Starting phenix.real_space_refine on Mon Sep 14 05:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ah3_9622/09_2026/6ah3_9622.map" } resolution = 3.48 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 449 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 16401 2.51 5 N 5095 2.21 5 O 6659 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28703 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 7861 Classifications: {'RNA': 369} Modifications used: {'rna2p_pur': 28, 'rna2p_pyr': 22, 'rna3p_pur': 160, 'rna3p_pyr': 159} Link IDs: {'rna2p': 50, 'rna3p': 318} Chain: "B" Number of atoms: 6389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6389 Classifications: {'peptide': 784} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 748} Chain breaks: 4 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1435 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "D" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1685 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1272 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1024 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1712 Classifications: {'RNA': 80} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 39, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 70} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 26565 SG CYS K 90 69.305 82.028 54.180 1.00 53.49 S ATOM 26762 SG CYS K 115 67.908 78.298 50.233 1.00 73.56 S ATOM 26772 SG CYS K 117 66.234 78.409 53.838 1.00 72.07 S Time building chain proxies: 6.06, per 1000 atoms: 0.21 Number of scatterers: 28703 At special positions: 0 Unit cell: (154.44, 130.68, 204.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 96 16.00 P 449 15.00 Mg 2 11.99 O 6659 8.00 N 5095 7.00 C 16401 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 939.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 115 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 117 " 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 43.9% alpha, 16.9% beta 99 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'B' and resid 58 through 84 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.758A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.855A pdb=" N SER B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.206A pdb=" N ARG B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 removed outlier: 4.291A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 166 removed outlier: 3.903A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.577A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.767A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.662A pdb=" N ARG B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 307 through 318 removed outlier: 4.439A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 422 through 435 removed outlier: 3.702A pdb=" N GLU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 465 through 469 removed outlier: 4.015A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 469 " --> pdb=" O GLN B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.913A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.604A pdb=" N ILE B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.803A pdb=" N ARG B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.572A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.739A pdb=" N TYR B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 660 through 678 Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.945A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.675A pdb=" N GLN B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 39 through 42 removed outlier: 3.620A pdb=" N LEU C 42 " --> pdb=" O ASP C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 42' Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.688A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.653A pdb=" N LEU C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.565A pdb=" N CYS C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.917A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.657A pdb=" N ASN D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.657A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.667A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 3.933A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.980A pdb=" N GLY D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.912A pdb=" N MET D 273 " --> pdb=" O CYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.523A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 123 through 147 Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.871A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.645A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.871A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.595A pdb=" N ASN F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.556A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 83 removed outlier: 3.888A pdb=" N GLN G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 removed outlier: 3.663A pdb=" N ASP H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.558A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 4.116A pdb=" N SER H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.764A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 removed outlier: 3.682A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 77 removed outlier: 4.470A pdb=" N LEU I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.711A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.663A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.616A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.683A pdb=" N LEU I 164 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 165' Processing helix chain 'I' and resid 167 through 185 removed outlier: 4.315A pdb=" N ARG I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 3.503A pdb=" N GLU I 200 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 197 through 201' Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 4.536A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 234 " --> pdb=" O SER I 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 36 removed outlier: 3.577A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.004A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.542A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.863A pdb=" N LEU J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.563A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 185 removed outlier: 4.022A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG J 185 " --> pdb=" O ILE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.766A pdb=" N GLU J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 201' Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 227 Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.722A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.913A pdb=" N ALA K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 3.762A pdb=" N ALA K 63 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.570A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.042A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 393 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.672A pdb=" N VAL B 546 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER B 400 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 827 through 830 removed outlier: 4.131A pdb=" N THR B 828 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 837 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 841 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 843 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.030A pdb=" N THR K 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C 17 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.915A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 78 removed outlier: 3.822A pdb=" N GLN E 73 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.287A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.287A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.565A pdb=" N ILE G 33 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N MET G 68 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.772A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR H 11 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU H 102 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS H 13 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.787A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 41 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.278A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU J 110 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU J 86 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 102 through 105 removed outlier: 3.540A pdb=" N LYS K 102 " --> pdb=" O MET K 114 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 99 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5546 1.33 - 1.45: 9280 1.45 - 1.58: 14311 1.58 - 1.70: 895 1.70 - 1.82: 146 Bond restraints: 30178 Sorted by residual: bond pdb=" O3' G T 4 " pdb=" P A T 5 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.20e-02 6.94e+03 7.43e+01 bond pdb=" C ILE C 108 " pdb=" N PRO C 109 " ideal model delta sigma weight residual 1.337 1.388 -0.052 1.11e-02 8.12e+03 2.19e+01 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" C PRO K 24 " pdb=" N PRO K 25 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.09e+00 ... (remaining 30173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 41740 2.54 - 5.09: 1085 5.09 - 7.63: 91 7.63 - 10.17: 17 10.17 - 12.71: 5 Bond angle restraints: 42938 Sorted by residual: angle pdb=" N ILE I 112 " pdb=" CA ILE I 112 " pdb=" C ILE I 112 " ideal model delta sigma weight residual 113.10 105.89 7.21 9.70e-01 1.06e+00 5.52e+01 angle pdb=" N1 C A 135 " pdb=" C2 C A 135 " pdb=" O2 C A 135 " ideal model delta sigma weight residual 118.90 123.26 -4.36 6.00e-01 2.78e+00 5.27e+01 angle pdb=" N1 C A 182 " pdb=" C2 C A 182 " pdb=" O2 C A 182 " ideal model delta sigma weight residual 118.90 123.13 -4.23 6.00e-01 2.78e+00 4.96e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 119.70 127.41 -7.71 1.20e+00 6.94e-01 4.13e+01 angle pdb=" C3' A A 367 " pdb=" O3' A A 367 " pdb=" P G A 368 " ideal model delta sigma weight residual 119.70 126.81 -7.11 1.20e+00 6.94e-01 3.51e+01 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 17706 35.32 - 70.63: 1166 70.63 - 105.95: 130 105.95 - 141.27: 3 141.27 - 176.59: 10 Dihedral angle restraints: 19015 sinusoidal: 12031 harmonic: 6984 Sorted by residual: dihedral pdb=" C4' U A 93 " pdb=" C3' U A 93 " pdb=" C2' U A 93 " pdb=" C1' U A 93 " ideal model delta sinusoidal sigma weight residual -35.00 36.00 -71.00 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' U A 93 " pdb=" C2' U A 93 " pdb=" C1' U A 93 " pdb=" C3' U A 93 " ideal model delta sinusoidal sigma weight residual -35.00 32.84 -67.84 1 8.00e+00 1.56e-02 9.34e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 200.00 42.99 157.01 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 19012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4318 0.072 - 0.144: 814 0.144 - 0.216: 84 0.216 - 0.288: 4 0.288 - 0.359: 2 Chirality restraints: 5222 Sorted by residual: chirality pdb=" C3' A A 367 " pdb=" C4' A A 367 " pdb=" O3' A A 367 " pdb=" C2' A A 367 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C3' G A 179 " pdb=" C4' G A 179 " pdb=" O3' G A 179 " pdb=" C2' G A 179 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C3' U A 266 " pdb=" C4' U A 266 " pdb=" O3' U A 266 " pdb=" C2' U A 266 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5219 not shown) Planarity restraints: 3770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 4 " -0.029 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 G T 4 " 0.013 2.00e-02 2.50e+03 pdb=" C8 G T 4 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G T 4 " -0.020 2.00e-02 2.50e+03 pdb=" C5 G T 4 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G T 4 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G T 4 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G T 4 " -0.040 2.00e-02 2.50e+03 pdb=" C2 G T 4 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G T 4 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G T 4 " 0.039 2.00e-02 2.50e+03 pdb=" C4 G T 4 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 728 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO B 729 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER F 93 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C SER F 93 " -0.047 2.00e-02 2.50e+03 pdb=" O SER F 93 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE F 94 " 0.016 2.00e-02 2.50e+03 ... (remaining 3767 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 16 2.16 - 2.85: 8530 2.85 - 3.53: 36466 3.53 - 4.22: 73409 4.22 - 4.90: 110059 Nonbonded interactions: 228480 Sorted by model distance: nonbonded pdb=" NH2 ARG B 87 " pdb=" O2 C T 2 " model vdw 1.476 3.120 nonbonded pdb=" C5' A A 344 " pdb=" O2' A T 0 " model vdw 1.530 3.440 nonbonded pdb=" O2 U A 311 " pdb=" C5 A A 344 " model vdw 1.725 3.260 nonbonded pdb=" O2' U A 93 " pdb=" O5' C A 94 " model vdw 1.853 3.040 nonbonded pdb=" O2 U A 311 " pdb=" N7 A A 344 " model vdw 1.922 3.120 ... (remaining 228475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 : 0.007 0.654 30181 Z= 0.307 Angle : 0.910 12.714 42938 Z= 0.655 Chirality : 0.057 0.359 5222 Planarity : 0.006 0.078 3770 Dihedral : 19.187 176.585 14479 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.57 (0.14), residues: 2350 helix: -2.57 (0.12), residues: 884 sheet: -0.89 (0.24), residues: 430 loop : -2.76 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 97 TYR 0.025 0.002 TYR B 597 PHE 0.031 0.002 PHE D 207 TRP 0.043 0.003 TRP C 44 HIS 0.007 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.24 (30178) covalent geometry : angle 0.91008 / 0.65 (42938) hydrogen bonds : bond 0.17348 / 19.07 ( 1052) hydrogen bonds : angle 7.06743 / 9.40 ( 2825) metal coordination : bond 0.58245 / 43.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 814 time to evaluate : 0.876 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 168 LEU cc_start: 0.6786 (pp) cc_final: 0.6551 (pp) REVERT: B 397 SER cc_start: 0.7668 (p) cc_final: 0.7432 (p) REVERT: C 95 ASN cc_start: 0.4908 (OUTLIER) cc_final: 0.4206 (t0) REVERT: D 277 ILE cc_start: 0.4970 (mm) cc_final: 0.4178 (mt) REVERT: I 158 ILE cc_start: 0.8527 (mt) cc_final: 0.7831 (mt) REVERT: I 204 ILE cc_start: 0.7760 (tt) cc_final: 0.7535 (tt) REVERT: J 261 ASN cc_start: 0.7521 (m-40) cc_final: 0.7250 (m-40) outliers start: 4 outliers final: 2 residues processed: 816 average time/residue: 0.2135 time to fit residues: 265.5534 Evaluate side-chains 408 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN B 243 HIS B 251 HIS B 335 GLN B 437 HIS B 463 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 590 GLN B 595 GLN B 642 HIS B 665 GLN B 677 ASN B 704 ASN B 808 HIS B 832 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 95 ASN F 8 ASN F 37 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 65 GLN F 87 HIS F 111 GLN F 113 ASN G 18 HIS G 85 GLN H 27 HIS ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 143 HIS J 151 ASN J 172 GLN J 243 HIS ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.205384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.175225 restraints weight = 51804.749| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.16 r_work: 0.4076 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 30181 Z= 0.182 Angle : 0.685 12.203 42938 Z= 0.359 Chirality : 0.044 0.509 5222 Planarity : 0.006 0.074 3770 Dihedral : 21.613 177.061 9626 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 4.11 % Allowed : 13.21 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.19 (0.16), residues: 2350 helix: -0.93 (0.15), residues: 921 sheet: -0.54 (0.24), residues: 425 loop : -2.32 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 87 TYR 0.022 0.002 TYR D 143 PHE 0.025 0.002 PHE I 104 TRP 0.031 0.002 TRP C 44 HIS 0.009 0.002 HIS J 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (30178) covalent geometry : angle 0.68510 / 0.36 (42938) hydrogen bonds : bond 0.05741 / 5.80 ( 1052) hydrogen bonds : angle 4.87814 / 6.33 ( 2825) metal coordination : bond 0.05067 / 3.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 456 time to evaluate : 0.791 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: B 79 ASN cc_start: 0.7967 (t0) cc_final: 0.7755 (t0) REVERT: B 168 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7776 (pp) REVERT: B 312 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.6959 (m) REVERT: B 578 MET cc_start: 0.7090 (tpp) cc_final: 0.6852 (ttm) REVERT: B 720 MET cc_start: 0.4417 (mpp) cc_final: 0.2464 (ptt) REVERT: C 95 ASN cc_start: 0.4521 (t0) cc_final: 0.4306 (t0) REVERT: C 150 ASP cc_start: 0.4153 (m-30) cc_final: 0.2515 (t0) REVERT: D 91 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6209 (tt0) REVERT: D 177 ASP cc_start: 0.7956 (t0) cc_final: 0.7706 (t70) REVERT: D 207 PHE cc_start: 0.8549 (m-80) cc_final: 0.8338 (m-80) REVERT: E 135 SER cc_start: 0.8224 (t) cc_final: 0.7562 (m) REVERT: E 142 LYS cc_start: 0.7326 (mmtp) cc_final: 0.6974 (mmmt) REVERT: F 94 ILE cc_start: 0.6337 (mt) cc_final: 0.5989 (mp) REVERT: H 37 TRP cc_start: 0.8431 (t60) cc_final: 0.8188 (t60) REVERT: H 51 GLU cc_start: 0.7452 (tt0) cc_final: 0.7128 (tt0) REVERT: H 111 VAL cc_start: 0.4638 (OUTLIER) cc_final: 0.4387 (t) REVERT: I 157 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8129 (tm-30) REVERT: I 159 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8278 (p) REVERT: I 171 ARG cc_start: 0.6328 (mpt-90) cc_final: 0.6090 (mpt-90) outliers start: 89 outliers final: 49 residues processed: 514 average time/residue: 0.1958 time to fit residues: 160.0249 Evaluate side-chains 407 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 354 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 212 LYS Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 100 optimal weight: 0.0770 chunk 266 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 40.0000 chunk 277 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 189 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 123 GLN D 99 ASN D 197 GLN D 231 GLN G 18 HIS J 44 ASN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.203349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.172187 restraints weight = 51519.319| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.21 r_work: 0.4036 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30181 Z= 0.117 Angle : 0.562 16.661 42938 Z= 0.293 Chirality : 0.038 0.437 5222 Planarity : 0.005 0.065 3770 Dihedral : 21.424 176.171 9622 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.88 % Allowed : 16.03 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2350 helix: 0.04 (0.17), residues: 911 sheet: -0.40 (0.25), residues: 422 loop : -2.08 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 53 TYR 0.024 0.002 TYR E 76 PHE 0.020 0.002 PHE H 12 TRP 0.031 0.002 TRP C 66 HIS 0.005 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (30178) covalent geometry : angle 0.56173 / 0.29 (42938) hydrogen bonds : bond 0.04494 / 4.64 ( 1052) hydrogen bonds : angle 4.48887 / 5.73 ( 2825) metal coordination : bond 0.01114 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 401 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 578 MET cc_start: 0.7010 (tpp) cc_final: 0.6756 (ttm) REVERT: C 17 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6547 (pp30) REVERT: C 95 ASN cc_start: 0.4484 (t0) cc_final: 0.4257 (t0) REVERT: C 125 PRO cc_start: 0.5715 (Cg_endo) cc_final: 0.5354 (Cg_exo) REVERT: D 91 GLU cc_start: 0.6474 (mm-30) cc_final: 0.6181 (tt0) REVERT: D 106 LEU cc_start: 0.8281 (mt) cc_final: 0.6962 (tp) REVERT: D 151 ILE cc_start: 0.6539 (mm) cc_final: 0.6058 (mm) REVERT: D 177 ASP cc_start: 0.8106 (t0) cc_final: 0.7864 (t0) REVERT: D 207 PHE cc_start: 0.8600 (m-80) cc_final: 0.8366 (m-80) REVERT: D 233 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6896 (tt0) REVERT: E 135 SER cc_start: 0.8238 (t) cc_final: 0.7511 (m) REVERT: E 142 LYS cc_start: 0.7154 (mmtp) cc_final: 0.6902 (mmmt) REVERT: F 97 ILE cc_start: 0.6560 (pt) cc_final: 0.6177 (pt) REVERT: G 118 GLU cc_start: 0.6548 (tm-30) cc_final: 0.6006 (tm-30) REVERT: H 31 GLN cc_start: 0.7538 (tm-30) cc_final: 0.6985 (tm-30) REVERT: H 37 TRP cc_start: 0.8350 (t60) cc_final: 0.8130 (t60) REVERT: H 51 GLU cc_start: 0.7420 (tt0) cc_final: 0.7101 (tt0) REVERT: H 111 VAL cc_start: 0.4773 (OUTLIER) cc_final: 0.4408 (t) REVERT: I 157 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8134 (tm-30) REVERT: I 159 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (p) REVERT: J 95 GLN cc_start: 0.4585 (pp30) cc_final: 0.4301 (tm-30) REVERT: K 102 LYS cc_start: 0.5425 (tmtt) cc_final: 0.5109 (tptt) outliers start: 84 outliers final: 52 residues processed: 455 average time/residue: 0.1874 time to fit residues: 136.7144 Evaluate side-chains 411 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 0.0040 chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 270 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 263 optimal weight: 0.5980 chunk 277 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 832 ASN C 17 GLN C 25 ASN E 36 HIS F 113 ASN G 18 HIS K 38 ASN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.200816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.169145 restraints weight = 50891.298| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.20 r_work: 0.3997 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30181 Z= 0.110 Angle : 0.531 14.126 42938 Z= 0.278 Chirality : 0.036 0.359 5222 Planarity : 0.005 0.064 3770 Dihedral : 21.320 175.699 9622 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.83 % Allowed : 17.27 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2350 helix: 0.44 (0.17), residues: 919 sheet: -0.28 (0.25), residues: 422 loop : -1.97 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 252 TYR 0.020 0.001 TYR D 121 PHE 0.021 0.002 PHE D 265 TRP 0.012 0.001 TRP C 66 HIS 0.009 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (30178) covalent geometry : angle 0.53142 / 0.28 (42938) hydrogen bonds : bond 0.04066 / 4.14 ( 1052) hydrogen bonds : angle 4.32738 / 5.48 ( 2825) metal coordination : bond 0.00642 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 378 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8191 (tp) cc_final: 0.7678 (tp) REVERT: B 578 MET cc_start: 0.7174 (tpp) cc_final: 0.6939 (ttm) REVERT: C 129 MET cc_start: 0.2174 (tpp) cc_final: 0.1467 (tpp) REVERT: C 140 MET cc_start: 0.4515 (mmp) cc_final: 0.4216 (mmp) REVERT: D 91 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6301 (tt0) REVERT: D 106 LEU cc_start: 0.8270 (mt) cc_final: 0.6958 (tp) REVERT: D 151 ILE cc_start: 0.6616 (mm) cc_final: 0.6138 (mm) REVERT: D 207 PHE cc_start: 0.8622 (m-80) cc_final: 0.8392 (m-80) REVERT: D 233 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7025 (tt0) REVERT: D 265 PHE cc_start: 0.7789 (m-10) cc_final: 0.7534 (m-10) REVERT: F 94 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6313 (mp) REVERT: F 97 ILE cc_start: 0.6721 (pt) cc_final: 0.6276 (pt) REVERT: H 31 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7059 (tm-30) REVERT: H 44 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.6846 (tpp-160) REVERT: H 51 GLU cc_start: 0.7476 (tt0) cc_final: 0.7181 (tt0) REVERT: H 123 MET cc_start: 0.6224 (tpt) cc_final: 0.5808 (tmm) REVERT: I 105 ASP cc_start: 0.7433 (t70) cc_final: 0.7074 (t70) REVERT: I 106 ILE cc_start: 0.8710 (mt) cc_final: 0.8486 (mt) REVERT: I 157 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8177 (tm-30) REVERT: I 159 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8191 (p) REVERT: I 166 ASP cc_start: 0.5888 (m-30) cc_final: 0.5668 (m-30) REVERT: I 239 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7362 (mpt180) REVERT: K 102 LYS cc_start: 0.5420 (tmtt) cc_final: 0.5145 (tmtt) outliers start: 83 outliers final: 56 residues processed: 432 average time/residue: 0.1860 time to fit residues: 129.7111 Evaluate side-chains 400 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 342 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 140 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 123 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 257 optimal weight: 0.0980 chunk 153 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 258 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 704 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS G 58 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.190915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.156646 restraints weight = 49620.712| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.20 r_work: 0.3827 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 30181 Z= 0.174 Angle : 0.598 16.228 42938 Z= 0.311 Chirality : 0.039 0.381 5222 Planarity : 0.005 0.070 3770 Dihedral : 21.227 175.227 9622 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.53 % Allowed : 17.60 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.87 (0.17), residues: 2350 helix: 0.62 (0.17), residues: 925 sheet: -0.29 (0.25), residues: 426 loop : -1.87 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 15 TYR 0.021 0.002 TYR K 41 PHE 0.021 0.002 PHE B 657 TRP 0.014 0.002 TRP B 256 HIS 0.009 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (30178) covalent geometry : angle 0.59779 / 0.31 (42938) hydrogen bonds : bond 0.04449 / 4.64 ( 1052) hydrogen bonds : angle 4.36123 / 5.56 ( 2825) metal coordination : bond 0.00668 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 406 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6476 (tm-30) REVERT: B 469 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.5107 (p) REVERT: B 578 MET cc_start: 0.7706 (tpp) cc_final: 0.7380 (ttm) REVERT: B 757 PHE cc_start: 0.6227 (t80) cc_final: 0.5992 (t80) REVERT: B 758 PHE cc_start: 0.6343 (m-80) cc_final: 0.5982 (m-80) REVERT: C 129 MET cc_start: 0.2335 (tpp) cc_final: 0.2085 (tpp) REVERT: D 91 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6557 (tt0) REVERT: D 142 MET cc_start: 0.6347 (tmm) cc_final: 0.5879 (tpt) REVERT: D 151 ILE cc_start: 0.7500 (mm) cc_final: 0.7021 (mm) REVERT: D 259 ASP cc_start: 0.6652 (m-30) cc_final: 0.6344 (m-30) REVERT: E 124 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8189 (tttm) REVERT: F 94 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7050 (mp) REVERT: F 97 ILE cc_start: 0.7169 (pt) cc_final: 0.6762 (pt) REVERT: F 133 LEU cc_start: 0.6152 (mt) cc_final: 0.5898 (mt) REVERT: H 31 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7196 (tm-30) REVERT: H 37 TRP cc_start: 0.8719 (t60) cc_final: 0.8292 (t60) REVERT: H 44 ARG cc_start: 0.7738 (tpp-160) cc_final: 0.7467 (tpp-160) REVERT: H 123 MET cc_start: 0.6164 (tpt) cc_final: 0.5729 (tmm) REVERT: I 157 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8264 (tm-30) REVERT: I 159 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8313 (p) REVERT: I 225 MET cc_start: 0.4661 (tpp) cc_final: 0.4288 (tpp) REVERT: I 239 ARG cc_start: 0.7948 (mmt-90) cc_final: 0.7722 (mmt180) REVERT: J 185 ARG cc_start: 0.8359 (mtp85) cc_final: 0.7849 (mtp85) REVERT: K 51 ARG cc_start: 0.5350 (ttp80) cc_final: 0.4349 (ttp-170) outliers start: 98 outliers final: 65 residues processed: 474 average time/residue: 0.1836 time to fit residues: 140.3699 Evaluate side-chains 432 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 363 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 262 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 219 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN C 123 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 ASN ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** 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 = 0.4395 r_free = 0.4395 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.153886 restraints weight = 49390.994| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.20 r_work: 0.3789 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30181 Z= 0.134 Angle : 0.561 15.568 42938 Z= 0.291 Chirality : 0.038 0.366 5222 Planarity : 0.005 0.059 3770 Dihedral : 21.224 175.717 9622 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.20 % Allowed : 18.48 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.74 (0.17), residues: 2350 helix: 0.82 (0.17), residues: 927 sheet: -0.46 (0.24), residues: 434 loop : -1.77 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 136 TYR 0.023 0.002 TYR E 76 PHE 0.020 0.002 PHE D 265 TRP 0.016 0.001 TRP B 256 HIS 0.006 0.001 HIS J 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (30178) covalent geometry : angle 0.56102 / 0.29 (42938) hydrogen bonds : bond 0.04011 / 4.13 ( 1052) hydrogen bonds : angle 4.30613 / 5.53 ( 2825) metal coordination : bond 0.00269 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 377 time to evaluate : 0.818 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: B 193 LYS cc_start: 0.7687 (mttt) cc_final: 0.7223 (tptt) REVERT: B 469 THR cc_start: 0.5479 (OUTLIER) cc_final: 0.4987 (p) REVERT: B 645 LYS cc_start: 0.6788 (mmtt) cc_final: 0.6403 (pptt) REVERT: B 758 PHE cc_start: 0.6656 (m-80) cc_final: 0.6306 (m-80) REVERT: B 786 GLU cc_start: 0.8247 (pm20) cc_final: 0.7214 (pt0) REVERT: B 835 ASN cc_start: 0.8261 (p0) cc_final: 0.7711 (p0) REVERT: D 91 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6673 (tt0) REVERT: D 142 MET cc_start: 0.6233 (tmm) cc_final: 0.5725 (tpt) REVERT: D 259 ASP cc_start: 0.6618 (m-30) cc_final: 0.6370 (m-30) REVERT: E 124 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8202 (tttm) REVERT: E 134 ASN cc_start: 0.8693 (t0) cc_final: 0.8341 (m-40) REVERT: F 94 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7087 (mp) REVERT: F 97 ILE cc_start: 0.7415 (pt) cc_final: 0.6997 (pt) REVERT: F 133 LEU cc_start: 0.6562 (mt) cc_final: 0.6298 (mt) REVERT: G 33 ILE cc_start: 0.9092 (mp) cc_final: 0.8729 (mt) REVERT: G 118 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6510 (tm-30) REVERT: H 31 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7242 (tm-30) REVERT: I 157 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8236 (tm-30) REVERT: I 159 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8246 (p) REVERT: I 225 MET cc_start: 0.5306 (tpp) cc_final: 0.4614 (tmm) REVERT: J 187 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: K 51 ARG cc_start: 0.5529 (ttp80) cc_final: 0.5019 (ttp-170) REVERT: K 70 MET cc_start: 0.8104 (ttp) cc_final: 0.7890 (ttm) outliers start: 91 outliers final: 67 residues processed: 441 average time/residue: 0.1828 time to fit residues: 130.5921 Evaluate side-chains 425 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 354 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 161 optimal weight: 0.0570 chunk 102 optimal weight: 0.3980 chunk 258 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN G 58 GLN I 203 ASN ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.187851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152846 restraints weight = 48923.945| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.19 r_work: 0.3779 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30181 Z= 0.115 Angle : 0.546 15.377 42938 Z= 0.283 Chirality : 0.037 0.364 5222 Planarity : 0.005 0.060 3770 Dihedral : 21.194 176.034 9622 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.70 % Allowed : 19.49 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.18), residues: 2350 helix: 0.91 (0.17), residues: 928 sheet: -0.35 (0.24), residues: 447 loop : -1.74 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 202 TYR 0.015 0.001 TYR K 66 PHE 0.018 0.002 PHE J 104 TRP 0.015 0.001 TRP H 37 HIS 0.006 0.001 HIS J 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (30178) covalent geometry : angle 0.54597 / 0.28 (42938) hydrogen bonds : bond 0.03821 / 3.90 ( 1052) hydrogen bonds : angle 4.20821 / 5.36 ( 2825) metal coordination : bond 0.00209 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 369 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 LYS cc_start: 0.7686 (mttt) cc_final: 0.7212 (tptt) REVERT: B 204 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7803 (tp) REVERT: B 235 LYS cc_start: 0.6483 (tttt) cc_final: 0.6256 (ptpt) REVERT: B 655 ASP cc_start: 0.7308 (t70) cc_final: 0.6980 (t70) REVERT: B 786 GLU cc_start: 0.8087 (pm20) cc_final: 0.7219 (pt0) REVERT: B 835 ASN cc_start: 0.8233 (p0) cc_final: 0.7686 (p0) REVERT: D 91 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6759 (tt0) REVERT: D 142 MET cc_start: 0.6076 (tmm) cc_final: 0.5624 (tpt) REVERT: D 259 ASP cc_start: 0.6674 (m-30) cc_final: 0.6432 (m-30) REVERT: E 124 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8367 (tttm) REVERT: E 134 ASN cc_start: 0.8801 (t0) cc_final: 0.8368 (m-40) REVERT: F 94 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7162 (mp) REVERT: F 97 ILE cc_start: 0.7518 (pt) cc_final: 0.7091 (pt) REVERT: F 106 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6246 (p0) REVERT: F 133 LEU cc_start: 0.6716 (mt) cc_final: 0.6458 (mt) REVERT: G 33 ILE cc_start: 0.9104 (mp) cc_final: 0.8705 (mt) REVERT: G 58 GLN cc_start: 0.7852 (tp40) cc_final: 0.7531 (tp40) REVERT: G 118 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6700 (tm-30) REVERT: H 7 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7653 (tpp80) REVERT: H 31 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7255 (tm-30) REVERT: I 97 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6923 (mt) REVERT: I 157 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8187 (tm-30) REVERT: I 159 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8149 (p) REVERT: I 225 MET cc_start: 0.5153 (tpp) cc_final: 0.4493 (tmm) REVERT: J 187 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7745 (mtm-85) outliers start: 80 outliers final: 65 residues processed: 423 average time/residue: 0.1863 time to fit residues: 126.5573 Evaluate side-chains 423 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 57 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 123 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN F 111 GLN F 113 ASN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.178350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141301 restraints weight = 47964.228| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.17 r_work: 0.3611 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30181 Z= 0.183 Angle : 0.651 17.905 42938 Z= 0.338 Chirality : 0.040 0.384 5222 Planarity : 0.006 0.064 3770 Dihedral : 21.187 176.022 9622 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 4.34 % Allowed : 19.31 % Favored : 76.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.79 (0.17), residues: 2350 helix: 0.73 (0.17), residues: 936 sheet: -0.44 (0.25), residues: 419 loop : -1.79 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 136 TYR 0.023 0.002 TYR K 66 PHE 0.031 0.003 PHE H 49 TRP 0.020 0.002 TRP B 661 HIS 0.012 0.002 HIS J 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (30178) covalent geometry : angle 0.65066 / 0.34 (42938) hydrogen bonds : bond 0.04875 / 5.10 ( 1052) hydrogen bonds : angle 4.46970 / 5.68 ( 2825) metal coordination : bond 0.00452 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 399 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 LYS cc_start: 0.7838 (mttt) cc_final: 0.7394 (tptt) REVERT: B 204 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (tp) REVERT: B 786 GLU cc_start: 0.8359 (pm20) cc_final: 0.7556 (pt0) REVERT: C 113 TYR cc_start: 0.6496 (t80) cc_final: 0.6094 (t80) REVERT: D 91 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6958 (tt0) REVERT: E 124 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8483 (tttm) REVERT: E 134 ASN cc_start: 0.8856 (t0) cc_final: 0.8501 (m-40) REVERT: F 94 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7949 (mp) REVERT: G 58 GLN cc_start: 0.8072 (tp40) cc_final: 0.7809 (tp40) REVERT: G 118 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6883 (tm-30) REVERT: H 31 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7340 (tm-30) REVERT: I 97 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7656 (mt) REVERT: I 157 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8311 (tm-30) REVERT: I 159 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8321 (p) REVERT: I 225 MET cc_start: 0.5159 (tpp) cc_final: 0.4708 (tmm) REVERT: J 266 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7250 (mt) outliers start: 94 outliers final: 72 residues processed: 466 average time/residue: 0.1907 time to fit residues: 142.2439 Evaluate side-chains 421 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 343 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 109 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 122 optimal weight: 0.0370 chunk 33 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 231 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS H 39 ASN J 55 ASN J 143 HIS K 42 GLN ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.178758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141658 restraints weight = 47813.996| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.14 r_work: 0.3624 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30181 Z= 0.133 Angle : 0.593 15.892 42938 Z= 0.308 Chirality : 0.038 0.355 5222 Planarity : 0.005 0.063 3770 Dihedral : 21.192 176.987 9622 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.70 % Allowed : 22.17 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.68 (0.18), residues: 2350 helix: 0.85 (0.17), residues: 934 sheet: -0.43 (0.25), residues: 430 loop : -1.74 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 136 TYR 0.020 0.002 TYR K 66 PHE 0.033 0.002 PHE E 77 TRP 0.015 0.002 TRP C 44 HIS 0.010 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (30178) covalent geometry : angle 0.59285 / 0.31 (42938) hydrogen bonds : bond 0.04048 / 4.15 ( 1052) hydrogen bonds : angle 4.33563 / 5.56 ( 2825) metal coordination : bond 0.00172 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 372 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 LYS cc_start: 0.7736 (mttt) cc_final: 0.7353 (tptt) REVERT: B 204 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 645 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6667 (pptt) REVERT: B 786 GLU cc_start: 0.8308 (pm20) cc_final: 0.7600 (pt0) REVERT: C 113 TYR cc_start: 0.6402 (t80) cc_final: 0.6030 (t80) REVERT: C 140 MET cc_start: 0.3704 (mmp) cc_final: 0.3196 (mmm) REVERT: D 91 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6957 (tt0) REVERT: E 51 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 59 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8128 (t0) REVERT: E 124 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8401 (tttm) REVERT: E 134 ASN cc_start: 0.8779 (t0) cc_final: 0.8472 (m-40) REVERT: E 138 LEU cc_start: 0.8612 (tp) cc_final: 0.8368 (tt) REVERT: F 9 GLU cc_start: 0.8348 (mp0) cc_final: 0.8123 (pm20) REVERT: F 94 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8243 (mt) REVERT: G 33 ILE cc_start: 0.9338 (mp) cc_final: 0.9054 (mt) REVERT: G 58 GLN cc_start: 0.8060 (tp40) cc_final: 0.7725 (tp40) REVERT: G 118 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6853 (tm-30) REVERT: H 31 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7283 (tm-30) REVERT: H 107 ARG cc_start: 0.5276 (mmt90) cc_final: 0.5042 (mpt180) REVERT: I 1 MET cc_start: 0.8472 (tmm) cc_final: 0.8155 (ttp) REVERT: I 97 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7664 (mt) REVERT: I 157 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8142 (tm-30) REVERT: I 159 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8279 (p) REVERT: I 225 MET cc_start: 0.4811 (tpp) cc_final: 0.4595 (tmm) REVERT: J 225 MET cc_start: 0.4786 (mmp) cc_final: 0.3961 (ttm) outliers start: 80 outliers final: 58 residues processed: 427 average time/residue: 0.1900 time to fit residues: 129.9899 Evaluate side-chains 420 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 356 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 HIS Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 25 optimal weight: 30.0000 chunk 137 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 139 ASN F 89 GLN F 106 ASN H 27 HIS J 34 HIS ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137428 restraints weight = 47216.114| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.13 r_work: 0.3556 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 30181 Z= 0.186 Angle : 0.645 17.596 42938 Z= 0.335 Chirality : 0.040 0.371 5222 Planarity : 0.005 0.056 3770 Dihedral : 21.158 177.718 9622 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.60 % Allowed : 22.12 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.81 (0.17), residues: 2350 helix: 0.71 (0.17), residues: 945 sheet: -0.48 (0.25), residues: 420 loop : -1.80 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 136 TYR 0.023 0.002 TYR K 66 PHE 0.037 0.003 PHE J 104 TRP 0.023 0.002 TRP B 792 HIS 0.018 0.002 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (30178) covalent geometry : angle 0.64465 / 0.33 (42938) hydrogen bonds : bond 0.04624 / 4.73 ( 1052) hydrogen bonds : angle 4.46149 / 5.73 ( 2825) metal coordination : bond 0.00284 / 0.18 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 369 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 LYS cc_start: 0.7854 (mttt) cc_final: 0.7424 (tptt) REVERT: B 204 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 448 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8120 (p90) REVERT: B 645 LYS cc_start: 0.7222 (mmtt) cc_final: 0.6757 (pptt) REVERT: B 783 GLN cc_start: 0.7545 (mt0) cc_final: 0.7280 (mt0) REVERT: B 786 GLU cc_start: 0.8511 (pm20) cc_final: 0.7866 (pt0) REVERT: C 113 TYR cc_start: 0.6535 (t80) cc_final: 0.6133 (t80) REVERT: D 91 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7056 (tt0) REVERT: E 124 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8417 (tttm) REVERT: E 134 ASN cc_start: 0.8822 (t0) cc_final: 0.8515 (m-40) REVERT: F 30 VAL cc_start: 0.9082 (t) cc_final: 0.8710 (p) REVERT: F 94 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8475 (mp) REVERT: G 33 ILE cc_start: 0.9331 (mp) cc_final: 0.8933 (mt) REVERT: G 58 GLN cc_start: 0.8062 (tp40) cc_final: 0.7738 (tp40) REVERT: G 80 CYS cc_start: 0.7917 (m) cc_final: 0.7647 (m) REVERT: G 118 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6886 (tm-30) REVERT: H 31 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 107 ARG cc_start: 0.5389 (mmt90) cc_final: 0.5156 (mpt180) REVERT: I 81 TYR cc_start: 0.8528 (m-80) cc_final: 0.8178 (m-80) REVERT: I 157 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8213 (tm-30) REVERT: I 159 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8340 (p) REVERT: I 225 MET cc_start: 0.5007 (tpp) cc_final: 0.4706 (tmm) REVERT: J 225 MET cc_start: 0.4609 (mmp) cc_final: 0.3990 (ttm) outliers start: 78 outliers final: 62 residues processed: 421 average time/residue: 0.1946 time to fit residues: 130.9425 Evaluate side-chains 427 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 360 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 176 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 238 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 251 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 59 ASN E 139 ASN F 89 GLN F 106 ASN H 27 HIS J 34 HIS ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137337 restraints weight = 47579.683| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.13 r_work: 0.3555 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30181 Z= 0.146 Angle : 0.616 16.754 42938 Z= 0.320 Chirality : 0.039 0.356 5222 Planarity : 0.005 0.081 3770 Dihedral : 21.164 178.481 9622 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.42 % Allowed : 22.82 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.74 (0.17), residues: 2350 helix: 0.78 (0.17), residues: 943 sheet: -0.36 (0.25), residues: 414 loop : -1.82 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 136 TYR 0.021 0.002 TYR K 66 PHE 0.032 0.002 PHE C 92 TRP 0.028 0.002 TRP C 66 HIS 0.008 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (30178) covalent geometry : angle 0.61606 / 0.32 (42938) hydrogen bonds : bond 0.04270 / 4.36 ( 1052) hydrogen bonds : angle 4.42405 / 5.68 ( 2825) metal coordination : bond 0.00202 / 0.11 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7323.91 seconds wall clock time: 126 minutes 19.15 seconds (7579.15 seconds total)