Starting phenix.real_space_refine on Fri Feb 6 22:38:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.map" model { file = "/net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g44_51023/02_2026/9g44_51023.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 135 5.49 5 Mg 2 5.21 5 S 86 5.16 5 C 17336 2.51 5 N 4792 2.21 5 O 5700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28051 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1345 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2507 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "G" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2507 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "H" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2503 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2501 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1275 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Chain: "K" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 686 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 850 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2614 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6565 Classifications: {'peptide': 828} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 795} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2241 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 272} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2455 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 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} Time building chain proxies: 6.29, per 1000 atoms: 0.22 Number of scatterers: 28051 At special positions: 0 Unit cell: (211.11, 129.27, 145.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 135 15.00 Mg 2 11.99 O 5700 8.00 N 4792 7.00 C 17336 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: 2.29 Conformation dependent library (CDL) restraints added in 945.9 milliseconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5944 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 49 sheets defined 34.8% alpha, 24.1% beta 41 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'C' and resid 2 through 22 Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.320A pdb=" N GLY C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 105 through 119 removed outlier: 3.868A pdb=" N LYS C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 90 removed outlier: 3.906A pdb=" N PHE F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 94 Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 104 through 110 removed outlier: 4.343A pdb=" N VAL F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 117 Processing helix chain 'F' and resid 188 through 192 removed outlier: 4.358A pdb=" N PHE F 191 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 202 through 218 removed outlier: 3.561A pdb=" N ALA F 207 " --> pdb=" O GLY F 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.549A pdb=" N VAL F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 removed outlier: 3.923A pdb=" N ARG F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 81 through 90 removed outlier: 3.502A pdb=" N ILE G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS G 87 " --> pdb=" O ASN G 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 94 Processing helix chain 'G' and resid 96 through 100 Processing helix chain 'G' and resid 104 through 110 removed outlier: 4.279A pdb=" N VAL G 108 " --> pdb=" O ASN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 202 through 218 removed outlier: 3.503A pdb=" N ILE G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 265 removed outlier: 3.633A pdb=" N VAL G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 removed outlier: 3.788A pdb=" N ARG G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 4.065A pdb=" N ILE G 300 " --> pdb=" O GLU G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 81 through 90 removed outlier: 3.580A pdb=" N HIS H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 100 removed outlier: 5.640A pdb=" N PHE H 95 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP H 96 " --> pdb=" O GLN H 93 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU H 97 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 110 removed outlier: 4.324A pdb=" N VAL H 108 " --> pdb=" O ASN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 202 through 218 removed outlier: 3.789A pdb=" N LEU H 217 " --> pdb=" O TYR H 213 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN H 218 " --> pdb=" O ILE H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.563A pdb=" N ASN H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.663A pdb=" N ARG H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 90 removed outlier: 3.628A pdb=" N ILE I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 94 removed outlier: 3.661A pdb=" N ALA I 94 " --> pdb=" O ARG I 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 91 through 94' Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'I' and resid 104 through 110 removed outlier: 4.192A pdb=" N VAL I 108 " --> pdb=" O ASN I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 201 through 218 removed outlier: 4.789A pdb=" N VAL I 205 " --> pdb=" O GLY I 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 216 " --> pdb=" O ASN I 212 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU I 217 " --> pdb=" O TYR I 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN I 218 " --> pdb=" O ILE I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 291 through 296 removed outlier: 4.126A pdb=" N ARG I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 142 through 150 removed outlier: 4.466A pdb=" N ASP B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.359A pdb=" N VAL B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.737A pdb=" N THR B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.713A pdb=" N ASP B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.628A pdb=" N GLY B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.810A pdb=" N HIS A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 128 " --> pdb=" O HIS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.838A pdb=" N GLN A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.923A pdb=" N LYS A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 286 removed outlier: 3.778A pdb=" N ILE A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 325 through 354 removed outlier: 4.214A pdb=" N THR A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.900A pdb=" N LEU A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.728A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.692A pdb=" N GLN A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 519 through 526 removed outlier: 4.385A pdb=" N ASP A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.650A pdb=" N VAL A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 removed outlier: 3.814A pdb=" N LEU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.692A pdb=" N ALA A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 670 removed outlier: 3.984A pdb=" N PHE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 665 " --> pdb=" O TRP A 661 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.936A pdb=" N TYR A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 813 removed outlier: 3.548A pdb=" N ASP A 797 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.990A pdb=" N HIS A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 922 removed outlier: 4.040A pdb=" N LEU A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 939 removed outlier: 3.544A pdb=" N LEU A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 947 removed outlier: 6.483A pdb=" N GLY A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU A 944 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 945 " --> pdb=" O GLY A 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.905A pdb=" N ILE D 71 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.502A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 201 through 218 removed outlier: 4.551A pdb=" N VAL D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 81 through 90 removed outlier: 3.597A pdb=" N HIS E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 94 removed outlier: 3.661A pdb=" N ALA E 94 " --> pdb=" O ARG E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 91 through 94' Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.686A pdb=" N TYR E 99 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 removed outlier: 4.387A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 202 through 218 removed outlier: 3.692A pdb=" N ILE E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 291 through 295 Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.761A pdb=" N PHE C 140 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 81 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 79 through 80 removed outlier: 3.662A pdb=" N PHE F 137 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 138 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 172 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 79 through 80 removed outlier: 3.662A pdb=" N PHE F 137 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 138 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 172 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE F 12 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER F 9 " --> pdb=" O TYR F 284 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR F 284 " --> pdb=" O SER F 9 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP F 11 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL F 282 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS F 13 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE F 280 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS F 15 " --> pdb=" O ASP F 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.634A pdb=" N TRP F 24 " --> pdb=" O PRO F 44 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY F 26 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR F 42 " --> pdb=" O GLY F 26 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR F 28 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN F 40 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N VAL F 38 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N SER F 162 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN F 40 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR F 164 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR F 42 " --> pdb=" O THR F 164 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE F 161 " --> pdb=" O TYR F 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 56 removed outlier: 7.376A pdb=" N TYR F 64 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'F' and resid 184 through 186 removed outlier: 5.556A pdb=" N GLY F 244 " --> pdb=" O SER F 229 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER F 229 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU F 246 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE F 227 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 79 through 80 removed outlier: 3.637A pdb=" N PHE G 137 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 138 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 172 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 79 through 80 removed outlier: 3.637A pdb=" N PHE G 137 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 138 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 172 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 169 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER G 9 " --> pdb=" O ASN G 285 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP G 279 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU G 17 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL G 277 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HIS G 19 " --> pdb=" O MET G 275 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N MET G 275 " --> pdb=" O HIS G 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 24 through 31 removed outlier: 6.800A pdb=" N TRP G 24 " --> pdb=" O PRO G 44 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY G 26 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR G 42 " --> pdb=" O GLY G 26 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR G 28 " --> pdb=" O ASN G 40 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN G 40 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 52 through 56 removed outlier: 7.464A pdb=" N TYR G 64 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 119 through 120 Processing sheet with id=AB5, first strand: chain 'G' and resid 145 through 148 Processing sheet with id=AB6, first strand: chain 'G' and resid 184 through 186 removed outlier: 5.711A pdb=" N GLY G 244 " --> pdb=" O SER G 229 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER G 229 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU G 246 " --> pdb=" O PHE G 227 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE G 227 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR G 313 " --> pdb=" O VAL G 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 79 through 80 removed outlier: 3.514A pdb=" N PHE H 137 " --> pdb=" O ILE H 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 79 through 80 removed outlier: 3.514A pdb=" N PHE H 137 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY H 18 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 9 " --> pdb=" O ASN H 285 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP H 279 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU H 17 " --> pdb=" O VAL H 277 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL H 277 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N HIS H 19 " --> pdb=" O MET H 275 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N MET H 275 " --> pdb=" O HIS H 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 24 through 31 removed outlier: 3.897A pdb=" N GLY H 26 " --> pdb=" O LEU H 43 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 43 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N HIS H 41 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU H 30 " --> pdb=" O ASP H 39 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP H 39 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 52 through 56 removed outlier: 5.457A pdb=" N LYS H 55 " --> pdb=" O TYR H 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 119 through 120 Processing sheet with id=AC3, first strand: chain 'H' and resid 144 through 150 removed outlier: 4.024A pdb=" N PHE H 161 " --> pdb=" O TYR H 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 184 through 186 removed outlier: 5.634A pdb=" N GLY H 244 " --> pdb=" O SER H 229 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER H 229 " --> pdb=" O GLY H 244 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU H 246 " --> pdb=" O PHE H 227 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE H 227 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 79 through 80 Processing sheet with id=AC6, first strand: chain 'I' and resid 79 through 80 removed outlier: 3.780A pdb=" N SER I 9 " --> pdb=" O ASN I 285 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU I 17 " --> pdb=" O VAL I 277 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL I 277 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS I 19 " --> pdb=" O MET I 275 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N MET I 275 " --> pdb=" O HIS I 19 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 24 through 31 removed outlier: 6.802A pdb=" N TRP I 24 " --> pdb=" O PRO I 44 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY I 26 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR I 42 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR I 28 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN I 40 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N VAL I 38 " --> pdb=" O PHE I 160 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N SER I 162 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN I 40 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR I 164 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR I 42 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N PHE I 166 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE I 161 " --> pdb=" O TYR I 149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 52 through 56 removed outlier: 7.598A pdb=" N TYR I 64 " --> pdb=" O THR I 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 119 through 120 removed outlier: 3.572A pdb=" N TYR I 119 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 184 through 186 removed outlier: 5.871A pdb=" N GLY I 244 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER I 229 " --> pdb=" O GLY I 244 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU I 246 " --> pdb=" O PHE I 227 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE I 227 " --> pdb=" O LEU I 246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 89 through 93 Processing sheet with id=AD3, first strand: chain 'B' and resid 89 through 93 removed outlier: 7.635A pdb=" N THR B 289 " --> pdb=" O TRP B 11 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP B 11 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA B 291 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS B 2 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 334 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 4 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N CYS B 10 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 326 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 323 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 321 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.998A pdb=" N ALA B 14 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS B 45 " --> pdb=" O ALA B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AD6, first strand: chain 'B' and resid 273 through 278 Processing sheet with id=AD7, first strand: chain 'A' and resid 481 through 482 removed outlier: 3.793A pdb=" N PHE A 482 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 504 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 419 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 420 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.152A pdb=" N VAL A 647 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 624 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU A 700 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 626 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET A 697 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA A 729 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A 699 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR A 726 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN A 598 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A 728 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP A 600 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 730 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS A 602 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AE1, first strand: chain 'A' and resid 857 through 862 removed outlier: 3.626A pdb=" N ILE A 859 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL A 848 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 847 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 956 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 849 " --> pdb=" O VAL A 956 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 955 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 963 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.664A pdb=" N VAL D 138 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.664A pdb=" N VAL D 138 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 17 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL D 277 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N HIS D 19 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N MET D 275 " --> pdb=" O HIS D 19 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 24 through 30 removed outlier: 6.812A pdb=" N TRP D 24 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY D 26 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR D 42 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR D 28 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASN D 40 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.531A pdb=" N CYS D 126 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 145 through 149 Processing sheet with id=AE7, first strand: chain 'D' and resid 184 through 186 removed outlier: 4.882A pdb=" N GLU D 242 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN D 230 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 79 through 80 removed outlier: 3.514A pdb=" N PHE E 137 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 138 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 79 through 80 removed outlier: 3.514A pdb=" N PHE E 137 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 138 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E 18 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 17 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL E 277 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS E 19 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N MET E 275 " --> pdb=" O HIS E 19 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 24 through 31 removed outlier: 6.673A pdb=" N TRP E 24 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLY E 26 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR E 42 " --> pdb=" O GLY E 26 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR E 28 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASN E 40 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N SER E 162 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN E 40 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N THR E 164 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR E 42 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 52 through 56 removed outlier: 7.205A pdb=" N TYR E 64 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.596A pdb=" N TYR E 119 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 184 through 186 removed outlier: 5.287A pdb=" N GLY E 244 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER E 229 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU E 246 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE E 227 " --> pdb=" O LEU E 246 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 3.07 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: 7184 1.33 - 1.45: 5892 1.45 - 1.57: 15389 1.57 - 1.69: 267 1.69 - 1.81: 138 Bond restraints: 28870 Sorted by residual: bond pdb=" CA ALA A 752 " pdb=" CB ALA A 752 " ideal model delta sigma weight residual 1.539 1.514 0.025 1.36e-02 5.41e+03 3.45e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 28865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 38244 1.37 - 2.75: 1166 2.75 - 4.12: 182 4.12 - 5.50: 9 5.50 - 6.87: 4 Bond angle restraints: 39605 Sorted by residual: angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.90 109.28 2.62 8.10e-01 1.52e+00 1.05e+01 angle pdb=" CA ASP I 296 " pdb=" C ASP I 296 " pdb=" O ASP I 296 " ideal model delta sigma weight residual 120.52 124.91 -4.39 1.39e+00 5.18e-01 9.98e+00 angle pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" C GLN A 117 " ideal model delta sigma weight residual 113.43 109.54 3.89 1.26e+00 6.30e-01 9.51e+00 angle pdb=" N VAL B 122 " pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 106.21 109.41 -3.20 1.07e+00 8.73e-01 8.92e+00 angle pdb=" N THR B 210 " pdb=" CA THR B 210 " pdb=" C THR B 210 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.70e+00 ... (remaining 39600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 16587 34.82 - 69.64: 528 69.64 - 104.46: 64 104.46 - 139.29: 2 139.29 - 174.11: 7 Dihedral angle restraints: 17188 sinusoidal: 7944 harmonic: 9244 Sorted by residual: dihedral pdb=" O4' C J 18 " pdb=" C1' C J 18 " pdb=" N1 C J 18 " pdb=" C2 C J 18 " ideal model delta sinusoidal sigma weight residual 200.00 86.37 113.63 1 1.50e+01 4.44e-03 5.98e+01 dihedral pdb=" O4' C J 25 " pdb=" C1' C J 25 " pdb=" N1 C J 25 " pdb=" C2 C J 25 " ideal model delta sinusoidal sigma weight residual -128.00 -44.92 -83.08 1 1.70e+01 3.46e-03 2.92e+01 dihedral pdb=" O4' C J 7 " pdb=" C1' C J 7 " pdb=" N1 C J 7 " pdb=" C2 C J 7 " ideal model delta sinusoidal sigma weight residual -128.00 -58.65 -69.35 1 1.70e+01 3.46e-03 2.15e+01 ... (remaining 17185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2993 0.033 - 0.066: 1007 0.066 - 0.099: 240 0.099 - 0.131: 200 0.131 - 0.164: 9 Chirality restraints: 4449 Sorted by residual: chirality pdb=" C1' C J 25 " pdb=" O4' C J 25 " pdb=" C2' C J 25 " pdb=" N1 C J 25 " both_signs ideal model delta sigma weight residual False 2.45 2.28 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C1' G J 51 " pdb=" O4' G J 51 " pdb=" C2' G J 51 " pdb=" N9 G J 51 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C1' G J 19 " pdb=" O4' G J 19 " pdb=" C2' G J 19 " pdb=" N9 G J 19 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 4446 not shown) Planarity restraints: 4631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G J 17 " 0.034 2.00e-02 2.50e+03 1.49e-02 6.70e+00 pdb=" N9 G J 17 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G J 17 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G J 17 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G J 17 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G J 17 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G J 17 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G J 17 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G J 17 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G J 17 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G J 17 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G J 17 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G J 5 " 0.032 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G J 5 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G J 5 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G J 5 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G J 5 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G J 5 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G J 5 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G J 5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G J 5 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G J 5 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G J 5 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G J 5 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C J 11 " 0.031 2.00e-02 2.50e+03 1.55e-02 5.39e+00 pdb=" N1 C J 11 " -0.031 2.00e-02 2.50e+03 pdb=" C2 C J 11 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C J 11 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C J 11 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C J 11 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C J 11 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C J 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C J 11 " -0.009 2.00e-02 2.50e+03 ... (remaining 4628 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 3 1.84 - 2.61: 295 2.61 - 3.37: 35579 3.37 - 4.14: 62422 4.14 - 4.90: 116066 Nonbonded interactions: 214365 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb="MG MG A1002 " model vdw 1.081 1.300 nonbonded pdb=" OD2 ASP A 158 " pdb="MG MG A1001 " model vdw 1.791 2.170 nonbonded pdb=" OD2 ASP A 158 " pdb="MG MG A1002 " model vdw 1.821 2.170 nonbonded pdb=" OE1 GLN I 93 " pdb=" OG1 THR I 113 " model vdw 1.980 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OE2 GLU A 549 " model vdw 2.053 3.040 ... (remaining 214360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 278 or (resid 279 and (name N or na \ me CA or name C or name O or name CB )) or resid 280 through 298 or (resid 299 a \ nd (name N or name CA or name C or name O or name CB )) or resid 300 through 315 \ )) selection = (chain 'E' and (resid 1 through 32 or resid 37 through 52 or resid 65 through 69 \ or (resid 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 92 or resid 104 through 278 or (resid 279 and (name N or name CA or n \ ame C or name O or name CB )) or resid 280 through 298 or (resid 299 and (name N \ or name CA or name C or name O or name CB )) or resid 300 through 315)) selection = (chain 'F' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 32 or resid 37 through 52 or resid \ 65 through 69 or (resid 70 and (name N or name CA or name C or name O or name CB \ )) or resid 71 through 92 or resid 104 through 151 or resid 159 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 \ through 298 or (resid 299 and (name N or name CA or name C or name O or name CB \ )) or resid 300 through 315)) selection = (chain 'G' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 32 or resid 37 through 52 or resid \ 65 through 69 or (resid 70 and (name N or name CA or name C or name O or name CB \ )) or resid 71 through 92 or resid 104 through 151 or resid 159 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 \ through 298 or (resid 299 and (name N or name CA or name C or name O or name CB \ )) or resid 300 through 315)) selection = (chain 'H' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 32 or resid 37 through 52 or resid \ 65 through 69 or (resid 70 and (name N or name CA or name C or name O or name CB \ )) or resid 71 through 92 or resid 104 through 151 or resid 159 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 \ through 315)) selection = (chain 'I' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 32 or resid 37 through 52 or resid \ 65 through 69 or (resid 70 and (name N or name CA or name C or name O or name CB \ )) or resid 71 through 92 or resid 104 through 151 or resid 159 through 298 or \ (resid 299 and (name N or name CA or name C or name O or name CB )) or resid 300 \ through 315)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.210 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.004 0.046 28870 Z= 0.185 Angle : 0.570 6.870 39605 Z= 0.343 Chirality : 0.040 0.164 4449 Planarity : 0.003 0.044 4631 Dihedral : 16.754 174.108 11244 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3141 helix: 0.19 (0.18), residues: 854 sheet: -0.33 (0.23), residues: 459 loop : -1.07 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.012 0.001 TYR A 751 PHE 0.010 0.001 PHE H 73 TRP 0.009 0.001 TRP A 661 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00391 (28870) covalent geometry : angle 0.56976 (39605) hydrogen bonds : bond 0.26280 ( 997) hydrogen bonds : angle 7.78956 ( 2707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 MET cc_start: 0.8259 (ttm) cc_final: 0.7950 (ttm) REVERT: A 321 GLU cc_start: 0.8548 (pt0) cc_final: 0.8234 (pm20) REVERT: A 540 MET cc_start: 0.8550 (tpp) cc_final: 0.8189 (tpp) REVERT: A 700 GLU cc_start: 0.9036 (tt0) cc_final: 0.8267 (pp20) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1760 time to fit residues: 26.3928 Evaluate side-chains 84 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.4980 overall best weight: 3.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 HIS G 288 HIS ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 724 ASN A 807 GLN A 897 HIS D 87 HIS E 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.083536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.050749 restraints weight = 74252.422| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.47 r_work: 0.2580 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28870 Z= 0.190 Angle : 0.587 10.284 39605 Z= 0.329 Chirality : 0.044 0.213 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.577 175.840 5138 Min Nonbonded Distance : 1.050 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.55 % Allowed : 5.85 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3141 helix: 0.81 (0.18), residues: 921 sheet: -0.04 (0.23), residues: 466 loop : -1.15 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 233 TYR 0.013 0.001 TYR C 112 PHE 0.014 0.001 PHE F 146 TRP 0.008 0.001 TRP A 759 HIS 0.010 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00433 (28870) covalent geometry : angle 0.58668 (39605) hydrogen bonds : bond 0.05551 ( 997) hydrogen bonds : angle 4.99665 ( 2707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.8865 (pt0) cc_final: 0.8480 (pm20) REVERT: A 417 ASP cc_start: 0.8991 (p0) cc_final: 0.8713 (p0) REVERT: A 540 MET cc_start: 0.8882 (tpp) cc_final: 0.8520 (tpp) REVERT: A 700 GLU cc_start: 0.9106 (tt0) cc_final: 0.8332 (pp20) REVERT: A 705 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: D 202 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8660 (mp0) REVERT: D 291 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9109 (mmm) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.1950 time to fit residues: 33.4066 Evaluate side-chains 100 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 103 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 247 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 252 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 19 HIS ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052382 restraints weight = 74210.115| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.47 r_work: 0.2651 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28870 Z= 0.117 Angle : 0.502 9.557 39605 Z= 0.281 Chirality : 0.041 0.217 4449 Planarity : 0.003 0.042 4631 Dihedral : 17.624 174.196 5138 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.65 % Allowed : 6.80 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3141 helix: 1.03 (0.18), residues: 929 sheet: 0.05 (0.23), residues: 465 loop : -1.05 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 111 TYR 0.014 0.001 TYR C 112 PHE 0.012 0.001 PHE F 146 TRP 0.006 0.001 TRP A 759 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00253 (28870) covalent geometry : angle 0.50239 (39605) hydrogen bonds : bond 0.03918 ( 997) hydrogen bonds : angle 4.39248 ( 2707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4722 (OUTLIER) cc_final: 0.4273 (pt) REVERT: I 75 GLU cc_start: 0.8852 (mp0) cc_final: 0.8511 (mp0) REVERT: A 629 MET cc_start: 0.8332 (mtp) cc_final: 0.8080 (mtp) REVERT: A 700 GLU cc_start: 0.9110 (tt0) cc_final: 0.8328 (pp20) REVERT: A 705 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: D 202 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8620 (mp0) outliers start: 18 outliers final: 8 residues processed: 112 average time/residue: 0.1810 time to fit residues: 33.5040 Evaluate side-chains 95 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 813 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 258 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 88 HIS F 288 HIS G 23 ASN H 23 ASN I 183 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.048207 restraints weight = 75202.906| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.42 r_work: 0.2514 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 28870 Z= 0.401 Angle : 0.695 8.623 39605 Z= 0.381 Chirality : 0.048 0.325 4449 Planarity : 0.004 0.041 4631 Dihedral : 17.772 170.535 5138 Min Nonbonded Distance : 0.978 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.09 % Allowed : 7.81 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3141 helix: 0.96 (0.18), residues: 906 sheet: -0.13 (0.24), residues: 460 loop : -1.20 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 233 TYR 0.019 0.002 TYR E 171 PHE 0.022 0.002 PHE G 166 TRP 0.010 0.001 TRP A 759 HIS 0.009 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00934 (28870) covalent geometry : angle 0.69502 (39605) hydrogen bonds : bond 0.06449 ( 997) hydrogen bonds : angle 4.83784 ( 2707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4393 (pt) REVERT: A 540 MET cc_start: 0.8949 (tpp) cc_final: 0.8548 (tpp) REVERT: A 629 MET cc_start: 0.8553 (mtp) cc_final: 0.8281 (mtp) REVERT: A 700 GLU cc_start: 0.9132 (tt0) cc_final: 0.8326 (pp20) REVERT: A 705 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: A 921 GLU cc_start: 0.9270 (tp30) cc_final: 0.8822 (tp30) REVERT: D 275 MET cc_start: 0.9090 (tmm) cc_final: 0.8885 (tmm) REVERT: D 315 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7985 (tmmt) outliers start: 30 outliers final: 19 residues processed: 113 average time/residue: 0.1892 time to fit residues: 35.6514 Evaluate side-chains 105 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 64 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 GLN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.083933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.051116 restraints weight = 74413.327| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.45 r_work: 0.2597 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28870 Z= 0.145 Angle : 0.520 8.511 39605 Z= 0.291 Chirality : 0.042 0.212 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.761 172.698 5138 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.94 % Allowed : 8.94 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3141 helix: 1.17 (0.18), residues: 920 sheet: -0.03 (0.23), residues: 481 loop : -1.11 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 111 TYR 0.014 0.001 TYR I 119 PHE 0.013 0.001 PHE F 146 TRP 0.007 0.001 TRP A 759 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00333 (28870) covalent geometry : angle 0.51979 (39605) hydrogen bonds : bond 0.04092 ( 997) hydrogen bonds : angle 4.35143 ( 2707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4363 (pt) REVERT: H 75 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8919 (mp0) REVERT: I 75 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: A 540 MET cc_start: 0.8964 (tpp) cc_final: 0.8501 (tpp) REVERT: A 629 MET cc_start: 0.8364 (mtp) cc_final: 0.8085 (mtp) REVERT: A 700 GLU cc_start: 0.9135 (tt0) cc_final: 0.8340 (pp20) REVERT: A 705 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: D 222 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8717 (p0) REVERT: D 275 MET cc_start: 0.9111 (tmm) cc_final: 0.8895 (tmm) REVERT: D 315 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7908 (tmmt) outliers start: 26 outliers final: 12 residues processed: 111 average time/residue: 0.1690 time to fit residues: 31.5951 Evaluate side-chains 101 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 165 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 238 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 215 GLN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052362 restraints weight = 74286.685| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.47 r_work: 0.2613 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28870 Z= 0.142 Angle : 0.512 9.090 39605 Z= 0.285 Chirality : 0.041 0.199 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.696 170.959 5138 Min Nonbonded Distance : 1.068 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.16 % Allowed : 9.16 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3141 helix: 1.31 (0.18), residues: 920 sheet: -0.22 (0.23), residues: 521 loop : -1.00 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.019 0.001 TYR C 112 PHE 0.013 0.001 PHE F 146 TRP 0.007 0.001 TRP C 58 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00326 (28870) covalent geometry : angle 0.51156 (39605) hydrogen bonds : bond 0.03990 ( 997) hydrogen bonds : angle 4.22059 ( 2707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4495 (pt) REVERT: H 1 MET cc_start: 0.8057 (ppp) cc_final: 0.7775 (ppp) REVERT: A 246 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7626 (p) REVERT: A 629 MET cc_start: 0.8491 (mtp) cc_final: 0.8211 (mtp) REVERT: A 700 GLU cc_start: 0.9135 (tt0) cc_final: 0.8447 (pp20) REVERT: A 705 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: D 222 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8735 (p0) REVERT: D 275 MET cc_start: 0.9139 (tmm) cc_final: 0.8898 (tmm) REVERT: D 315 LYS cc_start: 0.8221 (ttpt) cc_final: 0.8014 (tmmt) outliers start: 32 outliers final: 18 residues processed: 117 average time/residue: 0.1619 time to fit residues: 31.6551 Evaluate side-chains 104 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 165 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 20 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.083890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.051219 restraints weight = 74009.508| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.39 r_work: 0.2620 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28870 Z= 0.139 Angle : 0.507 9.694 39605 Z= 0.281 Chirality : 0.041 0.200 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.668 170.919 5138 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.20 % Allowed : 9.48 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3141 helix: 1.37 (0.18), residues: 923 sheet: -0.20 (0.23), residues: 527 loop : -0.98 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.014 0.001 TYR C 112 PHE 0.013 0.001 PHE F 146 TRP 0.005 0.001 TRP A 759 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00320 (28870) covalent geometry : angle 0.50727 (39605) hydrogen bonds : bond 0.03818 ( 997) hydrogen bonds : angle 4.16699 ( 2707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4556 (pt) REVERT: I 75 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: B 8 ASP cc_start: 0.8500 (t0) cc_final: 0.8232 (t0) REVERT: B 196 TYR cc_start: 0.8473 (m-80) cc_final: 0.8245 (m-80) REVERT: A 246 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7608 (p) REVERT: A 475 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 629 MET cc_start: 0.8495 (mtp) cc_final: 0.8216 (mtp) REVERT: A 700 GLU cc_start: 0.9133 (tt0) cc_final: 0.8444 (pp20) REVERT: A 705 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: D 222 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (p0) REVERT: D 315 LYS cc_start: 0.8221 (ttpt) cc_final: 0.8012 (tmmt) outliers start: 33 outliers final: 22 residues processed: 118 average time/residue: 0.1582 time to fit residues: 31.7399 Evaluate side-chains 113 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 19 HIS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 165 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 279 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 272 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 HIS B 145 GLN A 307 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.048765 restraints weight = 74982.705| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.41 r_work: 0.2531 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 28870 Z= 0.339 Angle : 0.641 10.050 39605 Z= 0.351 Chirality : 0.046 0.210 4449 Planarity : 0.004 0.041 4631 Dihedral : 17.739 168.232 5138 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.27 % Allowed : 9.81 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3141 helix: 1.25 (0.18), residues: 909 sheet: -0.06 (0.24), residues: 476 loop : -1.19 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 128 TYR 0.021 0.002 TYR C 112 PHE 0.020 0.002 PHE H 146 TRP 0.008 0.001 TRP A 169 HIS 0.008 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00790 (28870) covalent geometry : angle 0.64059 (39605) hydrogen bonds : bond 0.05685 ( 997) hydrogen bonds : angle 4.53293 ( 2707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4535 (pt) REVERT: I 75 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: B 8 ASP cc_start: 0.8685 (t0) cc_final: 0.8359 (t0) REVERT: B 196 TYR cc_start: 0.8477 (m-80) cc_final: 0.8258 (m-80) REVERT: A 246 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 475 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7046 (tt) REVERT: A 540 MET cc_start: 0.8927 (tpp) cc_final: 0.8462 (tpp) REVERT: A 629 MET cc_start: 0.8495 (mtp) cc_final: 0.8216 (mtp) REVERT: A 652 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8573 (ptmt) REVERT: A 700 GLU cc_start: 0.9153 (tt0) cc_final: 0.8387 (pp20) REVERT: A 705 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: D 222 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8768 (p0) REVERT: D 315 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7951 (tmmt) outliers start: 35 outliers final: 25 residues processed: 119 average time/residue: 0.1615 time to fit residues: 31.8501 Evaluate side-chains 116 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 315 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 314 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN D 19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.083903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.051149 restraints weight = 73825.706| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.44 r_work: 0.2599 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28870 Z= 0.134 Angle : 0.521 9.862 39605 Z= 0.289 Chirality : 0.041 0.200 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.700 169.588 5138 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.16 % Allowed : 10.28 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3141 helix: 1.41 (0.18), residues: 916 sheet: -0.30 (0.23), residues: 523 loop : -1.05 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 97 TYR 0.017 0.001 TYR C 112 PHE 0.013 0.001 PHE F 146 TRP 0.007 0.001 TRP A 661 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00303 (28870) covalent geometry : angle 0.52129 (39605) hydrogen bonds : bond 0.03957 ( 997) hydrogen bonds : angle 4.22510 ( 2707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.4582 (pt) REVERT: I 75 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 196 TYR cc_start: 0.8503 (m-80) cc_final: 0.8281 (m-80) REVERT: A 246 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 475 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6944 (tt) REVERT: A 629 MET cc_start: 0.8364 (mtp) cc_final: 0.8095 (mtp) REVERT: A 700 GLU cc_start: 0.9158 (tt0) cc_final: 0.8399 (pp20) REVERT: A 705 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: D 222 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8760 (p0) REVERT: D 315 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7897 (tmmt) outliers start: 32 outliers final: 22 residues processed: 116 average time/residue: 0.1648 time to fit residues: 32.3817 Evaluate side-chains 114 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 79 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 306 optimal weight: 0.0370 chunk 178 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 305 optimal weight: 8.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.084565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.051914 restraints weight = 73874.971| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.42 r_work: 0.2641 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28870 Z= 0.120 Angle : 0.497 9.946 39605 Z= 0.274 Chirality : 0.040 0.190 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.580 169.808 5138 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.02 % Allowed : 10.47 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3141 helix: 1.47 (0.18), residues: 920 sheet: -0.23 (0.22), residues: 554 loop : -0.93 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 97 TYR 0.013 0.001 TYR C 112 PHE 0.013 0.001 PHE F 146 TRP 0.005 0.001 TRP A 759 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00270 (28870) covalent geometry : angle 0.49680 (39605) hydrogen bonds : bond 0.03476 ( 997) hydrogen bonds : angle 4.08435 ( 2707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4729 (pt) REVERT: I 75 GLU cc_start: 0.8856 (mp0) cc_final: 0.8575 (mp0) REVERT: A 246 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7506 (p) REVERT: A 629 MET cc_start: 0.8465 (mtp) cc_final: 0.8206 (mtp) REVERT: A 700 GLU cc_start: 0.9151 (tt0) cc_final: 0.8428 (pp20) REVERT: A 705 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: D 222 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (p0) REVERT: D 315 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7948 (tmmt) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.1779 time to fit residues: 35.1969 Evaluate side-chains 111 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 36 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.051005 restraints weight = 74166.795| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.43 r_work: 0.2615 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28870 Z= 0.152 Angle : 0.518 10.463 39605 Z= 0.286 Chirality : 0.041 0.193 4449 Planarity : 0.003 0.043 4631 Dihedral : 17.516 169.308 5138 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.94 % Allowed : 10.65 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3141 helix: 1.52 (0.18), residues: 917 sheet: -0.20 (0.23), residues: 542 loop : -0.94 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 97 TYR 0.036 0.001 TYR B 196 PHE 0.013 0.001 PHE F 146 TRP 0.005 0.001 TRP I 24 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00351 (28870) covalent geometry : angle 0.51787 (39605) hydrogen bonds : bond 0.03895 ( 997) hydrogen bonds : angle 4.12903 ( 2707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6871.27 seconds wall clock time: 118 minutes 18.85 seconds (7098.85 seconds total)