Starting phenix.real_space_refine on Sat Aug 8 16:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.cif Found real_map, /net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.map" model { file = "/net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9taw_55757/08_2026/9taw_55757.cif" } resolution = 3.54 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= 0.002 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 138 5.16 5 C 17931 2.51 5 N 4942 2.21 5 O 5673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28846 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1682 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} Chain: "B" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1641 Classifications: {'DNA': 80} Link IDs: {'rna3p': 79} Chain: "H" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5014 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "K" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1922 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2502 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 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: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2613 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "U" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1365 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "b" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 291 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Time building chain proxies: 5.60, per 1000 atoms: 0.19 Number of scatterers: 28846 At special positions: 0 Unit cell: (126.875, 208.075, 218.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 162 15.00 O 5673 8.00 N 4942 7.00 C 17931 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: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 17 sheets defined 66.7% alpha, 10.6% beta 75 base pairs and 143 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 removed outlier: 3.520A pdb=" N ARG H 39 " --> pdb=" O CYS H 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 115 Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 124 through 189 removed outlier: 4.378A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 224 removed outlier: 3.741A pdb=" N LYS H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 229 removed outlier: 3.622A pdb=" N GLU H 229 " --> pdb=" O ASN H 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 226 through 229' Processing helix chain 'H' and resid 230 through 241 removed outlier: 4.085A pdb=" N GLU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 removed outlier: 3.780A pdb=" N GLY I 76 " --> pdb=" O TYR I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.595A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.732A pdb=" N GLY I 154 " --> pdb=" O TRP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 172 through 175 removed outlier: 3.965A pdb=" N ILE I 175 " --> pdb=" O PHE I 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 172 through 175' Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 184 through 191 Processing helix chain 'I' and resid 192 through 194 No H-bonds generated for 'chain 'I' and resid 192 through 194' Processing helix chain 'I' and resid 197 through 209 Processing helix chain 'I' and resid 210 through 214 removed outlier: 3.501A pdb=" N VAL I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 Processing helix chain 'I' and resid 269 through 282 Processing helix chain 'I' and resid 328 through 333 Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 346 through 353 removed outlier: 3.508A pdb=" N LEU I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.968A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 380 removed outlier: 4.176A pdb=" N ARG I 380 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 400 Processing helix chain 'I' and resid 411 through 428 removed outlier: 3.696A pdb=" N THR I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 removed outlier: 4.006A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 460 removed outlier: 3.890A pdb=" N SER I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 Proline residue: I 472 - end of helix Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.894A pdb=" N THR I 484 " --> pdb=" O GLN I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 514 removed outlier: 3.724A pdb=" N MET I 514 " --> pdb=" O MET I 510 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 551 removed outlier: 3.510A pdb=" N SER I 529 " --> pdb=" O THR I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 576 removed outlier: 3.773A pdb=" N LEU I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP I 570 " --> pdb=" O GLU I 566 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR I 572 " --> pdb=" O VAL I 568 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE I 573 " --> pdb=" O CYS I 569 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.599A pdb=" N LEU I 593 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 625 removed outlier: 3.585A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 652 removed outlier: 4.152A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER I 646 " --> pdb=" O HIS I 642 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP I 652 " --> pdb=" O VAL I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 Processing helix chain 'I' and resid 685 through 687 No H-bonds generated for 'chain 'I' and resid 685 through 687' Processing helix chain 'I' and resid 688 through 697 removed outlier: 3.825A pdb=" N SER I 694 " --> pdb=" O SER I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 719 through 727 removed outlier: 3.639A pdb=" N GLY I 727 " --> pdb=" O LEU I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 740 removed outlier: 3.507A pdb=" N HIS I 740 " --> pdb=" O ARG I 736 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 44 Processing helix chain 'K' and resid 54 through 77 removed outlier: 3.704A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 149 removed outlier: 3.720A pdb=" N LEU K 89 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 188 Processing helix chain 'K' and resid 211 through 226 Processing helix chain 'K' and resid 239 through 249 Processing helix chain 'L' and resid 27 through 37 removed outlier: 3.574A pdb=" N GLN L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 68 removed outlier: 3.508A pdb=" N LEU L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 104 removed outlier: 3.929A pdb=" N TYR L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER L 92 " --> pdb=" O LEU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 172 Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.668A pdb=" N THR L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 269 Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.715A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.511A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 38 removed outlier: 3.716A pdb=" N LEU M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 86 removed outlier: 4.117A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.628A pdb=" N PHE M 92 " --> pdb=" O ASP M 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 114 through 124 Processing helix chain 'M' and resid 135 through 155 removed outlier: 3.653A pdb=" N GLY M 155 " --> pdb=" O GLN M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.770A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 removed outlier: 3.585A pdb=" N ILE N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.857A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 32 through 37' Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.569A pdb=" N LYS N 59 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 78 removed outlier: 3.846A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 Processing helix chain 'N' and resid 166 through 170 removed outlier: 4.004A pdb=" N ARG N 169 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 320 through 325 removed outlier: 3.647A pdb=" N THR N 324 " --> pdb=" O SER N 320 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS N 325 " --> pdb=" O PRO N 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 320 through 325' Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.752A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 160 through 169 removed outlier: 3.935A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 201 Processing helix chain 'O' and resid 261 through 278 removed outlier: 4.247A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 289 Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 Processing helix chain 'P' and resid 162 through 191 removed outlier: 3.754A pdb=" N PHE P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.711A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP P 250 " --> pdb=" O ALA P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 256 removed outlier: 3.988A pdb=" N GLU P 256 " --> pdb=" O ARG P 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 257 through 269 removed outlier: 3.636A pdb=" N SER P 261 " --> pdb=" O THR P 257 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'Q' and resid 69 through 73 removed outlier: 3.628A pdb=" N TRP Q 73 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 69 through 73' Processing helix chain 'Q' and resid 77 through 99 removed outlier: 3.793A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 124 Processing helix chain 'Q' and resid 133 through 135 No H-bonds generated for 'chain 'Q' and resid 133 through 135' Processing helix chain 'Q' and resid 136 through 199 removed outlier: 3.732A pdb=" N LEU Q 140 " --> pdb=" O ASN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 Processing helix chain 'Q' and resid 223 through 232 removed outlier: 4.312A pdb=" N ILE Q 232 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 248 removed outlier: 4.132A pdb=" N LEU Q 238 " --> pdb=" O ASN Q 234 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER Q 248 " --> pdb=" O ILE Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 268 removed outlier: 3.524A pdb=" N SER Q 268 " --> pdb=" O LYS Q 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 107 removed outlier: 4.350A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 114 removed outlier: 4.009A pdb=" N GLN R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.768A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 3.892A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 Processing helix chain 'S' and resid 2 through 39 Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.628A pdb=" N GLU S 59 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 87 removed outlier: 3.840A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'T' and resid 454 through 472 removed outlier: 4.099A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 477 through 506 removed outlier: 3.947A pdb=" N GLU T 481 " --> pdb=" O ARG T 477 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.697A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.547A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 Processing helix chain 'U' and resid 254 through 267 removed outlier: 4.269A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 375 Proline residue: U 332 - end of helix Processing helix chain 'U' and resid 386 through 399 Processing helix chain 'U' and resid 399 through 417 Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.936A pdb=" N LEU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER W 65 " --> pdb=" O ASN W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 86 Processing helix chain 'X' and resid 11 through 23 removed outlier: 4.025A pdb=" N HIS X 22 " --> pdb=" O LEU X 18 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 61 removed outlier: 3.730A pdb=" N GLU X 40 " --> pdb=" O GLN X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 81 Proline residue: X 75 - end of helix Processing helix chain 'b' and resid 261 through 273 removed outlier: 3.661A pdb=" N LYS b 273 " --> pdb=" O THR b 269 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 303 removed outlier: 4.033A pdb=" N GLU b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA2, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.526A pdb=" N PHE L 137 " --> pdb=" O PHE L 162 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE L 141 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY L 188 " --> pdb=" O GLN L 71 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N GLN L 71 " --> pdb=" O GLY L 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 117 through 123 removed outlier: 3.526A pdb=" N PHE L 137 " --> pdb=" O PHE L 162 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE L 141 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY L 188 " --> pdb=" O GLN L 71 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N GLN L 71 " --> pdb=" O GLY L 188 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 240 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL L 307 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU L 238 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU L 250 " --> pdb=" O VAL L 243 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N LEU N 294 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N GLU N 272 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N LYS N 296 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N LYS N 270 " --> pdb=" O LYS N 296 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N SER N 298 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N GLN N 268 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE N 266 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU N 264 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'M' and resid 128 through 131 removed outlier: 3.770A pdb=" N LEU M 65 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 126 removed outlier: 3.802A pdb=" N ALA N 130 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.535A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE O 139 " --> pdb=" O HIS O 153 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS O 153 " --> pdb=" O PHE O 139 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP O 141 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG O 149 " --> pdb=" O VAL O 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 217 through 224 Processing sheet with id=AB2, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.313A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.313A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.567A pdb=" N TYR P 196 " --> pdb=" O GLY P 207 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 76 through 77 Processing sheet with id=AB6, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AB7, first strand: chain 'T' and resid 509 through 510 Processing sheet with id=AB8, first strand: chain 'T' and resid 550 through 552 removed outlier: 3.662A pdb=" N CYS T 550 " --> pdb=" O PHE T 558 " (cutoff:3.500A) 1713 hydrogen bonds defined for protein. 5031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 348 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 143 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 3.21 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: 6299 1.33 - 1.45: 7005 1.45 - 1.58: 15867 1.58 - 1.70: 322 1.70 - 1.82: 214 Bond restraints: 29707 Sorted by residual: bond pdb=" C3' DA B 93 " pdb=" C2' DA B 93 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DT A-106 " pdb=" C2' DT A-106 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG B 72 " pdb=" C2' DG B 72 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DC B 83 " pdb=" C2' DC B 83 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DA B 104 " pdb=" C2' DA B 104 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 29702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 40407 2.99 - 5.98: 305 5.98 - 8.98: 38 8.98 - 11.97: 10 11.97 - 14.96: 5 Bond angle restraints: 40765 Sorted by residual: angle pdb=" N3 DT A-122 " pdb=" C4 DT A-122 " pdb=" O4 DT A-122 " ideal model delta sigma weight residual 119.90 123.63 -3.73 6.00e-01 2.78e+00 3.87e+01 angle pdb=" N3 DT B 137 " pdb=" C4 DT B 137 " pdb=" O4 DT B 137 " ideal model delta sigma weight residual 119.90 123.45 -3.55 6.00e-01 2.78e+00 3.50e+01 angle pdb=" O4 DT B 137 " pdb=" C4 DT B 137 " pdb=" C5 DT B 137 " ideal model delta sigma weight residual 124.90 121.34 3.56 7.00e-01 2.04e+00 2.58e+01 angle pdb=" O4 DT A-122 " pdb=" C4 DT A-122 " pdb=" C5 DT A-122 " ideal model delta sigma weight residual 124.90 121.40 3.50 7.00e-01 2.04e+00 2.50e+01 angle pdb=" CB MET R 143 " pdb=" CG MET R 143 " pdb=" SD MET R 143 " ideal model delta sigma weight residual 112.70 127.66 -14.96 3.00e+00 1.11e-01 2.49e+01 ... (remaining 40760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 16644 35.29 - 70.59: 1102 70.59 - 105.88: 54 105.88 - 141.17: 0 141.17 - 176.47: 1 Dihedral angle restraints: 17801 sinusoidal: 8435 harmonic: 9366 Sorted by residual: dihedral pdb=" CA LEU Q 124 " pdb=" C LEU Q 124 " pdb=" N LYS Q 125 " pdb=" CA LYS Q 125 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA VAL I 405 " pdb=" C VAL I 405 " pdb=" N ASN I 406 " pdb=" CA ASN I 406 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA HIS N 239 " pdb=" C HIS N 239 " pdb=" N GLU N 240 " pdb=" CA GLU N 240 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 17798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4335 0.081 - 0.163: 330 0.163 - 0.244: 2 0.244 - 0.325: 1 0.325 - 0.407: 2 Chirality restraints: 4670 Sorted by residual: chirality pdb=" P DT A-142 " pdb=" OP1 DT A-142 " pdb=" OP2 DT A-142 " pdb=" O5' DT A-142 " both_signs ideal model delta sigma weight residual True 2.34 2.74 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CG LEU S 108 " pdb=" CB LEU S 108 " pdb=" CD1 LEU S 108 " pdb=" CD2 LEU S 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB VAL I 405 " pdb=" CA VAL I 405 " pdb=" CG1 VAL I 405 " pdb=" CG2 VAL I 405 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4667 not shown) Planarity restraints: 4566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 164 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C LYS Q 164 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS Q 164 " -0.018 2.00e-02 2.50e+03 pdb=" N MET Q 165 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE K 188 " -0.043 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO K 189 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 92 " -0.002 2.00e-02 2.50e+03 1.38e-02 5.68e+00 pdb=" N9 DG B 92 " -0.003 2.00e-02 2.50e+03 pdb=" C8 DG B 92 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG B 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG B 92 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG B 92 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG B 92 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG B 92 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG B 92 " 0.034 2.00e-02 2.50e+03 pdb=" N2 DG B 92 " -0.029 2.00e-02 2.50e+03 pdb=" N3 DG B 92 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DG B 92 " 0.002 2.00e-02 2.50e+03 ... (remaining 4563 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9421 2.86 - 3.37: 28227 3.37 - 3.88: 46957 3.88 - 4.39: 51646 4.39 - 4.90: 85598 Nonbonded interactions: 221849 Sorted by model distance: nonbonded pdb=" N GLN Q 202 " pdb=" OE1 GLN Q 202 " model vdw 2.346 3.120 nonbonded pdb=" O ILE I 115 " pdb=" OG SER I 118 " model vdw 2.347 3.040 nonbonded pdb=" O MET R 136 " pdb=" OG1 THR R 139 " model vdw 2.382 3.040 nonbonded pdb=" OE2 GLU Q 132 " pdb=" OG SER U 296 " model vdw 2.389 3.040 nonbonded pdb=" O LYS K 117 " pdb=" OD1 ASP K 121 " model vdw 2.395 3.040 ... (remaining 221844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 0.050 29707 Z= 0.310 Angle : 0.762 14.959 40765 Z= 0.484 Chirality : 0.043 0.407 4670 Planarity : 0.005 0.067 4566 Dihedral : 19.878 176.465 11651 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 0.04 % Allowed : 17.74 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.89 (0.15), residues: 3099 helix: 2.22 (0.12), residues: 1926 sheet: 0.65 (0.30), residues: 299 loop : -0.74 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 70 TYR 0.019 0.001 TYR L 91 PHE 0.025 0.002 PHE I 164 TRP 0.017 0.001 TRP K 239 HIS 0.010 0.001 HIS S 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.31 (29707) covalent geometry : angle 0.76154 / 0.48 (40765) hydrogen bonds : bond 0.12181 / 13.51 ( 1851) hydrogen bonds : angle 4.94847 / 6.48 ( 5379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 766 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 104 ASP cc_start: 0.8284 (m-30) cc_final: 0.8022 (m-30) REVERT: H 138 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8480 (ptpp) REVERT: H 218 ASN cc_start: 0.6525 (m-40) cc_final: 0.6215 (m110) REVERT: I 133 MET cc_start: 0.2498 (mmm) cc_final: 0.1401 (mmp) REVERT: I 596 ASP cc_start: 0.7004 (t0) cc_final: 0.6532 (t0) REVERT: I 635 LYS cc_start: 0.9067 (tttm) cc_final: 0.8836 (ptmm) REVERT: I 651 LEU cc_start: 0.8162 (mt) cc_final: 0.7636 (mt) REVERT: K 84 LEU cc_start: 0.8492 (tp) cc_final: 0.8067 (tp) REVERT: K 226 VAL cc_start: 0.8522 (t) cc_final: 0.8254 (p) REVERT: O 167 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8103 (ttpp) REVERT: P 100 LYS cc_start: 0.8174 (mppt) cc_final: 0.7689 (ttpt) REVERT: P 101 VAL cc_start: 0.8212 (t) cc_final: 0.7999 (t) REVERT: P 114 VAL cc_start: 0.9570 (t) cc_final: 0.9350 (t) REVERT: P 158 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7827 (mm-30) REVERT: P 161 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7701 (mtpt) REVERT: P 179 TYR cc_start: 0.8295 (m-10) cc_final: 0.7929 (m-10) REVERT: P 185 LYS cc_start: 0.9182 (tppt) cc_final: 0.8845 (mmtm) REVERT: P 268 LEU cc_start: 0.9224 (tp) cc_final: 0.8937 (mt) REVERT: Q 85 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8942 (pt0) REVERT: Q 115 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7666 (mtmt) REVERT: Q 136 ASN cc_start: 0.9164 (m-40) cc_final: 0.8938 (m-40) REVERT: Q 145 ARG cc_start: 0.9178 (mtt180) cc_final: 0.8785 (mtt180) REVERT: R 119 LEU cc_start: 0.8735 (tt) cc_final: 0.8418 (pt) REVERT: T 482 MET cc_start: 0.7327 (mtm) cc_final: 0.6623 (ttp) REVERT: W 76 LEU cc_start: 0.9163 (tp) cc_final: 0.8953 (tp) outliers start: 1 outliers final: 0 residues processed: 766 average time/residue: 0.2065 time to fit residues: 245.2909 Evaluate side-chains 456 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 144 GLN H 243 ASN I 345 GLN I 362 GLN K 187 HIS K 249 ASN M 80 ASN N 43 GLN O 193 GLN O 271 HIS P 252 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 159 GLN S 11 GLN U 297 GLN U 306 ASN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.171069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116179 restraints weight = 57440.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112370 restraints weight = 35889.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113594 restraints weight = 31162.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113648 restraints weight = 27069.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113641 restraints weight = 25561.964| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29707 Z= 0.272 Angle : 0.832 12.680 40765 Z= 0.440 Chirality : 0.047 0.277 4670 Planarity : 0.006 0.075 4566 Dihedral : 20.214 169.543 5191 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 4.87 % Allowed : 17.78 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.37 (0.15), residues: 3099 helix: 1.83 (0.11), residues: 1949 sheet: 0.05 (0.30), residues: 295 loop : -0.91 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 196 TYR 0.024 0.003 TYR I 572 PHE 0.024 0.003 PHE O 233 TRP 0.034 0.003 TRP Q 73 HIS 0.010 0.002 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (29707) covalent geometry : angle 0.83205 / 0.44 (40765) hydrogen bonds : bond 0.07448 / 8.27 ( 1851) hydrogen bonds : angle 4.40897 / 5.60 ( 5379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 485 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8437 (pp) REVERT: H 104 ASP cc_start: 0.8157 (m-30) cc_final: 0.7760 (m-30) REVERT: H 115 ASN cc_start: 0.8223 (t0) cc_final: 0.7699 (t0) REVERT: H 138 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8275 (ptpp) REVERT: I 495 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6614 (tm-30) REVERT: I 596 ASP cc_start: 0.7228 (t0) cc_final: 0.6955 (t0) REVERT: I 651 LEU cc_start: 0.7669 (mt) cc_final: 0.7329 (mt) REVERT: K 84 LEU cc_start: 0.8357 (tp) cc_final: 0.7953 (tp) REVERT: K 155 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: K 166 MET cc_start: 0.6909 (tpp) cc_final: 0.6549 (tmm) REVERT: K 218 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8948 (mt) REVERT: K 247 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8501 (mm) REVERT: M 82 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: N 29 ASP cc_start: 0.8469 (t0) cc_final: 0.8148 (t70) REVERT: O 255 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7429 (mm110) REVERT: O 278 LYS cc_start: 0.8845 (tppp) cc_final: 0.8564 (tptp) REVERT: P 114 VAL cc_start: 0.9491 (t) cc_final: 0.9245 (t) REVERT: P 158 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7593 (mm-30) REVERT: P 161 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7300 (mtpt) REVERT: P 162 ASP cc_start: 0.6526 (m-30) cc_final: 0.5141 (t0) REVERT: P 231 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7414 (tptp) REVERT: Q 88 MET cc_start: 0.9304 (mpp) cc_final: 0.8373 (mpp) REVERT: Q 119 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: Q 177 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8644 (tp-100) REVERT: R 101 MET cc_start: 0.4990 (mpp) cc_final: 0.4752 (mmm) REVERT: S 14 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.8060 (p) REVERT: T 482 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6847 (ttp) REVERT: T 496 ASP cc_start: 0.8701 (m-30) cc_final: 0.8474 (m-30) REVERT: U 281 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6656 (p90) REVERT: U 352 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8504 (ptm160) REVERT: W 46 ASN cc_start: 0.8223 (t0) cc_final: 0.7931 (m-40) REVERT: X 17 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: X 69 GLN cc_start: 0.8055 (mp10) cc_final: 0.7741 (mp10) outliers start: 139 outliers final: 62 residues processed: 586 average time/residue: 0.1899 time to fit residues: 173.7418 Evaluate side-chains 499 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 427 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 546 THR Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 587 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 336 THR Chi-restraints excluded: chain M residue 40 CYS Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain Q residue 92 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 14 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 482 MET Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 102 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 272 optimal weight: 3.9990 chunk 236 optimal weight: 0.0870 chunk 2 optimal weight: 50.0000 overall best weight: 1.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 137 ASN H 176 GLN I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 249 ASN L 96 ASN M 125 GLN M 151 GLN O 153 HIS ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 265 HIS ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN W 74 HIS ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.172142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118450 restraints weight = 57711.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113989 restraints weight = 35864.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115044 restraints weight = 32839.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115260 restraints weight = 26922.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115277 restraints weight = 25684.912| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29707 Z= 0.170 Angle : 0.701 12.060 40765 Z= 0.368 Chirality : 0.042 0.286 4670 Planarity : 0.005 0.072 4566 Dihedral : 20.178 178.683 5191 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.33 % Allowed : 20.79 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.66 (0.15), residues: 3099 helix: 2.12 (0.12), residues: 1945 sheet: 0.11 (0.30), residues: 295 loop : -0.93 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG U 352 TYR 0.031 0.001 TYR S 15 PHE 0.025 0.002 PHE U 392 TRP 0.036 0.001 TRP Q 73 HIS 0.012 0.001 HIS I 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (29707) covalent geometry : angle 0.70073 / 0.37 (40765) hydrogen bonds : bond 0.06667 / 7.46 ( 1851) hydrogen bonds : angle 4.11433 / 5.25 ( 5379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 459 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8414 (pp) REVERT: H 104 ASP cc_start: 0.8208 (m-30) cc_final: 0.7694 (m-30) REVERT: H 115 ASN cc_start: 0.8319 (t0) cc_final: 0.7786 (t0) REVERT: H 204 MET cc_start: 0.7489 (tpp) cc_final: 0.7257 (tpt) REVERT: I 495 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6570 (tm-30) REVERT: I 638 GLN cc_start: 0.9190 (tp40) cc_final: 0.8784 (tp40) REVERT: I 651 LEU cc_start: 0.7726 (mt) cc_final: 0.7419 (mt) REVERT: K 52 ASP cc_start: 0.7581 (t0) cc_final: 0.7364 (t0) REVERT: K 84 LEU cc_start: 0.8409 (tp) cc_final: 0.7996 (tp) REVERT: K 131 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: K 166 MET cc_start: 0.6915 (tpp) cc_final: 0.6515 (tmm) REVERT: K 218 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8893 (mt) REVERT: M 82 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: M 134 GLU cc_start: 0.7982 (pm20) cc_final: 0.7759 (pm20) REVERT: N 29 ASP cc_start: 0.8534 (t0) cc_final: 0.8294 (t70) REVERT: O 255 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7468 (mm-40) REVERT: O 278 LYS cc_start: 0.8718 (tppp) cc_final: 0.8245 (tptp) REVERT: P 114 VAL cc_start: 0.9475 (t) cc_final: 0.9225 (p) REVERT: P 117 GLN cc_start: 0.8373 (mp10) cc_final: 0.7919 (mp10) REVERT: P 158 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7560 (mm-30) REVERT: P 161 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7511 (mtpt) REVERT: P 162 ASP cc_start: 0.6614 (m-30) cc_final: 0.5124 (t0) REVERT: P 218 LEU cc_start: 0.9348 (pt) cc_final: 0.8547 (tt) REVERT: P 231 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7115 (tptp) REVERT: Q 88 MET cc_start: 0.9243 (mpp) cc_final: 0.8213 (mpp) REVERT: Q 116 ARG cc_start: 0.7349 (ptm-80) cc_final: 0.6983 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: Q 145 ARG cc_start: 0.9044 (mtt180) cc_final: 0.8695 (mtt90) REVERT: Q 201 HIS cc_start: 0.8781 (t70) cc_final: 0.8577 (t70) REVERT: S 10 GLN cc_start: 0.8828 (pp30) cc_final: 0.8608 (pp30) REVERT: S 12 ARG cc_start: 0.8906 (mmp80) cc_final: 0.8628 (mmp80) REVERT: T 482 MET cc_start: 0.7568 (mtm) cc_final: 0.7099 (ttp) REVERT: U 320 MET cc_start: 0.7708 (ttt) cc_final: 0.7489 (ttm) REVERT: W 46 ASN cc_start: 0.8172 (t0) cc_final: 0.7929 (m-40) REVERT: W 76 LEU cc_start: 0.9114 (tp) cc_final: 0.8858 (tp) REVERT: X 66 ASP cc_start: 0.8049 (t70) cc_final: 0.7814 (t70) outliers start: 95 outliers final: 55 residues processed: 528 average time/residue: 0.1644 time to fit residues: 137.1813 Evaluate side-chains 478 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 418 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 579 LEU Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 550 CYS Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 259 optimal weight: 0.0000 chunk 8 optimal weight: 50.0000 chunk 72 optimal weight: 0.0980 chunk 232 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN N 35 GLN ** N 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN Q 107 GLN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** 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 = 0.4378 r_free = 0.4378 target = 0.170395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116121 restraints weight = 57439.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111183 restraints weight = 36079.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112242 restraints weight = 33792.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112392 restraints weight = 28970.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112425 restraints weight = 26728.575| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29707 Z= 0.197 Angle : 0.700 13.589 40765 Z= 0.366 Chirality : 0.042 0.355 4670 Planarity : 0.004 0.066 4566 Dihedral : 20.200 175.177 5191 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.17 % Allowed : 20.72 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.71 (0.15), residues: 3099 helix: 2.19 (0.12), residues: 1941 sheet: 0.02 (0.30), residues: 295 loop : -0.96 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 64 TYR 0.025 0.002 TYR P 191 PHE 0.020 0.002 PHE I 482 TRP 0.037 0.001 TRP Q 73 HIS 0.006 0.001 HIS I 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (29707) covalent geometry : angle 0.69951 / 0.37 (40765) hydrogen bonds : bond 0.06597 / 7.33 ( 1851) hydrogen bonds : angle 4.07170 / 5.20 ( 5379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 441 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8483 (pp) REVERT: H 104 ASP cc_start: 0.8241 (m-30) cc_final: 0.7684 (m-30) REVERT: H 115 ASN cc_start: 0.8352 (t0) cc_final: 0.7075 (p0) REVERT: H 204 MET cc_start: 0.7674 (tpp) cc_final: 0.7354 (tpt) REVERT: I 495 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6868 (tm-30) REVERT: I 548 MET cc_start: 0.8897 (ttp) cc_final: 0.8492 (ttm) REVERT: I 596 ASP cc_start: 0.7543 (t0) cc_final: 0.7004 (t0) REVERT: I 638 GLN cc_start: 0.9195 (tp40) cc_final: 0.8406 (tp40) REVERT: I 642 HIS cc_start: 0.8031 (m90) cc_final: 0.7282 (m-70) REVERT: I 651 LEU cc_start: 0.7787 (mt) cc_final: 0.7455 (mt) REVERT: I 668 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8253 (tt) REVERT: K 52 ASP cc_start: 0.7531 (t0) cc_final: 0.7316 (t0) REVERT: K 84 LEU cc_start: 0.8460 (tp) cc_final: 0.8022 (tp) REVERT: K 103 ASP cc_start: 0.7544 (m-30) cc_final: 0.6817 (t0) REVERT: K 131 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: K 166 MET cc_start: 0.6992 (tpp) cc_final: 0.6595 (tmm) REVERT: K 218 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8908 (mt) REVERT: K 247 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8521 (mm) REVERT: M 82 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: N 29 ASP cc_start: 0.8708 (t0) cc_final: 0.8454 (t70) REVERT: O 167 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8396 (ptmm) REVERT: O 168 TYR cc_start: 0.7703 (m-80) cc_final: 0.7440 (m-80) REVERT: O 255 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7495 (mm110) REVERT: P 100 LYS cc_start: 0.8262 (mppt) cc_final: 0.7983 (ttpt) REVERT: P 111 CYS cc_start: 0.8738 (t) cc_final: 0.8450 (t) REVERT: P 114 VAL cc_start: 0.9450 (t) cc_final: 0.9171 (t) REVERT: P 158 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7766 (mm-30) REVERT: P 161 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7880 (mtpt) REVERT: P 188 LYS cc_start: 0.9254 (mttm) cc_final: 0.8935 (mttm) REVERT: P 218 LEU cc_start: 0.9372 (pt) cc_final: 0.8604 (tt) REVERT: P 231 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7558 (tptp) REVERT: Q 88 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: Q 116 ARG cc_start: 0.7435 (ptm-80) cc_final: 0.7066 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: Q 145 ARG cc_start: 0.9152 (mtt180) cc_final: 0.8646 (mtt90) REVERT: Q 177 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8747 (tp-100) REVERT: Q 201 HIS cc_start: 0.8859 (t70) cc_final: 0.8593 (t70) REVERT: R 119 LEU cc_start: 0.8465 (tp) cc_final: 0.7796 (pp) REVERT: S 10 GLN cc_start: 0.8916 (pp30) cc_final: 0.8673 (pp30) REVERT: T 466 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8386 (tp) REVERT: T 482 MET cc_start: 0.7637 (mtm) cc_final: 0.7260 (ttm) REVERT: U 320 MET cc_start: 0.7771 (ttt) cc_final: 0.7566 (ttm) REVERT: W 59 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7866 (ttm170) REVERT: X 17 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8248 (tpp80) REVERT: X 69 GLN cc_start: 0.7879 (mp10) cc_final: 0.7524 (mp10) outliers start: 119 outliers final: 74 residues processed: 532 average time/residue: 0.1784 time to fit residues: 148.1885 Evaluate side-chains 502 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 418 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 546 THR Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 579 LEU Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain P residue 253 ARG Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 550 CYS Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 314 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 309 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 14 optimal weight: 50.0000 chunk 162 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.171719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117487 restraints weight = 57438.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113089 restraints weight = 36377.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114248 restraints weight = 32714.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114393 restraints weight = 26892.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114406 restraints weight = 25624.793| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29707 Z= 0.151 Angle : 0.664 12.373 40765 Z= 0.349 Chirality : 0.040 0.263 4670 Planarity : 0.004 0.068 4566 Dihedral : 20.174 176.848 5191 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 3.72 % Allowed : 22.05 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.89 (0.15), residues: 3099 helix: 2.34 (0.12), residues: 1937 sheet: 0.16 (0.30), residues: 297 loop : -0.90 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 268 TYR 0.014 0.001 TYR I 572 PHE 0.021 0.001 PHE P 233 TRP 0.038 0.001 TRP Q 73 HIS 0.010 0.001 HIS U 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (29707) covalent geometry : angle 0.66380 / 0.35 (40765) hydrogen bonds : bond 0.06137 / 6.83 ( 1851) hydrogen bonds : angle 3.94645 / 5.06 ( 5379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 438 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8531 (pp) REVERT: H 115 ASN cc_start: 0.8341 (t0) cc_final: 0.7109 (p0) REVERT: H 204 MET cc_start: 0.7645 (tpp) cc_final: 0.7343 (tpt) REVERT: I 495 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6854 (tm-30) REVERT: I 548 MET cc_start: 0.8826 (ttp) cc_final: 0.8430 (ttm) REVERT: I 558 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8147 (tt) REVERT: I 596 ASP cc_start: 0.7493 (t0) cc_final: 0.6954 (t0) REVERT: I 638 GLN cc_start: 0.9175 (tp40) cc_final: 0.8330 (tp40) REVERT: I 642 HIS cc_start: 0.8012 (m90) cc_final: 0.7259 (m90) REVERT: I 651 LEU cc_start: 0.7710 (mt) cc_final: 0.7482 (mt) REVERT: I 668 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8203 (tt) REVERT: K 84 LEU cc_start: 0.8381 (tp) cc_final: 0.7938 (tp) REVERT: K 103 ASP cc_start: 0.7392 (m-30) cc_final: 0.6716 (t0) REVERT: K 131 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: K 166 MET cc_start: 0.6937 (tpp) cc_final: 0.6558 (tmm) REVERT: K 218 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8867 (mt) REVERT: M 82 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: M 132 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7968 (t0) REVERT: N 29 ASP cc_start: 0.8681 (t0) cc_final: 0.8446 (t70) REVERT: O 255 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7516 (mm110) REVERT: P 100 LYS cc_start: 0.8268 (mppt) cc_final: 0.8006 (ttpt) REVERT: P 111 CYS cc_start: 0.8635 (t) cc_final: 0.8097 (t) REVERT: P 158 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7633 (mm-30) REVERT: P 161 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7821 (mtpt) REVERT: P 188 LYS cc_start: 0.9215 (mttm) cc_final: 0.8911 (mttm) REVERT: P 191 TYR cc_start: 0.7819 (t80) cc_final: 0.7561 (t80) REVERT: P 231 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7729 (tptp) REVERT: Q 88 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8327 (mpp) REVERT: Q 116 ARG cc_start: 0.7470 (ptm-80) cc_final: 0.7236 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: Q 145 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8657 (mtt90) REVERT: Q 201 HIS cc_start: 0.8809 (t70) cc_final: 0.8521 (t70) REVERT: Q 251 MET cc_start: 0.8836 (pmm) cc_final: 0.8575 (pmm) REVERT: R 119 LEU cc_start: 0.8421 (tp) cc_final: 0.7787 (pp) REVERT: S 10 GLN cc_start: 0.8909 (pp30) cc_final: 0.8639 (pp30) REVERT: S 98 ASP cc_start: 0.8195 (m-30) cc_final: 0.7169 (p0) REVERT: S 102 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8248 (mp0) REVERT: T 481 GLU cc_start: 0.7710 (mp0) cc_final: 0.7321 (mp0) REVERT: T 482 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7452 (tpp) REVERT: X 69 GLN cc_start: 0.7892 (mp10) cc_final: 0.7656 (mp10) outliers start: 106 outliers final: 72 residues processed: 516 average time/residue: 0.1742 time to fit residues: 140.0086 Evaluate side-chains 493 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 411 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 579 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 661 ILE Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain P residue 237 ASP Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 482 MET Chi-restraints excluded: chain T residue 484 GLU Chi-restraints excluded: chain T residue 550 CYS Chi-restraints excluded: chain W residue 11 LYS Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 296 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 545 GLN U 284 ASN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** 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 = 0.4371 r_free = 0.4371 target = 0.169798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115239 restraints weight = 57022.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110598 restraints weight = 35783.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111545 restraints weight = 32904.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111731 restraints weight = 28054.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111727 restraints weight = 26389.165| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29707 Z= 0.195 Angle : 0.701 13.385 40765 Z= 0.366 Chirality : 0.042 0.357 4670 Planarity : 0.004 0.062 4566 Dihedral : 20.176 176.080 5191 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.14 % Allowed : 22.09 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.82 (0.15), residues: 3099 helix: 2.30 (0.12), residues: 1939 sheet: 0.05 (0.30), residues: 307 loop : -0.95 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 35 TYR 0.016 0.002 TYR I 403 PHE 0.020 0.002 PHE P 233 TRP 0.040 0.002 TRP Q 73 HIS 0.033 0.001 HIS I 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (29707) covalent geometry : angle 0.70116 / 0.37 (40765) hydrogen bonds : bond 0.06381 / 7.07 ( 1851) hydrogen bonds : angle 4.00016 / 5.14 ( 5379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 424 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8531 (pp) REVERT: H 112 LEU cc_start: 0.9237 (tp) cc_final: 0.9005 (tp) REVERT: H 115 ASN cc_start: 0.8416 (t0) cc_final: 0.7195 (p0) REVERT: H 189 MET cc_start: 0.7906 (tpp) cc_final: 0.7142 (tpp) REVERT: H 204 MET cc_start: 0.7824 (tpp) cc_final: 0.7473 (tpt) REVERT: I 133 MET cc_start: 0.3556 (mmm) cc_final: 0.1615 (mtm) REVERT: I 495 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6999 (tm-30) REVERT: I 558 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8276 (tt) REVERT: I 596 ASP cc_start: 0.7661 (t0) cc_final: 0.7036 (t0) REVERT: I 638 GLN cc_start: 0.9194 (tp40) cc_final: 0.8380 (tp40) REVERT: I 642 HIS cc_start: 0.8139 (m90) cc_final: 0.7426 (m90) REVERT: I 651 LEU cc_start: 0.7760 (mt) cc_final: 0.7505 (mt) REVERT: I 668 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8261 (tt) REVERT: K 84 LEU cc_start: 0.8436 (tp) cc_final: 0.7991 (tp) REVERT: K 103 ASP cc_start: 0.7436 (m-30) cc_final: 0.6797 (t0) REVERT: K 131 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: K 166 MET cc_start: 0.7091 (tpp) cc_final: 0.6688 (tmm) REVERT: K 218 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8884 (mt) REVERT: K 247 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8572 (mm) REVERT: L 338 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8354 (mp) REVERT: M 82 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: M 132 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8197 (t0) REVERT: O 255 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7537 (mm110) REVERT: P 111 CYS cc_start: 0.8721 (t) cc_final: 0.8483 (t) REVERT: P 158 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7687 (mm-30) REVERT: P 231 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7803 (tptp) REVERT: Q 88 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8410 (mpp) REVERT: Q 119 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: Q 145 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8741 (mtt90) REVERT: Q 201 HIS cc_start: 0.8881 (t70) cc_final: 0.8581 (t70) REVERT: Q 251 MET cc_start: 0.8926 (pmm) cc_final: 0.8637 (pmm) REVERT: R 87 MET cc_start: 0.7159 (mmp) cc_final: 0.6808 (mmp) REVERT: R 101 MET cc_start: 0.4048 (mmt) cc_final: 0.3766 (mmt) REVERT: S 102 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8356 (mp0) REVERT: T 480 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7746 (mt) REVERT: X 69 GLN cc_start: 0.7940 (mp10) cc_final: 0.7708 (mp10) outliers start: 118 outliers final: 90 residues processed: 507 average time/residue: 0.1864 time to fit residues: 148.3061 Evaluate side-chains 506 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 404 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 579 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain P residue 237 ASP Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 550 CYS Chi-restraints excluded: chain W residue 11 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 109 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN M 80 ASN M 164 ASN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 545 GLN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.167550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112531 restraints weight = 56807.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107384 restraints weight = 37875.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108095 restraints weight = 34626.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108540 restraints weight = 29182.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108567 restraints weight = 27407.854| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29707 Z= 0.205 Angle : 0.738 15.513 40765 Z= 0.383 Chirality : 0.043 0.357 4670 Planarity : 0.004 0.059 4566 Dihedral : 20.175 176.496 5191 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 4.42 % Allowed : 22.69 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.68 (0.15), residues: 3099 helix: 2.19 (0.12), residues: 1938 sheet: -0.03 (0.30), residues: 310 loop : -1.00 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 116 TYR 0.016 0.002 TYR I 403 PHE 0.035 0.002 PHE P 233 TRP 0.047 0.002 TRP Q 73 HIS 0.013 0.001 HIS I 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (29707) covalent geometry : angle 0.73755 / 0.38 (40765) hydrogen bonds : bond 0.06491 / 7.19 ( 1851) hydrogen bonds : angle 4.05017 / 5.20 ( 5379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 411 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8566 (pp) REVERT: H 115 ASN cc_start: 0.8423 (t0) cc_final: 0.7961 (t0) REVERT: H 189 MET cc_start: 0.7914 (tpp) cc_final: 0.7178 (tpp) REVERT: H 204 MET cc_start: 0.7911 (tpp) cc_final: 0.7689 (tpp) REVERT: I 495 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7147 (tm-30) REVERT: I 558 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8222 (tt) REVERT: I 596 ASP cc_start: 0.7796 (t0) cc_final: 0.7271 (t0) REVERT: I 637 TYR cc_start: 0.8853 (t80) cc_final: 0.8646 (t80) REVERT: I 638 GLN cc_start: 0.9165 (tp40) cc_final: 0.8428 (tp40) REVERT: I 642 HIS cc_start: 0.8219 (m90) cc_final: 0.7479 (m90) REVERT: I 651 LEU cc_start: 0.7778 (mt) cc_final: 0.7474 (mt) REVERT: I 668 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8262 (tt) REVERT: I 681 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7480 (p0) REVERT: K 52 ASP cc_start: 0.7420 (t0) cc_final: 0.7201 (t0) REVERT: K 84 LEU cc_start: 0.8425 (tp) cc_final: 0.7958 (tp) REVERT: K 103 ASP cc_start: 0.7625 (m-30) cc_final: 0.6850 (t0) REVERT: K 131 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: K 166 MET cc_start: 0.7189 (tpp) cc_final: 0.6729 (tmm) REVERT: K 218 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8898 (mt) REVERT: K 247 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8568 (mm) REVERT: L 30 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: L 338 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8390 (mp) REVERT: M 82 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: M 92 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8726 (t80) REVERT: M 132 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8388 (t0) REVERT: O 255 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7623 (mm110) REVERT: O 265 GLU cc_start: 0.8921 (mp0) cc_final: 0.8603 (pm20) REVERT: O 278 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8408 (tppp) REVERT: P 111 CYS cc_start: 0.8854 (t) cc_final: 0.8590 (t) REVERT: P 158 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7669 (mm-30) REVERT: P 228 GLU cc_start: 0.9102 (mp0) cc_final: 0.8884 (pm20) REVERT: P 231 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7754 (tptp) REVERT: Q 88 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: Q 93 MET cc_start: 0.9072 (ttt) cc_final: 0.8843 (ttt) REVERT: Q 119 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: Q 121 CYS cc_start: 0.8889 (p) cc_final: 0.8207 (t) REVERT: Q 145 ARG cc_start: 0.9188 (mtt180) cc_final: 0.8783 (mtt90) REVERT: Q 177 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8783 (tp-100) REVERT: Q 201 HIS cc_start: 0.8920 (t70) cc_final: 0.8623 (t70) REVERT: R 101 MET cc_start: 0.3901 (mmt) cc_final: 0.3622 (mmt) REVERT: S 10 GLN cc_start: 0.8841 (pp30) cc_final: 0.8610 (pp30) REVERT: S 98 ASP cc_start: 0.8306 (m-30) cc_final: 0.7325 (p0) REVERT: S 102 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8377 (mp0) REVERT: T 482 MET cc_start: 0.7990 (tpp) cc_final: 0.7718 (mmt) REVERT: W 57 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7742 (mm-30) REVERT: X 11 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7485 (mmp80) REVERT: X 69 GLN cc_start: 0.7908 (mp10) cc_final: 0.7681 (mp10) outliers start: 126 outliers final: 92 residues processed: 506 average time/residue: 0.1915 time to fit residues: 151.8020 Evaluate side-chains 506 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 400 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 681 ASN Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 232 VAL Chi-restraints excluded: chain P residue 237 ASP Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 550 CYS Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain W residue 11 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 7 optimal weight: 70.0000 chunk 30 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 ASN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113528 restraints weight = 57046.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108947 restraints weight = 37801.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110017 restraints weight = 34750.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110087 restraints weight = 29528.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110092 restraints weight = 27718.385| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29707 Z= 0.162 Angle : 0.718 15.965 40765 Z= 0.370 Chirality : 0.041 0.387 4670 Planarity : 0.004 0.058 4566 Dihedral : 20.137 177.158 5191 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.00 % Allowed : 23.53 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.81 (0.15), residues: 3099 helix: 2.29 (0.12), residues: 1934 sheet: 0.05 (0.30), residues: 310 loop : -0.94 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 12 TYR 0.015 0.001 TYR I 572 PHE 0.034 0.001 PHE P 233 TRP 0.052 0.001 TRP Q 73 HIS 0.007 0.001 HIS I 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (29707) covalent geometry : angle 0.71773 / 0.37 (40765) hydrogen bonds : bond 0.06111 / 6.78 ( 1851) hydrogen bonds : angle 3.94473 / 5.06 ( 5379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 418 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 115 ASN cc_start: 0.8386 (t0) cc_final: 0.7940 (t0) REVERT: H 189 MET cc_start: 0.7807 (tpp) cc_final: 0.7269 (tpp) REVERT: H 204 MET cc_start: 0.7860 (tpp) cc_final: 0.7475 (tpt) REVERT: I 68 MET cc_start: 0.7746 (mpp) cc_final: 0.7481 (mpp) REVERT: I 495 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7200 (tm-30) REVERT: I 558 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8139 (tt) REVERT: I 596 ASP cc_start: 0.7802 (t0) cc_final: 0.7283 (t0) REVERT: I 637 TYR cc_start: 0.8818 (t80) cc_final: 0.8608 (t80) REVERT: I 638 GLN cc_start: 0.9145 (tp40) cc_final: 0.8379 (tp40) REVERT: I 642 HIS cc_start: 0.8205 (m90) cc_final: 0.7453 (m-70) REVERT: I 651 LEU cc_start: 0.7790 (mt) cc_final: 0.7494 (mt) REVERT: I 668 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8229 (tt) REVERT: I 681 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7441 (p0) REVERT: K 52 ASP cc_start: 0.7443 (t0) cc_final: 0.7222 (t0) REVERT: K 84 LEU cc_start: 0.8363 (tp) cc_final: 0.7907 (tp) REVERT: K 131 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: K 166 MET cc_start: 0.7173 (tpp) cc_final: 0.6715 (tmm) REVERT: K 218 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8870 (mt) REVERT: K 247 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8524 (mm) REVERT: L 30 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: L 190 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: L 338 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8361 (mp) REVERT: M 82 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: M 92 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8764 (t80) REVERT: N 147 TYR cc_start: 0.7786 (m-80) cc_final: 0.7550 (m-10) REVERT: O 255 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7652 (mm110) REVERT: P 158 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7587 (mm-30) REVERT: P 185 LYS cc_start: 0.9190 (tppt) cc_final: 0.8911 (mptt) REVERT: P 228 GLU cc_start: 0.9074 (mp0) cc_final: 0.8870 (pm20) REVERT: P 231 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7865 (tptp) REVERT: P 238 LEU cc_start: 0.8852 (tt) cc_final: 0.8416 (tp) REVERT: Q 88 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8570 (mpp) REVERT: Q 116 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7328 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: Q 121 CYS cc_start: 0.8843 (p) cc_final: 0.8175 (t) REVERT: Q 145 ARG cc_start: 0.9162 (mtt180) cc_final: 0.8796 (mtt90) REVERT: Q 177 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8827 (tp-100) REVERT: Q 201 HIS cc_start: 0.8878 (t70) cc_final: 0.8578 (t70) REVERT: R 87 MET cc_start: 0.7096 (mmp) cc_final: 0.6757 (mmp) REVERT: R 101 MET cc_start: 0.3832 (mmt) cc_final: 0.3573 (mmt) REVERT: R 141 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8581 (pm20) REVERT: S 10 GLN cc_start: 0.8859 (pp30) cc_final: 0.8601 (pp30) REVERT: S 15 TYR cc_start: 0.8977 (t80) cc_final: 0.8693 (t80) REVERT: S 98 ASP cc_start: 0.8272 (m-30) cc_final: 0.7178 (p0) REVERT: S 102 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8396 (mp0) REVERT: T 480 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7992 (mt) REVERT: T 482 MET cc_start: 0.7975 (tpp) cc_final: 0.7632 (mmt) REVERT: T 484 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: U 264 GLU cc_start: 0.8424 (pt0) cc_final: 0.7907 (pt0) REVERT: W 57 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7758 (mm-30) REVERT: X 11 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7382 (mmp80) REVERT: X 69 GLN cc_start: 0.7850 (mp10) cc_final: 0.7626 (mp10) outliers start: 114 outliers final: 81 residues processed: 501 average time/residue: 0.1859 time to fit residues: 145.4320 Evaluate side-chains 493 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 396 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 513 HIS Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 681 ASN Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 237 ASP Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 141 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 78 ASN Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 484 GLU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 11 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 182 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 195 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 286 optimal weight: 0.5980 chunk 279 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 638 GLN K 143 HIS K 249 ASN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN ** X 36 GLN ** 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 = 0.4353 r_free = 0.4353 target = 0.169080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.114752 restraints weight = 57283.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109804 restraints weight = 37303.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110883 restraints weight = 34472.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110963 restraints weight = 29180.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110983 restraints weight = 27700.517| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29707 Z= 0.152 Angle : 0.719 17.341 40765 Z= 0.370 Chirality : 0.041 0.363 4670 Planarity : 0.004 0.066 4566 Dihedral : 20.118 177.372 5191 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 3.68 % Allowed : 24.09 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.87 (0.15), residues: 3099 helix: 2.34 (0.12), residues: 1936 sheet: 0.07 (0.30), residues: 310 loop : -0.93 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 268 TYR 0.040 0.001 TYR P 191 PHE 0.038 0.001 PHE P 233 TRP 0.051 0.001 TRP Q 73 HIS 0.008 0.001 HIS U 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (29707) covalent geometry : angle 0.71888 / 0.37 (40765) hydrogen bonds : bond 0.05921 / 6.55 ( 1851) hydrogen bonds : angle 3.88860 / 5.01 ( 5379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 407 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8436 (pp) REVERT: H 107 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6638 (mtm-85) REVERT: H 115 ASN cc_start: 0.8368 (t0) cc_final: 0.7931 (t0) REVERT: H 189 MET cc_start: 0.7818 (tpp) cc_final: 0.7294 (tpp) REVERT: H 204 MET cc_start: 0.7856 (tpp) cc_final: 0.7470 (tpt) REVERT: I 68 MET cc_start: 0.7819 (mpp) cc_final: 0.7550 (mpp) REVERT: I 143 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8579 (m) REVERT: I 495 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7201 (tm-30) REVERT: I 558 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8097 (tt) REVERT: I 596 ASP cc_start: 0.7809 (t0) cc_final: 0.7264 (t0) REVERT: I 637 TYR cc_start: 0.8833 (t80) cc_final: 0.8617 (t80) REVERT: I 638 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8395 (tp40) REVERT: I 642 HIS cc_start: 0.8245 (m90) cc_final: 0.7473 (m-70) REVERT: I 651 LEU cc_start: 0.7783 (mt) cc_final: 0.7502 (mt) REVERT: I 668 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8249 (tt) REVERT: I 681 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7457 (p0) REVERT: K 131 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: K 166 MET cc_start: 0.7165 (tpp) cc_final: 0.6693 (tmm) REVERT: K 218 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (mt) REVERT: K 247 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8518 (mm) REVERT: L 30 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7326 (mtm-85) REVERT: L 190 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: L 338 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (mp) REVERT: M 82 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: M 92 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (t80) REVERT: N 147 TYR cc_start: 0.7750 (m-80) cc_final: 0.7532 (m-10) REVERT: O 195 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: O 255 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7710 (mm110) REVERT: O 278 LYS cc_start: 0.8682 (tppp) cc_final: 0.8334 (tppp) REVERT: P 158 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7597 (mm-30) REVERT: P 185 LYS cc_start: 0.9209 (tppt) cc_final: 0.8917 (mptt) REVERT: P 228 GLU cc_start: 0.9095 (mp0) cc_final: 0.8876 (pm20) REVERT: P 231 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7891 (tptp) REVERT: P 238 LEU cc_start: 0.8716 (tt) cc_final: 0.8483 (tp) REVERT: Q 88 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8570 (mpp) REVERT: Q 116 ARG cc_start: 0.7618 (ptm-80) cc_final: 0.7348 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: Q 121 CYS cc_start: 0.8854 (p) cc_final: 0.8217 (t) REVERT: Q 145 ARG cc_start: 0.9183 (mtt180) cc_final: 0.8820 (mtt90) REVERT: Q 177 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8842 (tp-100) REVERT: Q 201 HIS cc_start: 0.8900 (t70) cc_final: 0.8589 (t70) REVERT: R 87 MET cc_start: 0.7155 (mmp) cc_final: 0.6792 (mmp) REVERT: R 101 MET cc_start: 0.3884 (mmt) cc_final: 0.3639 (mmt) REVERT: R 141 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: S 10 GLN cc_start: 0.8888 (pp30) cc_final: 0.8655 (pp30) REVERT: S 15 TYR cc_start: 0.8952 (t80) cc_final: 0.8733 (t80) REVERT: S 98 ASP cc_start: 0.8331 (m-30) cc_final: 0.7243 (p0) REVERT: S 102 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8410 (mp0) REVERT: T 480 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8064 (mt) REVERT: T 482 MET cc_start: 0.7932 (tpp) cc_final: 0.7578 (mmp) REVERT: T 484 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: W 57 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7757 (mm-30) REVERT: X 11 ARG cc_start: 0.7664 (mmp80) cc_final: 0.7450 (mmp80) outliers start: 105 outliers final: 79 residues processed: 481 average time/residue: 0.2002 time to fit residues: 150.5538 Evaluate side-chains 493 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 395 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 513 HIS Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 681 ASN Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 338 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 195 ASP Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 219 SER Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 237 ASP Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 141 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 58 CYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 484 GLU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 11 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 275 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 183 optimal weight: 0.0980 chunk 283 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 246 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 HIS P 252 ASN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 32 GLN X 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117009 restraints weight = 57105.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111901 restraints weight = 37604.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112697 restraints weight = 34808.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.112961 restraints weight = 28736.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113839 restraints weight = 27709.417| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29707 Z= 0.144 Angle : 0.737 18.175 40765 Z= 0.378 Chirality : 0.041 0.364 4670 Planarity : 0.004 0.061 4566 Dihedral : 20.090 177.988 5191 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 3.12 % Allowed : 24.79 % Favored : 72.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % 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: 1.96 (0.15), residues: 3099 helix: 2.40 (0.12), residues: 1936 sheet: 0.15 (0.30), residues: 310 loop : -0.90 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 12 TYR 0.023 0.001 TYR P 191 PHE 0.038 0.001 PHE P 233 TRP 0.057 0.002 TRP Q 73 HIS 0.009 0.001 HIS U 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (29707) covalent geometry : angle 0.73711 / 0.38 (40765) hydrogen bonds : bond 0.05562 / 6.19 ( 1851) hydrogen bonds : angle 3.81899 / 4.93 ( 5379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 408 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 103 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8230 (pp) REVERT: H 115 ASN cc_start: 0.8342 (t0) cc_final: 0.7792 (t0) REVERT: H 189 MET cc_start: 0.7665 (tpp) cc_final: 0.7182 (tpp) REVERT: H 204 MET cc_start: 0.7749 (tpp) cc_final: 0.7375 (tpt) REVERT: I 68 MET cc_start: 0.7833 (mpp) cc_final: 0.7592 (mpp) REVERT: I 133 MET cc_start: 0.3865 (mmm) cc_final: 0.1908 (mtm) REVERT: I 143 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8530 (m) REVERT: I 495 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7172 (tm-30) REVERT: I 558 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (tt) REVERT: I 570 ASP cc_start: 0.7411 (t0) cc_final: 0.6707 (t0) REVERT: I 596 ASP cc_start: 0.7777 (t0) cc_final: 0.7245 (t0) REVERT: I 637 TYR cc_start: 0.8795 (t80) cc_final: 0.8575 (t80) REVERT: I 638 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8306 (tp40) REVERT: I 642 HIS cc_start: 0.8177 (m90) cc_final: 0.7329 (m90) REVERT: I 651 LEU cc_start: 0.7782 (mt) cc_final: 0.7572 (mt) REVERT: I 668 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (tt) REVERT: I 681 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7375 (p0) REVERT: K 131 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: K 166 MET cc_start: 0.7063 (tpp) cc_final: 0.6622 (tmm) REVERT: K 218 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8832 (mt) REVERT: L 30 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7314 (mtm-85) REVERT: M 82 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: N 10 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8489 (ttpt) REVERT: N 101 MET cc_start: 0.7535 (mmm) cc_final: 0.7201 (tpt) REVERT: N 147 TYR cc_start: 0.7702 (m-80) cc_final: 0.7469 (m-10) REVERT: O 255 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7725 (mm110) REVERT: O 278 LYS cc_start: 0.8611 (tppp) cc_final: 0.8258 (tppp) REVERT: P 158 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7538 (mm-30) REVERT: P 185 LYS cc_start: 0.9181 (tppt) cc_final: 0.8904 (mptt) REVERT: P 228 GLU cc_start: 0.9051 (mp0) cc_final: 0.8820 (pm20) REVERT: P 231 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7894 (tptp) REVERT: Q 88 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8597 (mpp) REVERT: Q 116 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.7348 (ptm-80) REVERT: Q 119 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: Q 121 CYS cc_start: 0.8789 (p) cc_final: 0.8330 (t) REVERT: Q 136 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8629 (p0) REVERT: Q 145 ARG cc_start: 0.9131 (mtt180) cc_final: 0.8826 (mtt90) REVERT: Q 177 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8825 (tp-100) REVERT: Q 201 HIS cc_start: 0.8866 (t70) cc_final: 0.8543 (t70) REVERT: R 87 MET cc_start: 0.7138 (mmp) cc_final: 0.6775 (mmp) REVERT: R 101 MET cc_start: 0.3877 (mmt) cc_final: 0.3621 (mmt) REVERT: R 141 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: S 10 GLN cc_start: 0.8864 (pp30) cc_final: 0.8622 (pp30) REVERT: S 57 GLN cc_start: 0.8150 (tp40) cc_final: 0.7950 (tp-100) REVERT: S 98 ASP cc_start: 0.8295 (m-30) cc_final: 0.7239 (p0) REVERT: T 480 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7914 (mt) REVERT: T 482 MET cc_start: 0.7858 (tpp) cc_final: 0.7533 (mmp) REVERT: W 57 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7722 (mm-30) outliers start: 89 outliers final: 63 residues processed: 466 average time/residue: 0.2078 time to fit residues: 150.7512 Evaluate side-chains 474 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 513 HIS Chi-restraints excluded: chain I residue 550 LEU Chi-restraints excluded: chain I residue 558 LEU Chi-restraints excluded: chain I residue 568 VAL Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 681 ASN Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 HIS Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 223 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 119 GLN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 141 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 67 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 14 optimal weight: 50.0000 chunk 269 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** 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 = 0.4352 r_free = 0.4352 target = 0.169022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114718 restraints weight = 57230.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110289 restraints weight = 38170.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111176 restraints weight = 34942.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111303 restraints weight = 29866.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111319 restraints weight = 27999.761| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29707 Z= 0.162 Angle : 0.751 17.912 40765 Z= 0.385 Chirality : 0.042 0.364 4670 Planarity : 0.004 0.059 4566 Dihedral : 20.095 177.877 5191 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.77 % Allowed : 25.42 % Favored : 71.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.00 % 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: 1.91 (0.15), residues: 3099 helix: 2.36 (0.12), residues: 1930 sheet: 0.11 (0.30), residues: 308 loop : -0.87 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 268 TYR 0.038 0.002 TYR P 191 PHE 0.041 0.001 PHE P 233 TRP 0.056 0.002 TRP Q 73 HIS 0.007 0.001 HIS U 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (29707) covalent geometry : angle 0.75143 / 0.39 (40765) hydrogen bonds : bond 0.05743 / 6.36 ( 1851) hydrogen bonds : angle 3.88263 / 5.05 ( 5379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5977.72 seconds wall clock time: 103 minutes 28.52 seconds (6208.52 seconds total)