Starting phenix.real_space_refine on Wed Nov 19 22:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_9622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_9622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_9622.map" model { file = "/net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_9622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ah3_9622/11_2025/6ah3_9622_neut.cif" } 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-2.0-5881/lib/python3.9/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: 7.04, per 1000 atoms: 0.25 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.95 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: 6.81 Time building geometry restraints manager: 3.59 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 1.50e-02 4.44e+03 4.76e+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: 42103 2.54 - 5.09: 723 5.09 - 7.63: 91 7.63 - 10.17: 16 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=" C VAL B 361 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N ASN D 215 " pdb=" CA ASN D 215 " pdb=" C ASN D 215 " ideal model delta sigma weight residual 111.14 105.88 5.26 1.08e+00 8.57e-01 2.38e+01 angle pdb=" N VAL H 111 " pdb=" CA VAL H 111 " pdb=" C VAL H 111 " ideal model delta sigma weight residual 108.82 102.91 5.91 1.22e+00 6.72e-01 2.34e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 120.20 127.41 -7.21 1.50e+00 4.44e-01 2.31e+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: 4696 0.072 - 0.144: 410 0.144 - 0.216: 110 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.020 Find NCS groups from input model: 0.140 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 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= 0.283 Angle : 0.829 12.714 42938 Z= 0.485 Chirality : 0.046 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 covalent geometry : bond 0.00352 (30178) covalent geometry : angle 0.82864 (42938) hydrogen bonds : bond 0.17348 ( 1052) hydrogen bonds : angle 7.06743 ( 2825) metal coordination : bond 0.58245 ( 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 : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 LEU cc_start: 0.6786 (pp) cc_final: 0.6550 (pp) REVERT: B 397 SER cc_start: 0.7668 (p) cc_final: 0.7433 (p) REVERT: C 95 ASN cc_start: 0.4908 (OUTLIER) cc_final: 0.4205 (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: 0.7832 (mt) REVERT: I 204 ILE cc_start: 0.7760 (tt) cc_final: 0.7530 (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: 0.2278 time to fit residues: 280.1596 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 : 0.935 ------------------------------------------------------------------------------- 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: 10.0000 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: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 251 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 463 ASN B 505 ASN B 506 ASN B 590 GLN B 677 ASN B 704 ASN B 808 HIS C 17 GLN C 25 ASN C 95 ASN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 89 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 143 HIS J 172 GLN J 243 HIS ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.193256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159245 restraints weight = 50349.742| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.24 r_work: 0.3863 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30181 Z= 0.214 Angle : 0.714 11.991 42938 Z= 0.364 Chirality : 0.041 0.309 5222 Planarity : 0.006 0.080 3770 Dihedral : 21.556 169.118 9626 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 4.34 % Allowed : 13.21 % Favored : 82.45 % 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: -2.03 (0.16), residues: 2350 helix: -0.80 (0.15), residues: 929 sheet: -0.76 (0.24), residues: 424 loop : -2.07 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 47 TYR 0.028 0.003 TYR K 66 PHE 0.026 0.003 PHE I 104 TRP 0.030 0.003 TRP C 44 HIS 0.010 0.002 HIS J 34 Details of bonding type rmsd covalent geometry : bond 0.00455 (30178) covalent geometry : angle 0.71395 (42938) hydrogen bonds : bond 0.04941 ( 1052) hydrogen bonds : angle 4.74105 ( 2825) metal coordination : bond 0.01367 ( 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 608 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 514 time to evaluate : 0.924 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 66 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7630 (mtt-85) REVERT: B 79 ASN cc_start: 0.7934 (t0) cc_final: 0.7697 (t0) REVERT: B 314 ILE cc_start: 0.6427 (mm) cc_final: 0.6026 (mm) REVERT: B 433 MET cc_start: 0.8221 (ptp) cc_final: 0.7914 (ptt) REVERT: B 720 MET cc_start: 0.4260 (mpp) cc_final: 0.2128 (ptt) REVERT: B 758 PHE cc_start: 0.6292 (m-80) cc_final: 0.6055 (m-80) REVERT: B 803 ASN cc_start: 0.8304 (t0) cc_final: 0.8080 (t0) REVERT: C 17 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.5366 (pp30) REVERT: C 33 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6564 (ttm) REVERT: C 95 ASN cc_start: 0.4711 (t0) cc_final: 0.4440 (t0) REVERT: C 125 PRO cc_start: 0.5693 (Cg_endo) cc_final: 0.5451 (Cg_exo) REVERT: C 129 MET cc_start: 0.4448 (tpp) cc_final: 0.4118 (tpp) REVERT: D 91 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6470 (tt0) REVERT: D 179 ASN cc_start: 0.7946 (m-40) cc_final: 0.7702 (m110) REVERT: F 94 ILE cc_start: 0.7109 (mp) cc_final: 0.6697 (mp) REVERT: F 133 LEU cc_start: 0.6351 (mt) cc_final: 0.6034 (mt) REVERT: G 84 ASP cc_start: 0.7883 (m-30) cc_final: 0.7637 (m-30) REVERT: H 37 TRP cc_start: 0.8512 (t60) cc_final: 0.8310 (t60) REVERT: H 111 VAL cc_start: 0.4907 (OUTLIER) cc_final: 0.4435 (t) REVERT: I 64 ASP cc_start: 0.6646 (m-30) cc_final: 0.6378 (m-30) REVERT: I 110 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8213 (tp) REVERT: I 159 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8433 (p) REVERT: I 166 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5861 (m-30) REVERT: I 168 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 225 MET cc_start: 0.4744 (tpp) cc_final: 0.4305 (tpp) REVERT: J 212 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7238 (ttpp) REVERT: J 222 SER cc_start: 0.5072 (m) cc_final: 0.4721 (p) REVERT: K 42 GLN cc_start: 0.7592 (mt0) cc_final: 0.7242 (mt0) outliers start: 94 outliers final: 47 residues processed: 572 average time/residue: 0.2001 time to fit residues: 179.2674 Evaluate side-chains 426 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG 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 258 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU 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 622 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 ASP 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 114 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 124 THR 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 81 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 159 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 100 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 488 ASN B 595 GLN B 665 GLN B 818 HIS B 850 GLN C 158 GLN E 36 HIS F 89 GLN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS K 38 ASN K 42 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146922 restraints weight = 48488.268| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.23 r_work: 0.3684 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6179 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= 0.166 Angle : 0.631 14.889 42938 Z= 0.321 Chirality : 0.038 0.214 5222 Planarity : 0.006 0.088 3770 Dihedral : 21.319 174.272 9622 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.67 % Allowed : 17.32 % Favored : 78.01 % 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: -1.33 (0.17), residues: 2350 helix: 0.01 (0.16), residues: 930 sheet: -0.69 (0.24), residues: 454 loop : -1.80 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 277 TYR 0.021 0.002 TYR K 66 PHE 0.024 0.002 PHE B 657 TRP 0.017 0.002 TRP C 44 HIS 0.008 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00365 (30178) covalent geometry : angle 0.63112 (42938) hydrogen bonds : bond 0.04277 ( 1052) hydrogen bonds : angle 4.54097 ( 2825) metal coordination : bond 0.00788 ( 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 536 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 435 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8230 (t0) cc_final: 0.8012 (t0) REVERT: B 193 LYS cc_start: 0.7715 (mttt) cc_final: 0.7300 (tptt) REVERT: B 204 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 488 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (m-40) REVERT: B 758 PHE cc_start: 0.6793 (m-80) cc_final: 0.6579 (m-80) REVERT: C 125 PRO cc_start: 0.6020 (Cg_endo) cc_final: 0.5779 (Cg_exo) REVERT: C 133 LYS cc_start: 0.5735 (mttt) cc_final: 0.5528 (mttp) REVERT: D 91 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6881 (tt0) REVERT: D 125 LYS cc_start: 0.7179 (mppt) cc_final: 0.6829 (ptmt) REVERT: D 167 SER cc_start: 0.8240 (t) cc_final: 0.7868 (t) REVERT: D 273 MET cc_start: 0.8089 (tpp) cc_final: 0.7649 (mpp) REVERT: E 62 ASP cc_start: 0.5280 (OUTLIER) cc_final: 0.4551 (m-30) REVERT: E 134 ASN cc_start: 0.8861 (t0) cc_final: 0.8565 (m-40) REVERT: F 94 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7887 (mp) REVERT: G 58 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7269 (tp40) REVERT: G 84 ASP cc_start: 0.8125 (m-30) cc_final: 0.7799 (m-30) REVERT: H 31 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7293 (tm-30) REVERT: H 37 TRP cc_start: 0.8517 (t60) cc_final: 0.8227 (t60) REVERT: H 44 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7161 (tpp-160) REVERT: I 81 TYR cc_start: 0.8596 (m-80) cc_final: 0.8117 (m-80) REVERT: I 97 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7268 (mt) REVERT: I 159 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8376 (p) REVERT: I 166 ASP cc_start: 0.6195 (t70) cc_final: 0.5819 (m-30) REVERT: I 200 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7428 (mt-10) REVERT: I 225 MET cc_start: 0.4886 (tpp) cc_final: 0.4449 (tmm) REVERT: J 63 ILE cc_start: 0.9028 (mm) cc_final: 0.8803 (mt) REVERT: J 168 GLN cc_start: 0.8004 (tp40) cc_final: 0.7560 (tp40) REVERT: J 246 THR cc_start: 0.8834 (m) cc_final: 0.8626 (p) outliers start: 101 outliers final: 59 residues processed: 503 average time/residue: 0.2020 time to fit residues: 159.4425 Evaluate side-chains 427 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 362 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 153 SER 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 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 415 CYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 488 ASN 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 559 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 850 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 70 SER 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 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 122 ARG 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 87 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 196 MET 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 60 THR Chi-restraints excluded: chain K residue 65 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 67 optimal weight: 3.9990 chunk 139 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 262 optimal weight: 0.0870 chunk 263 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 226 optimal weight: 0.0980 chunk 182 optimal weight: 0.3980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 488 ASN B 808 HIS C 123 GLN D 179 ASN E 139 ASN F 111 GLN F 113 ASN G 58 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 ASN K 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.185725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149626 restraints weight = 48558.106| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.21 r_work: 0.3732 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30181 Z= 0.105 Angle : 0.546 14.465 42938 Z= 0.276 Chirality : 0.035 0.199 5222 Planarity : 0.005 0.066 3770 Dihedral : 21.178 173.452 9622 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.93 % Allowed : 19.08 % Favored : 77.00 % 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: -0.82 (0.17), residues: 2350 helix: 0.59 (0.17), residues: 933 sheet: -0.35 (0.25), residues: 436 loop : -1.73 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 67 TYR 0.017 0.001 TYR J 160 PHE 0.015 0.002 PHE J 104 TRP 0.014 0.001 TRP C 44 HIS 0.005 0.001 HIS J 34 Details of bonding type rmsd covalent geometry : bond 0.00221 (30178) covalent geometry : angle 0.54584 (42938) hydrogen bonds : bond 0.03410 ( 1052) hydrogen bonds : angle 4.20065 ( 2825) metal coordination : bond 0.00161 ( 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 486 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 401 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8313 (mmt-90) REVERT: B 112 MET cc_start: 0.8515 (mtp) cc_final: 0.8192 (mtp) REVERT: B 193 LYS cc_start: 0.7664 (mttt) cc_final: 0.7265 (tptt) REVERT: B 204 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7677 (tp) REVERT: B 645 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6606 (pptt) REVERT: B 758 PHE cc_start: 0.6950 (m-80) cc_final: 0.6632 (m-80) REVERT: C 113 TYR cc_start: 0.6097 (t80) cc_final: 0.5839 (t80) REVERT: C 125 PRO cc_start: 0.5965 (Cg_endo) cc_final: 0.5618 (Cg_exo) REVERT: C 140 MET cc_start: 0.4496 (mmp) cc_final: 0.4243 (mmp) REVERT: D 91 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6831 (tt0) REVERT: D 125 LYS cc_start: 0.7500 (mppt) cc_final: 0.7151 (ptmt) REVERT: D 142 MET cc_start: 0.5868 (tpt) cc_final: 0.5425 (tpt) REVERT: D 151 ILE cc_start: 0.8136 (mm) cc_final: 0.7766 (mm) REVERT: D 167 SER cc_start: 0.8117 (t) cc_final: 0.7766 (t) REVERT: D 178 TYR cc_start: 0.8577 (m-80) cc_final: 0.8163 (m-80) REVERT: D 273 MET cc_start: 0.7980 (tpp) cc_final: 0.7622 (mpp) REVERT: E 50 GLN cc_start: 0.7486 (pp30) cc_final: 0.7061 (pt0) REVERT: E 134 ASN cc_start: 0.8756 (t0) cc_final: 0.8515 (m-40) REVERT: E 138 LEU cc_start: 0.8462 (tp) cc_final: 0.8241 (tt) REVERT: F 9 GLU cc_start: 0.8309 (mp0) cc_final: 0.8109 (pm20) REVERT: F 30 VAL cc_start: 0.8653 (t) cc_final: 0.8439 (p) REVERT: G 58 GLN cc_start: 0.7528 (tp40) cc_final: 0.7166 (tp40) REVERT: G 76 LEU cc_start: 0.8018 (mt) cc_final: 0.7472 (mt) REVERT: G 80 CYS cc_start: 0.7670 (m) cc_final: 0.7317 (m) REVERT: G 84 ASP cc_start: 0.8194 (m-30) cc_final: 0.7980 (m-30) REVERT: G 118 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6542 (tm-30) REVERT: H 31 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7347 (tm-30) REVERT: H 37 TRP cc_start: 0.8528 (t60) cc_final: 0.8227 (t60) REVERT: H 44 ARG cc_start: 0.7575 (tpp-160) cc_final: 0.7014 (tpp-160) REVERT: H 101 GLN cc_start: 0.5876 (pp30) cc_final: 0.5588 (pp30) REVERT: H 123 MET cc_start: 0.7117 (tpp) cc_final: 0.6311 (tmm) REVERT: I 81 TYR cc_start: 0.8454 (m-80) cc_final: 0.7978 (m-80) REVERT: I 97 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7476 (mt) REVERT: I 159 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8356 (p) REVERT: I 166 ASP cc_start: 0.6285 (t70) cc_final: 0.6017 (m-30) REVERT: J 137 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8350 (mp) REVERT: J 212 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7498 (ttpp) REVERT: J 219 ASP cc_start: 0.7977 (t0) cc_final: 0.7736 (m-30) REVERT: J 246 THR cc_start: 0.8877 (m) cc_final: 0.8670 (p) REVERT: J 266 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.6327 (mt) REVERT: K 72 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7765 (tt) REVERT: K 92 LYS cc_start: 0.7989 (tmtt) cc_final: 0.7667 (ttpt) REVERT: K 102 LYS cc_start: 0.6543 (tptp) cc_final: 0.6117 (tptp) outliers start: 85 outliers final: 51 residues processed: 447 average time/residue: 0.2066 time to fit residues: 144.8087 Evaluate side-chains 418 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 359 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 100 THR 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 228 VAL Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 250 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 419 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 566 LEU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU 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 139 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ARG 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 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 97 LEU 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 30 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 212 LYS 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 32 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 123 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 246 ASN ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN F 89 GLN F 106 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN J 55 ASN J 245 GLN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.161930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122701 restraints weight = 46600.566| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.22 r_work: 0.3334 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.9117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 30181 Z= 0.395 Angle : 0.908 18.935 42938 Z= 0.459 Chirality : 0.048 0.254 5222 Planarity : 0.007 0.072 3770 Dihedral : 21.482 176.171 9622 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 7.02 % Allowed : 17.78 % Favored : 75.20 % 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: -1.53 (0.17), residues: 2350 helix: -0.16 (0.16), residues: 938 sheet: -0.93 (0.24), residues: 429 loop : -1.84 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 202 TYR 0.037 0.004 TYR K 66 PHE 0.047 0.004 PHE H 49 TRP 0.054 0.004 TRP C 66 HIS 0.014 0.003 HIS J 34 Details of bonding type rmsd covalent geometry : bond 0.00874 (30178) covalent geometry : angle 0.90759 (42938) hydrogen bonds : bond 0.06902 ( 1052) hydrogen bonds : angle 5.27584 ( 2825) metal coordination : bond 0.00737 ( 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 554 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 402 time to evaluate : 0.832 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: B 57 LEU cc_start: 0.7733 (pt) cc_final: 0.6897 (pt) REVERT: B 112 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: B 448 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8410 (p90) REVERT: B 461 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8146 (ptmm) REVERT: B 621 LYS cc_start: 0.8844 (tttp) cc_final: 0.8419 (ttpt) REVERT: B 629 MET cc_start: 0.8406 (tpp) cc_final: 0.8120 (ttt) REVERT: B 645 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7520 (pptt) REVERT: B 652 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: B 672 ASP cc_start: 0.7856 (t0) cc_final: 0.7512 (m-30) REVERT: B 786 GLU cc_start: 0.8519 (pm20) cc_final: 0.8010 (pt0) REVERT: C 74 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7097 (tt0) REVERT: C 113 TYR cc_start: 0.6531 (t80) cc_final: 0.6224 (t80) REVERT: C 173 LYS cc_start: 0.7427 (tptt) cc_final: 0.7160 (tptt) REVERT: C 183 LYS cc_start: 0.8217 (mttt) cc_final: 0.8001 (mtmm) REVERT: D 93 ILE cc_start: 0.8663 (pp) cc_final: 0.8417 (mt) REVERT: D 110 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7750 (t0) REVERT: D 142 MET cc_start: 0.6389 (tpt) cc_final: 0.6137 (tpt) REVERT: D 167 SER cc_start: 0.8755 (t) cc_final: 0.8316 (m) REVERT: E 124 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8679 (tttm) REVERT: E 134 ASN cc_start: 0.8640 (t0) cc_final: 0.8437 (m-40) REVERT: F 9 GLU cc_start: 0.8356 (mp0) cc_final: 0.8113 (pm20) REVERT: F 94 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8983 (mt) REVERT: F 106 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6879 (p0) REVERT: G 58 GLN cc_start: 0.8550 (tp40) cc_final: 0.8161 (tp40) REVERT: G 80 CYS cc_start: 0.8128 (m) cc_final: 0.7892 (m) REVERT: G 84 ASP cc_start: 0.8254 (m-30) cc_final: 0.8019 (m-30) REVERT: H 31 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7276 (tm-30) REVERT: H 37 TRP cc_start: 0.8730 (t60) cc_final: 0.8478 (t60) REVERT: H 87 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7183 (t) REVERT: H 123 MET cc_start: 0.6939 (tpp) cc_final: 0.6214 (tmm) REVERT: H 126 GLU cc_start: 0.7537 (pt0) cc_final: 0.7030 (pt0) REVERT: I 73 MET cc_start: 0.8359 (mmm) cc_final: 0.7721 (mtp) REVERT: I 196 MET cc_start: 0.8080 (mpp) cc_final: 0.7710 (mtm) REVERT: I 238 LEU cc_start: 0.8141 (tt) cc_final: 0.7830 (mt) REVERT: J 183 SER cc_start: 0.9631 (OUTLIER) cc_final: 0.9416 (p) REVERT: J 204 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (tp) REVERT: J 266 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.7639 (mt) REVERT: K 46 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5733 (m-80) outliers start: 152 outliers final: 73 residues processed: 517 average time/residue: 0.2152 time to fit residues: 172.5144 Evaluate side-chains 419 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 333 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 THR 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 335 GLN 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 448 PHE Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 546 VAL 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 581 ILE Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 131 THR 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 158 THR Chi-restraints excluded: chain D residue 218 ASP 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 26 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 96 VAL 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 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 108 LYS 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 90 ILE Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 234 LEU 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 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 262 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.0070 chunk 219 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 808 HIS B 850 GLN C 17 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 106 ASN I 40 HIS I 240 ASN J 34 HIS J 49 HIS K 33 HIS K 38 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129337 restraints weight = 46373.294| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.14 r_work: 0.3451 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.9128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30181 Z= 0.132 Angle : 0.617 16.456 42938 Z= 0.315 Chirality : 0.037 0.208 5222 Planarity : 0.005 0.057 3770 Dihedral : 21.314 178.675 9622 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.43 % Allowed : 21.66 % Favored : 73.90 % 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: -0.97 (0.17), residues: 2350 helix: 0.45 (0.17), residues: 947 sheet: -0.60 (0.25), residues: 417 loop : -1.73 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 321 TYR 0.023 0.002 TYR F 110 PHE 0.035 0.002 PHE J 104 TRP 0.032 0.002 TRP C 44 HIS 0.006 0.001 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.00283 (30178) covalent geometry : angle 0.61731 (42938) hydrogen bonds : bond 0.03907 ( 1052) hydrogen bonds : angle 4.56152 ( 2825) metal coordination : bond 0.00154 ( 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 481 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 385 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 486 GLU cc_start: 0.7271 (pm20) cc_final: 0.6947 (pm20) REVERT: B 621 LYS cc_start: 0.8754 (tttp) cc_final: 0.8204 (ttpt) REVERT: B 652 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: B 672 ASP cc_start: 0.7710 (t0) cc_final: 0.7431 (m-30) REVERT: B 675 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8228 (mm-40) REVERT: C 17 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6460 (pp30) REVERT: C 33 MET cc_start: 0.5899 (mtp) cc_final: 0.5470 (mmt) REVERT: C 113 TYR cc_start: 0.6388 (t80) cc_final: 0.6066 (t80) REVERT: C 151 LYS cc_start: 0.6906 (pttt) cc_final: 0.6318 (mmtm) REVERT: D 167 SER cc_start: 0.8698 (t) cc_final: 0.8295 (m) REVERT: D 238 ASP cc_start: 0.5038 (OUTLIER) cc_final: 0.4046 (p0) REVERT: E 12 GLU cc_start: 0.7748 (tt0) cc_final: 0.7497 (tt0) REVERT: E 108 ASP cc_start: 0.5869 (p0) cc_final: 0.5596 (p0) REVERT: E 124 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8600 (tttm) REVERT: F 30 VAL cc_start: 0.9045 (t) cc_final: 0.8701 (p) REVERT: F 49 ILE cc_start: 0.8663 (mt) cc_final: 0.8403 (mt) REVERT: F 94 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (mt) REVERT: F 106 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6470 (p0) REVERT: F 130 GLU cc_start: 0.7303 (tt0) cc_final: 0.6942 (tt0) REVERT: F 131 GLU cc_start: 0.6785 (mt-10) cc_final: 0.5827 (pm20) REVERT: G 26 HIS cc_start: 0.7875 (t-90) cc_final: 0.7521 (t-90) REVERT: G 58 GLN cc_start: 0.8230 (tp40) cc_final: 0.7777 (tp40) REVERT: G 80 CYS cc_start: 0.8092 (m) cc_final: 0.7669 (m) REVERT: G 118 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7110 (tm-30) REVERT: H 31 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7641 (tm-30) REVERT: H 117 LEU cc_start: 0.7793 (tt) cc_final: 0.7591 (tp) REVERT: I 5 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8011 (pp) REVERT: I 196 MET cc_start: 0.7765 (mpp) cc_final: 0.7511 (mtm) REVERT: J 137 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8176 (mt) outliers start: 96 outliers final: 53 residues processed: 453 average time/residue: 0.2030 time to fit residues: 145.6111 Evaluate side-chains 408 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 434 ILE 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 652 GLU Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU 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 16 ILE 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 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 103 SER 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 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 127 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 161 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 chunk 81 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 0.0270 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 106 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 HIS J 151 ASN K 31 GLN K 59 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131723 restraints weight = 46445.594| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.13 r_work: 0.3475 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.9146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30181 Z= 0.114 Angle : 0.578 14.825 42938 Z= 0.294 Chirality : 0.036 0.214 5222 Planarity : 0.004 0.060 3770 Dihedral : 21.142 174.860 9622 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.42 % Allowed : 23.37 % Favored : 73.21 % 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: -0.66 (0.18), residues: 2350 helix: 0.81 (0.17), residues: 944 sheet: -0.56 (0.25), residues: 425 loop : -1.60 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 16 TYR 0.019 0.001 TYR C 19 PHE 0.020 0.002 PHE B 657 TRP 0.016 0.001 TRP C 44 HIS 0.011 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00245 (30178) covalent geometry : angle 0.57799 (42938) hydrogen bonds : bond 0.03586 ( 1052) hydrogen bonds : angle 4.36469 ( 2825) metal coordination : bond 0.00150 ( 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 460 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 386 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 486 GLU cc_start: 0.7212 (pm20) cc_final: 0.6969 (pm20) REVERT: B 652 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: B 672 ASP cc_start: 0.7789 (t0) cc_final: 0.7480 (m-30) REVERT: B 786 GLU cc_start: 0.8697 (pm20) cc_final: 0.8184 (pt0) REVERT: B 819 ASP cc_start: 0.8092 (t0) cc_final: 0.7773 (t70) REVERT: C 33 MET cc_start: 0.5687 (mtp) cc_final: 0.5397 (mmt) REVERT: C 113 TYR cc_start: 0.6447 (t80) cc_final: 0.6130 (t80) REVERT: D 167 SER cc_start: 0.8821 (t) cc_final: 0.8304 (m) REVERT: D 203 ASP cc_start: 0.8371 (t0) cc_final: 0.8098 (t0) REVERT: D 238 ASP cc_start: 0.4951 (OUTLIER) cc_final: 0.4383 (p0) REVERT: E 12 GLU cc_start: 0.7805 (tt0) cc_final: 0.7543 (tt0) REVERT: E 101 MET cc_start: 0.8859 (tmm) cc_final: 0.8553 (tmm) REVERT: F 30 VAL cc_start: 0.9069 (t) cc_final: 0.8782 (p) REVERT: F 49 ILE cc_start: 0.8574 (mt) cc_final: 0.8356 (mt) REVERT: F 94 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8862 (mt) REVERT: F 106 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6468 (p0) REVERT: F 122 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7719 (mtm180) REVERT: F 131 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6022 (pm20) REVERT: G 26 HIS cc_start: 0.7685 (t-90) cc_final: 0.7328 (t-90) REVERT: G 58 GLN cc_start: 0.8308 (tp40) cc_final: 0.7938 (tp40) REVERT: G 118 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6992 (tm-30) REVERT: H 32 MET cc_start: 0.8082 (tpp) cc_final: 0.7864 (tpp) REVERT: H 117 LEU cc_start: 0.7864 (tt) cc_final: 0.7618 (tp) REVERT: I 5 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8044 (pp) REVERT: I 81 TYR cc_start: 0.8439 (m-80) cc_final: 0.8031 (m-80) REVERT: J 157 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7720 (tt0) outliers start: 74 outliers final: 42 residues processed: 436 average time/residue: 0.1981 time to fit residues: 137.6291 Evaluate side-chains 393 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 558 VAL 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 874 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU 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 126 ILE Chi-restraints excluded: chain F residue 20 THR 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 134 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 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 157 GLU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 57 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN B 236 HIS ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 573 ASN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS C 17 GLN C 40 GLN D 179 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 106 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123749 restraints weight = 46352.662| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.08 r_work: 0.3354 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.9758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30181 Z= 0.218 Angle : 0.697 17.540 42938 Z= 0.353 Chirality : 0.040 0.226 5222 Planarity : 0.005 0.064 3770 Dihedral : 21.150 169.624 9622 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.43 % Allowed : 22.54 % Favored : 73.03 % 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: -0.84 (0.18), residues: 2350 helix: 0.65 (0.17), residues: 950 sheet: -0.75 (0.25), residues: 429 loop : -1.64 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 136 TYR 0.026 0.002 TYR F 110 PHE 0.054 0.003 PHE D 253 TRP 0.018 0.002 TRP H 37 HIS 0.008 0.002 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00491 (30178) covalent geometry : angle 0.69657 (42938) hydrogen bonds : bond 0.04936 ( 1052) hydrogen bonds : angle 4.64847 ( 2825) metal coordination : bond 0.00384 ( 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 442 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 346 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.8271 (tpp) cc_final: 0.7973 (ttm) REVERT: B 672 ASP cc_start: 0.7918 (t0) cc_final: 0.7547 (m-30) REVERT: B 786 GLU cc_start: 0.8644 (pm20) cc_final: 0.8202 (pt0) REVERT: C 17 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6262 (pp30) REVERT: C 33 MET cc_start: 0.5637 (mtp) cc_final: 0.5436 (mmt) REVERT: C 113 TYR cc_start: 0.6639 (t80) cc_final: 0.6241 (t80) REVERT: D 167 SER cc_start: 0.8922 (t) cc_final: 0.8449 (m) REVERT: D 208 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6835 (t80) REVERT: E 12 GLU cc_start: 0.7906 (tt0) cc_final: 0.7528 (tt0) REVERT: E 124 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8642 (tttm) REVERT: F 30 VAL cc_start: 0.9092 (t) cc_final: 0.8832 (p) REVERT: F 46 TYR cc_start: 0.8156 (m-80) cc_final: 0.7792 (m-10) REVERT: F 94 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9038 (mt) REVERT: I 5 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8045 (pp) REVERT: I 73 MET cc_start: 0.8284 (mmm) cc_final: 0.7594 (mtp) REVERT: I 81 TYR cc_start: 0.8609 (m-80) cc_final: 0.8260 (m-80) REVERT: I 234 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8226 (mt) REVERT: J 157 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: J 225 MET cc_start: 0.5826 (mmp) cc_final: 0.5138 (mtt) REVERT: J 266 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.7748 (mt) outliers start: 96 outliers final: 68 residues processed: 414 average time/residue: 0.2033 time to fit residues: 134.7633 Evaluate side-chains 398 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 322 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 369 ARG 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 434 ILE Chi-restraints excluded: chain B residue 466 GLN 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 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 208 PHE 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 43 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 96 VAL 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 20 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 108 LYS 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 29 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 9 TRP 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 59 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 234 LEU 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 157 GLU Chi-restraints excluded: chain J residue 199 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 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 109 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 122 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 466 GLN B 573 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN D 179 ASN E 36 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 10 GLN H 27 HIS J 34 HIS J 245 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128181 restraints weight = 46299.747| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.09 r_work: 0.3429 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.9754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30181 Z= 0.123 Angle : 0.597 15.275 42938 Z= 0.303 Chirality : 0.037 0.212 5222 Planarity : 0.005 0.064 3770 Dihedral : 21.097 168.378 9622 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.83 % Allowed : 23.09 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2350 helix: 0.95 (0.17), residues: 945 sheet: -0.50 (0.26), residues: 413 loop : -1.62 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 136 TYR 0.018 0.001 TYR J 160 PHE 0.042 0.002 PHE D 253 TRP 0.013 0.002 TRP H 37 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00274 (30178) covalent geometry : angle 0.59723 (42938) hydrogen bonds : bond 0.03684 ( 1052) hydrogen bonds : angle 4.38266 ( 2825) metal coordination : bond 0.00164 ( 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 431 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 672 ASP cc_start: 0.7916 (t0) cc_final: 0.7533 (m-30) REVERT: B 676 ARG cc_start: 0.5127 (ttp-170) cc_final: 0.4765 (ttp80) REVERT: B 786 GLU cc_start: 0.8626 (pm20) cc_final: 0.8258 (pt0) REVERT: B 803 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: C 18 VAL cc_start: 0.7822 (t) cc_final: 0.7606 (t) REVERT: C 113 TYR cc_start: 0.6567 (t80) cc_final: 0.6187 (t80) REVERT: D 167 SER cc_start: 0.8859 (t) cc_final: 0.8380 (m) REVERT: D 208 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6636 (t80) REVERT: E 101 MET cc_start: 0.8860 (tmm) cc_final: 0.8572 (tmm) REVERT: E 103 MET cc_start: 0.8399 (ttm) cc_final: 0.8192 (ttp) REVERT: E 124 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (tttm) REVERT: F 30 VAL cc_start: 0.9070 (t) cc_final: 0.8761 (p) REVERT: F 46 TYR cc_start: 0.8110 (m-80) cc_final: 0.7678 (m-10) REVERT: F 122 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7582 (mtm180) REVERT: F 131 GLU cc_start: 0.7570 (pt0) cc_final: 0.6592 (pm20) REVERT: G 26 HIS cc_start: 0.7852 (t-90) cc_final: 0.7528 (t-90) REVERT: G 118 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6912 (tm-30) REVERT: H 31 GLN cc_start: 0.7556 (tp40) cc_final: 0.7149 (tm-30) REVERT: H 119 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7797 (mm) REVERT: I 5 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (pp) REVERT: I 81 TYR cc_start: 0.8495 (m-80) cc_final: 0.8119 (m-80) REVERT: I 234 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8122 (mt) REVERT: J 157 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: J 162 TYR cc_start: 0.8232 (m-10) cc_final: 0.8020 (m-10) REVERT: J 225 MET cc_start: 0.5240 (mmp) cc_final: 0.4732 (mtt) REVERT: J 266 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7434 (mt) outliers start: 83 outliers final: 62 residues processed: 407 average time/residue: 0.1882 time to fit residues: 124.6008 Evaluate side-chains 404 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 334 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 466 GLN 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 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU 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 20 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 109 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 G residue 96 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 HIS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 234 LEU 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 127 ASP Chi-restraints excluded: chain J residue 157 GLU 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 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 25 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 221 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN F 106 ASN H 27 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128813 restraints weight = 45854.513| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.08 r_work: 0.3440 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.9786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30181 Z= 0.122 Angle : 0.602 15.738 42938 Z= 0.303 Chirality : 0.037 0.205 5222 Planarity : 0.004 0.063 3770 Dihedral : 21.043 168.483 9622 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.37 % Allowed : 23.46 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.49 (0.18), residues: 2350 helix: 1.01 (0.17), residues: 947 sheet: -0.50 (0.26), residues: 420 loop : -1.58 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 136 TYR 0.018 0.001 TYR F 110 PHE 0.039 0.002 PHE D 253 TRP 0.013 0.001 TRP C 44 HIS 0.005 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00271 (30178) covalent geometry : angle 0.60154 (42938) hydrogen bonds : bond 0.03664 ( 1052) hydrogen bonds : angle 4.35827 ( 2825) metal coordination : bond 0.00146 ( 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 417 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 655 ASP cc_start: 0.5946 (p0) cc_final: 0.5656 (p0) REVERT: B 672 ASP cc_start: 0.7907 (t0) cc_final: 0.7520 (m-30) REVERT: B 786 GLU cc_start: 0.8643 (pm20) cc_final: 0.8241 (pt0) REVERT: B 803 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: C 113 TYR cc_start: 0.6619 (t80) cc_final: 0.6301 (t80) REVERT: C 133 LYS cc_start: 0.6306 (mmtt) cc_final: 0.6095 (tptt) REVERT: D 167 SER cc_start: 0.8842 (t) cc_final: 0.8361 (m) REVERT: D 203 ASP cc_start: 0.8371 (t0) cc_final: 0.8094 (t0) REVERT: D 208 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6542 (t80) REVERT: E 12 GLU cc_start: 0.7815 (tt0) cc_final: 0.7453 (tt0) REVERT: E 101 MET cc_start: 0.8858 (tmm) cc_final: 0.8601 (tmm) REVERT: E 103 MET cc_start: 0.8571 (ttm) cc_final: 0.8311 (ttp) REVERT: E 124 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8468 (tttm) REVERT: F 30 VAL cc_start: 0.9101 (t) cc_final: 0.8807 (p) REVERT: F 46 TYR cc_start: 0.8115 (m-80) cc_final: 0.7682 (m-10) REVERT: F 122 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7726 (mtm110) REVERT: F 131 GLU cc_start: 0.7630 (pt0) cc_final: 0.6567 (pm20) REVERT: G 26 HIS cc_start: 0.7876 (t-90) cc_final: 0.7531 (t-90) REVERT: G 118 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7021 (tm-30) REVERT: H 31 GLN cc_start: 0.7471 (tp40) cc_final: 0.7110 (tm-30) REVERT: H 119 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7793 (mm) REVERT: I 5 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8036 (pp) REVERT: I 81 TYR cc_start: 0.8473 (m-80) cc_final: 0.8101 (m-80) REVERT: I 234 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8072 (mt) REVERT: J 157 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: J 162 TYR cc_start: 0.8233 (m-10) cc_final: 0.8001 (m-10) REVERT: J 178 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7920 (mtp-110) REVERT: J 225 MET cc_start: 0.4937 (mmp) cc_final: 0.4434 (mtt) REVERT: J 266 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7441 (mt) outliers start: 73 outliers final: 59 residues processed: 396 average time/residue: 0.1882 time to fit residues: 121.4095 Evaluate side-chains 393 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 GLN 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 558 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 LEU 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 20 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 HIS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 234 LEU 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 157 GLU 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 32 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 176 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 573 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 197 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN F 129 GLN H 27 HIS K 130 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127703 restraints weight = 46159.624| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.06 r_work: 0.3421 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.9887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30181 Z= 0.137 Angle : 0.606 15.707 42938 Z= 0.306 Chirality : 0.037 0.217 5222 Planarity : 0.005 0.063 3770 Dihedral : 21.008 168.784 9622 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.46 % Allowed : 23.42 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.18), residues: 2350 helix: 1.03 (0.17), residues: 945 sheet: -0.51 (0.26), residues: 419 loop : -1.57 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 136 TYR 0.022 0.001 TYR F 110 PHE 0.039 0.002 PHE D 253 TRP 0.046 0.002 TRP C 168 HIS 0.005 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00307 (30178) covalent geometry : angle 0.60577 (42938) hydrogen bonds : bond 0.03811 ( 1052) hydrogen bonds : angle 4.36765 ( 2825) metal coordination : bond 0.00204 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.11 seconds wall clock time: 131 minutes 40.28 seconds (7900.28 seconds total)