: 0.8427 (mpp) REVERT: M 91 CYS cc_start: 0.9488 (m) cc_final: 0.9027 (t) REVERT: M 94 ARG cc_start: 0.9047 (mmt90) cc_final: 0.8352 (mmm-85) REVERT: M 111 PHE cc_start: 0.9216 (m-80) cc_final: 0.8741 (m-80) REVERT: M 173 ASN cc_start: 0.9278 (m-40) cc_final: 0.9069 (m-40) REVERT: M 225 ASP cc_start: 0.9399 (t0) cc_final: 0.9053 (t0) REVERT: M 238 PHE cc_start: 0.9238 (m-80) cc_final: 0.8904 (m-80) outliers start: 57 outliers final: 48 residues processed: 314 average time/residue: 0.1848 time to fit residues: 92.4935 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 : 0.977 ------------------------------------------------------------------------------- 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 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 606 VAL 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 C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU 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 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 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 F residue 135 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 102 THR 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 J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 282 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 HIS ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN 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 = 0.3478 r_free = 0.3478 target = 0.065618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046758 restraints weight = 155558.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048199 restraints weight = 80597.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049123 restraints weight = 53992.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049694 restraints weight = 42221.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050052 restraints weight = 36376.240| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28558 Z= 0.133 Angle : 0.636 16.784 39937 Z= 0.306 Chirality : 0.038 0.195 4781 Planarity : 0.004 0.082 4056 Dihedral : 19.223 172.767 7258 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.29 % Allowed : 30.00 % 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: 1.62 (0.16), residues: 1079 sheet: 0.47 (0.23), residues: 526 loop : -1.39 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 95 TYR 0.027 0.001 TYR K 24 PHE 0.022 0.001 PHE M 157 TRP 0.015 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00291 (28554) covalent geometry : angle 0.63482 (39931) hydrogen bonds : bond 0.03559 ( 1018) hydrogen bonds : angle 4.46160 ( 2895) metal coordination : bond 0.00490 ( 4) metal coordination : angle 3.49615 ( 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 310 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 0.744 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: B 628 MET cc_start: 0.9164 (mmm) cc_final: 0.8380 (mmm) REVERT: B 846 LEU cc_start: 0.9359 (tt) cc_final: 0.9018 (pp) REVERT: C 119 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6936 (mp0) REVERT: D 41 ARG cc_start: 0.9093 (mmp80) cc_final: 0.8819 (mmp80) REVERT: D 160 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8584 (tm-30) REVERT: D 172 ASP cc_start: 0.8859 (p0) cc_final: 0.8624 (p0) REVERT: E 39 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8803 (ttp80) REVERT: E 71 LYS cc_start: 0.9597 (tppp) cc_final: 0.9094 (tppp) REVERT: E 144 ARG cc_start: 0.8749 (ptm-80) cc_final: 0.8337 (ttp80) REVERT: E 146 CYS cc_start: 0.8301 (m) cc_final: 0.8014 (m) REVERT: E 150 GLU cc_start: 0.7782 (mp0) cc_final: 0.7064 (tp30) REVERT: G 39 VAL cc_start: 0.9570 (t) cc_final: 0.9275 (p) REVERT: G 87 GLN cc_start: 0.9591 (tp40) cc_final: 0.9183 (mp10) REVERT: H 102 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: I 57 LEU cc_start: 0.9069 (tp) cc_final: 0.8319 (mt) REVERT: I 58 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8534 (t80) REVERT: I 177 MET cc_start: 0.9260 (ttp) cc_final: 0.8431 (tpp) REVERT: J 177 MET cc_start: 0.8929 (tmm) cc_final: 0.8720 (mtm) REVERT: K 8 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7998 (tt0) REVERT: K 109 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8522 (mmm-85) REVERT: K 113 HIS cc_start: 0.8990 (m-70) cc_final: 0.8743 (m-70) REVERT: L 114 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8950 (ptpp) REVERT: M 14 ARG cc_start: 0.8675 (mmp80) cc_final: 0.8446 (mmp80) REVERT: M 45 GLU cc_start: 0.8997 (tp30) cc_final: 0.8703 (tp30) REVERT: M 91 CYS cc_start: 0.9507 (m) cc_final: 0.9052 (t) REVERT: M 94 ARG cc_start: 0.9100 (mmt90) cc_final: 0.8387 (mmm-85) REVERT: M 111 PHE cc_start: 0.9213 (m-80) cc_final: 0.8738 (m-80) REVERT: M 173 ASN cc_start: 0.9331 (m-40) cc_final: 0.9107 (m-40) REVERT: M 225 ASP cc_start: 0.9336 (t0) cc_final: 0.9014 (t0) REVERT: M 238 PHE cc_start: 0.9263 (m-80) cc_final: 0.8919 (m-80) outliers start: 55 outliers final: 48 residues processed: 296 average time/residue: 0.1695 time to fit residues: 80.7909 Evaluate side-chains 299 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 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 606 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 133 LEU 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 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 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 F residue 135 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain M residue 153 CYS Chi-restraints excluded: chain M residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 144 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** M 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045893 restraints weight = 158092.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047322 restraints weight = 82972.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048146 restraints weight = 56408.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048783 restraints weight = 45072.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049129 restraints weight = 39139.159| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3583 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= 0.147 Angle : 0.644 16.570 39937 Z= 0.312 Chirality : 0.038 0.179 4781 Planarity : 0.004 0.049 4056 Dihedral : 19.263 172.357 7258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.50 % Allowed : 29.80 % 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: 0.30 (0.17), residues: 2699 helix: 1.60 (0.16), residues: 1079 sheet: 0.44 (0.23), residues: 526 loop : -1.39 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 147 TYR 0.026 0.001 TYR K 24 PHE 0.021 0.001 PHE M 108 TRP 0.010 0.001 TRP L 324 HIS 0.007 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00320 (28554) covalent geometry : angle 0.64231 (39931) hydrogen bonds : bond 0.03784 ( 1018) hydrogen bonds : angle 4.52667 ( 2895) metal coordination : bond 0.00553 ( 4) metal coordination : angle 3.86555 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5139.84 seconds wall clock time: 89 minutes 38.89 seconds (5378.89 seconds total)