Starting phenix.real_space_refine on Sat Jul 4 09:23:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5v_14341/07_2026/7r5v_14341.map" } resolution = 4.55 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= 0.005 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1691 atoms to isotropic. 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 63 5.49 5 S 92 5.16 5 C 11668 2.51 5 N 3126 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18507 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1013 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2686 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 6 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "K" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1026 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 125} Chain breaks: 1 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: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2397 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 2 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: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2452 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: {'PTRANS': 8, '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: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1732 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1346 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 3.69, per 1000 atoms: 0.20 Number of scatterers: 18507 At special positions: 0 Unit cell: (113.847, 177.834, 191.13, 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 92 16.00 P 63 15.00 O 3558 8.00 N 3126 7.00 C 11668 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: 1.37 Conformation dependent library (CDL) restraints added in 724.4 milliseconds 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4170 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 11 sheets defined 63.6% alpha, 12.8% beta 20 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'H' and resid 40 through 64 Processing helix chain 'H' and resid 79 through 115 Processing helix chain 'H' and resid 125 through 183 removed outlier: 3.635A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 183 " --> pdb=" O LYS H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 364 through 369 removed outlier: 4.192A pdb=" N ASN I 368 " --> pdb=" O GLY I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 380 removed outlier: 3.516A pdb=" N LEU I 373 " --> pdb=" O ASN I 369 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS I 378 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG I 380 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 404 removed outlier: 3.706A pdb=" N LYS I 404 " --> pdb=" O CYS I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.559A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 443 Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.678A pdb=" N GLN I 457 " --> pdb=" O SER I 453 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 474 removed outlier: 3.679A pdb=" N LEU I 473 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 483 Processing helix chain 'I' and resid 486 through 509 Processing helix chain 'I' and resid 530 through 551 Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.512A pdb=" N LEU I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 576 Processing helix chain 'I' and resid 584 through 593 Processing helix chain 'I' and resid 596 through 617 Processing helix chain 'I' and resid 635 through 651 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 698 Processing helix chain 'I' and resid 719 through 726 Processing helix chain 'I' and resid 728 through 738 Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 54 through 77 Processing helix chain 'K' and resid 85 through 150 removed outlier: 3.660A pdb=" N LEU K 89 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 38 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 87 through 103 Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 189 through 205 Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 268 Processing helix chain 'L' and resid 276 through 296 Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 324 through 326 No H-bonds generated for 'chain 'L' and resid 324 through 326' Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.612A pdb=" N LEU L 338 " --> pdb=" O TYR L 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 36 Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.923A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 89 through 94 Processing helix chain 'M' and resid 113 through 125 removed outlier: 3.969A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 4.023A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 4.423A pdb=" N LEU N 116 " --> pdb=" O LEU N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 removed outlier: 4.186A pdb=" N LEU N 175 " --> pdb=" O ASN N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 304 through 313 removed outlier: 4.504A pdb=" N ALA N 310 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Proline residue: N 311 - end of helix Processing helix chain 'N' and resid 320 through 325 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.655A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 161 through 169 Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 201 through 204 removed outlier: 3.740A pdb=" N LEU O 204 " --> pdb=" O PHE O 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 201 through 204' Processing helix chain 'O' and resid 261 through 278 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 removed outlier: 4.070A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.577A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 256 No H-bonds generated for 'chain 'P' and resid 254 through 256' Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'P' and resid 271 through 282 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.626A 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 136 through 198 removed outlier: 4.157A pdb=" N GLU Q 170 " --> pdb=" O VAL Q 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Q 171 " --> pdb=" O GLU Q 167 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET Q 172 " --> pdb=" O THR Q 168 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY Q 174 " --> pdb=" O GLU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 229 removed outlier: 3.972A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 232 No H-bonds generated for 'chain 'Q' and resid 230 through 232' Processing helix chain 'Q' and resid 234 through 247 Processing helix chain 'Q' and resid 248 through 264 removed outlier: 3.903A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS Q 264 " --> pdb=" O GLU Q 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 269 Proline residue: U 256 - end of helix Processing helix chain 'U' and resid 271 through 375 Proline residue: U 332 - end of helix removed outlier: 4.376A pdb=" N LYS U 335 " --> pdb=" O GLU U 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN U 336 " --> pdb=" O PRO U 332 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU U 337 " --> pdb=" O GLN U 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 395 removed outlier: 3.822A pdb=" N LEU U 390 " --> pdb=" O SER U 386 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS U 393 " --> pdb=" O ALA U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 412 Processing helix chain 'R' and resid 168 through 177 Processing sheet with id=AA1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.810A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.810A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 252 " --> pdb=" O TRP L 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER N 298 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE N 334 " --> pdb=" O GLN N 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'M' and resid 128 through 131 removed outlier: 8.671A pdb=" N LEU M 129 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE M 99 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS M 131 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA M 101 " --> pdb=" O CYS M 131 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 120 through 124 removed outlier: 4.258A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 113 through 114 removed outlier: 6.536A pdb=" N VAL O 124 " --> pdb=" O PHE O 139 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE O 139 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE O 126 " --> pdb=" O SER O 137 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER O 137 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR O 128 " --> pdb=" O LEU O 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 210 through 211 removed outlier: 3.870A pdb=" N ASP O 249 " --> pdb=" O LEU O 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.710A pdb=" N LYS P 100 " --> pdb=" O LEU P 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.784A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 195 through 196 removed outlier: 4.018A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) 1142 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.76 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: 4311 1.33 - 1.45: 4111 1.45 - 1.58: 10300 1.58 - 1.70: 124 1.70 - 1.82: 140 Bond restraints: 18986 Sorted by residual: bond pdb=" C3' DC J 29 " pdb=" C2' DC J 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 bond pdb=" C3' DG J 28 " pdb=" C2' DG J 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DT J 40 " pdb=" C2' DT J 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.28e+00 bond pdb=" N ARG N 194 " pdb=" CA ARG N 194 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.24e-02 6.50e+03 8.66e+00 bond pdb=" C3' DT i 196 " pdb=" C2' DT i 196 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.59e+00 ... (remaining 18981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 25435 2.26 - 4.51: 415 4.51 - 6.77: 52 6.77 - 9.03: 7 9.03 - 11.29: 1 Bond angle restraints: 25910 Sorted by residual: angle pdb=" N3 DT i 196 " pdb=" C4 DT i 196 " pdb=" O4 DT i 196 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT i 219 " pdb=" C4 DT i 219 " pdb=" O4 DT i 219 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT J 20 " pdb=" C4 DT J 20 " pdb=" O4 DT J 20 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT J 39 " pdb=" C4 DT J 39 " pdb=" O4 DT J 39 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT i 210 " pdb=" C4 DT i 210 " pdb=" O4 DT i 210 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 25905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9910 17.72 - 35.45: 1045 35.45 - 53.17: 355 53.17 - 70.89: 61 70.89 - 88.61: 16 Dihedral angle restraints: 11387 sinusoidal: 5047 harmonic: 6340 Sorted by residual: dihedral pdb=" C ASN N 129 " pdb=" N ASN N 129 " pdb=" CA ASN N 129 " pdb=" CB ASN N 129 " ideal model delta harmonic sigma weight residual -122.60 -133.08 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA ARG H 105 " pdb=" C ARG H 105 " pdb=" N MET H 106 " pdb=" CA MET H 106 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N ASN N 129 " pdb=" C ASN N 129 " pdb=" CA ASN N 129 " pdb=" CB ASN N 129 " ideal model delta harmonic sigma weight residual 122.80 131.94 -9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 11384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2597 0.063 - 0.125: 367 0.125 - 0.188: 23 0.188 - 0.250: 3 0.250 - 0.313: 1 Chirality restraints: 2991 Sorted by residual: chirality pdb=" CA ASN N 129 " pdb=" N ASN N 129 " pdb=" C ASN N 129 " pdb=" CB ASN N 129 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE H 98 " pdb=" N ILE H 98 " pdb=" C ILE H 98 " pdb=" CB ILE H 98 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU N 193 " pdb=" N LEU N 193 " pdb=" C LEU N 193 " pdb=" CB LEU N 193 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 2988 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 225 " 0.029 2.00e-02 2.50e+03 2.86e-02 2.04e+01 pdb=" CG TRP L 225 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP L 225 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 225 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP L 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 105 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ARG H 105 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG H 105 " -0.015 2.00e-02 2.50e+03 pdb=" N MET H 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 163 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASP Q 163 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP Q 163 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS Q 164 " -0.012 2.00e-02 2.50e+03 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 754 2.71 - 3.26: 19524 3.26 - 3.81: 32280 3.81 - 4.35: 37551 4.35 - 4.90: 60219 Nonbonded interactions: 150328 Sorted by model distance: nonbonded pdb=" OD1 ASN M 71 " pdb=" OG1 THR M 102 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR O 128 " pdb=" O ASP O 136 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP I 596 " pdb=" OG SER I 598 " model vdw 2.189 3.040 nonbonded pdb=" O ARG O 23 " pdb=" OG1 THR O 26 " model vdw 2.191 3.040 nonbonded pdb=" CD1 ILE O 173 " pdb=" CB SER R 168 " model vdw 2.193 3.860 ... (remaining 150323 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.630 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 0.036 18986 Z= 0.264 Angle : 0.701 11.285 25910 Z= 0.455 Chirality : 0.042 0.313 2991 Planarity : 0.004 0.043 3026 Dihedral : 16.533 88.614 7217 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.21 % Allowed : 0.73 % Favored : 99.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.43 % 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: 1.11 (0.19), residues: 2078 helix: 1.34 (0.15), residues: 1263 sheet: 0.64 (0.32), residues: 251 loop : -0.48 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 120 TYR 0.016 0.001 TYR L 207 PHE 0.027 0.001 PHE K 97 TRP 0.077 0.001 TRP L 225 HIS 0.004 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.26 (18986) covalent geometry : angle 0.70057 / 0.45 (25910) hydrogen bonds : bond 0.14250 / 9.61 ( 1169) hydrogen bonds : angle 6.19056 / 4.55 ( 3453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 498 LYS cc_start: 0.9433 (pptt) cc_final: 0.9151 (pptt) REVERT: I 603 LEU cc_start: 0.9500 (mm) cc_final: 0.9199 (mm) REVERT: I 607 MET cc_start: 0.9355 (mpp) cc_final: 0.8714 (mpp) REVERT: L 230 MET cc_start: 0.7315 (tpt) cc_final: 0.6534 (tpp) REVERT: M 68 PHE cc_start: 0.9037 (m-80) cc_final: 0.8641 (m-10) REVERT: N 323 LEU cc_start: 0.9497 (mm) cc_final: 0.9271 (mm) REVERT: O 136 ASP cc_start: 0.8768 (t0) cc_final: 0.8551 (t0) REVERT: O 209 LEU cc_start: 0.9031 (pp) cc_final: 0.8821 (tt) REVERT: O 241 ASP cc_start: 0.8797 (t70) cc_final: 0.8500 (t0) REVERT: O 266 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8668 (tm-30) REVERT: Q 88 MET cc_start: -0.2589 (mmt) cc_final: -0.2790 (mtt) REVERT: U 309 MET cc_start: 0.8896 (mpp) cc_final: 0.8465 (mpp) outliers start: 4 outliers final: 0 residues processed: 217 average time/residue: 0.1283 time to fit residues: 43.8596 Evaluate side-chains 152 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 314 ASN I 353 ASN ** I 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.073331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056202 restraints weight = 153025.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055483 restraints weight = 109953.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.055793 restraints weight = 84386.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056064 restraints weight = 74447.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.056171 restraints weight = 65561.245| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18986 Z= 0.187 Angle : 0.623 8.780 25910 Z= 0.333 Chirality : 0.040 0.193 2991 Planarity : 0.004 0.041 3026 Dihedral : 16.665 67.342 2939 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.40 (0.19), residues: 2078 helix: 1.61 (0.14), residues: 1275 sheet: 0.57 (0.32), residues: 252 loop : -0.41 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 35 TYR 0.017 0.001 TYR L 207 PHE 0.024 0.002 PHE L 216 TRP 0.036 0.002 TRP L 225 HIS 0.005 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (18986) covalent geometry : angle 0.62266 / 0.33 (25910) hydrogen bonds : bond 0.05050 / 3.37 ( 1169) hydrogen bonds : angle 4.70601 / 3.45 ( 3453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.597 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: I 474 LEU cc_start: 0.9349 (tp) cc_final: 0.9046 (tp) REVERT: I 498 LYS cc_start: 0.9479 (pptt) cc_final: 0.9177 (pptt) REVERT: K 136 MET cc_start: 0.8490 (mmp) cc_final: 0.8276 (mmm) REVERT: L 214 ASN cc_start: 0.7784 (p0) cc_final: 0.7420 (p0) REVERT: L 230 MET cc_start: 0.7212 (tpt) cc_final: 0.6239 (tpp) REVERT: M 68 PHE cc_start: 0.9261 (m-80) cc_final: 0.8704 (m-10) REVERT: O 136 ASP cc_start: 0.8844 (t70) cc_final: 0.8348 (t0) REVERT: O 209 LEU cc_start: 0.9268 (pp) cc_final: 0.8929 (tt) REVERT: O 216 ASN cc_start: 0.9454 (p0) cc_final: 0.8280 (t0) REVERT: O 217 LEU cc_start: 0.9638 (tp) cc_final: 0.9345 (tp) REVERT: O 241 ASP cc_start: 0.9054 (t70) cc_final: 0.8800 (t0) REVERT: O 266 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8769 (tm-30) REVERT: Q 88 MET cc_start: -0.2713 (mmt) cc_final: -0.2948 (mtm) REVERT: U 325 ASP cc_start: 0.9247 (t0) cc_final: 0.9030 (t0) REVERT: U 342 ASP cc_start: 0.9243 (m-30) cc_final: 0.8918 (m-30) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1146 time to fit residues: 35.0716 Evaluate side-chains 147 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 163 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 30.0000 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 ASN ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 HIS U 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.072770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055852 restraints weight = 153593.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.055205 restraints weight = 107210.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055570 restraints weight = 84198.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055644 restraints weight = 84351.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055660 restraints weight = 70766.892| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18986 Z= 0.174 Angle : 0.587 7.869 25910 Z= 0.315 Chirality : 0.039 0.180 2991 Planarity : 0.003 0.042 3026 Dihedral : 16.940 63.418 2939 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.43 (0.19), residues: 2078 helix: 1.69 (0.14), residues: 1270 sheet: 0.47 (0.32), residues: 251 loop : -0.46 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 35 TYR 0.015 0.001 TYR Q 262 PHE 0.018 0.002 PHE L 216 TRP 0.016 0.001 TRP L 225 HIS 0.006 0.001 HIS M 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (18986) covalent geometry : angle 0.58716 / 0.32 (25910) hydrogen bonds : bond 0.04621 / 3.08 ( 1169) hydrogen bonds : angle 4.54428 / 3.33 ( 3453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.672 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: I 432 PHE cc_start: 0.8439 (m-80) cc_final: 0.7974 (m-80) REVERT: I 474 LEU cc_start: 0.9327 (tp) cc_final: 0.8991 (tp) REVERT: I 498 LYS cc_start: 0.9454 (pptt) cc_final: 0.9164 (pptt) REVERT: I 548 MET cc_start: 0.8881 (tpt) cc_final: 0.8627 (tpp) REVERT: I 603 LEU cc_start: 0.9628 (mm) cc_final: 0.9201 (mm) REVERT: I 607 MET cc_start: 0.9468 (mpp) cc_final: 0.9149 (mmt) REVERT: K 130 ASP cc_start: 0.9270 (m-30) cc_final: 0.8831 (p0) REVERT: K 136 MET cc_start: 0.8453 (mmp) cc_final: 0.8178 (mmm) REVERT: L 214 ASN cc_start: 0.8096 (p0) cc_final: 0.7673 (p0) REVERT: L 230 MET cc_start: 0.7184 (tpt) cc_final: 0.6202 (tpp) REVERT: N 167 MET cc_start: 0.7775 (tpt) cc_final: 0.6769 (tpt) REVERT: O 136 ASP cc_start: 0.8810 (t70) cc_final: 0.8254 (t0) REVERT: O 209 LEU cc_start: 0.9274 (pp) cc_final: 0.8973 (tt) REVERT: O 216 ASN cc_start: 0.9474 (p0) cc_final: 0.8354 (t0) REVERT: O 217 LEU cc_start: 0.9649 (tp) cc_final: 0.9375 (tp) REVERT: O 241 ASP cc_start: 0.9101 (t70) cc_final: 0.8870 (t0) REVERT: O 266 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8793 (tm-30) REVERT: Q 88 MET cc_start: -0.2976 (mmt) cc_final: -0.3186 (mtm) REVERT: U 342 ASP cc_start: 0.9237 (m-30) cc_final: 0.8907 (m-30) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.1208 time to fit residues: 36.0659 Evaluate side-chains 143 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 189 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 349 GLN I 602 GLN ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.073329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055278 restraints weight = 144424.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055323 restraints weight = 94263.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055229 restraints weight = 73903.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055399 restraints weight = 75642.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055674 restraints weight = 63419.775| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18986 Z= 0.121 Angle : 0.571 7.615 25910 Z= 0.299 Chirality : 0.039 0.176 2991 Planarity : 0.004 0.079 3026 Dihedral : 16.968 61.843 2939 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.46 (0.19), residues: 2078 helix: 1.74 (0.14), residues: 1269 sheet: 0.43 (0.32), residues: 251 loop : -0.50 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 116 TYR 0.016 0.001 TYR Q 262 PHE 0.026 0.001 PHE P 216 TRP 0.008 0.001 TRP L 225 HIS 0.006 0.001 HIS Q 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (18986) covalent geometry : angle 0.57053 / 0.30 (25910) hydrogen bonds : bond 0.04154 / 2.74 ( 1169) hydrogen bonds : angle 4.39188 / 3.21 ( 3453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.573 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: I 432 PHE cc_start: 0.8444 (m-80) cc_final: 0.7916 (m-80) REVERT: I 474 LEU cc_start: 0.9372 (tp) cc_final: 0.9048 (tp) REVERT: I 498 LYS cc_start: 0.9438 (pptt) cc_final: 0.9123 (pptt) REVERT: I 548 MET cc_start: 0.8936 (tpt) cc_final: 0.8685 (tpp) REVERT: I 603 LEU cc_start: 0.9614 (mm) cc_final: 0.9412 (mm) REVERT: K 130 ASP cc_start: 0.9180 (m-30) cc_final: 0.8788 (p0) REVERT: K 136 MET cc_start: 0.8475 (mmp) cc_final: 0.8205 (mmm) REVERT: L 214 ASN cc_start: 0.8103 (p0) cc_final: 0.7621 (p0) REVERT: L 230 MET cc_start: 0.7146 (tpt) cc_final: 0.6212 (tpp) REVERT: M 68 PHE cc_start: 0.9267 (m-80) cc_final: 0.8852 (m-10) REVERT: N 51 HIS cc_start: 0.9083 (m90) cc_final: 0.8640 (m-70) REVERT: N 167 MET cc_start: 0.7835 (tpt) cc_final: 0.6862 (tpt) REVERT: O 136 ASP cc_start: 0.8780 (t70) cc_final: 0.8234 (t0) REVERT: O 209 LEU cc_start: 0.9278 (pp) cc_final: 0.8974 (tt) REVERT: O 216 ASN cc_start: 0.9488 (p0) cc_final: 0.8396 (t0) REVERT: O 217 LEU cc_start: 0.9660 (tp) cc_final: 0.9349 (tp) REVERT: O 239 TYR cc_start: 0.9087 (m-80) cc_final: 0.7951 (m-80) REVERT: O 241 ASP cc_start: 0.9097 (t70) cc_final: 0.8865 (t0) REVERT: U 309 MET cc_start: 0.9256 (mmp) cc_final: 0.8917 (mmp) REVERT: U 325 ASP cc_start: 0.9191 (t70) cc_final: 0.8955 (t0) REVERT: U 342 ASP cc_start: 0.9219 (m-30) cc_final: 0.8920 (m-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1204 time to fit residues: 37.4947 Evaluate side-chains 157 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 151 optimal weight: 0.0470 chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 298 HIS ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN U 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.071480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054582 restraints weight = 152253.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053884 restraints weight = 105774.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054115 restraints weight = 85212.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054358 restraints weight = 76551.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054408 restraints weight = 67582.505| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18986 Z= 0.232 Angle : 0.642 8.556 25910 Z= 0.341 Chirality : 0.040 0.180 2991 Planarity : 0.004 0.061 3026 Dihedral : 17.041 60.839 2939 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.30 (0.18), residues: 2078 helix: 1.64 (0.14), residues: 1271 sheet: 0.21 (0.32), residues: 262 loop : -0.57 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 549 TYR 0.015 0.002 TYR I 488 PHE 0.024 0.002 PHE O 139 TRP 0.009 0.002 TRP I 446 HIS 0.007 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (18986) covalent geometry : angle 0.64201 / 0.34 (25910) hydrogen bonds : bond 0.04695 / 3.15 ( 1169) hydrogen bonds : angle 4.57575 / 3.36 ( 3453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.594 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: I 432 PHE cc_start: 0.8464 (m-80) cc_final: 0.7911 (m-80) REVERT: I 474 LEU cc_start: 0.9346 (tp) cc_final: 0.9032 (tp) REVERT: I 498 LYS cc_start: 0.9468 (pptt) cc_final: 0.9221 (pptt) REVERT: I 548 MET cc_start: 0.8943 (tpt) cc_final: 0.8716 (tpt) REVERT: I 603 LEU cc_start: 0.9639 (mm) cc_final: 0.9204 (mm) REVERT: I 607 MET cc_start: 0.9478 (mpp) cc_final: 0.9167 (mmt) REVERT: K 130 ASP cc_start: 0.9226 (m-30) cc_final: 0.8736 (p0) REVERT: L 207 TYR cc_start: 0.8409 (m-80) cc_final: 0.8197 (m-80) REVERT: L 214 ASN cc_start: 0.8350 (p0) cc_final: 0.7864 (p0) REVERT: L 221 MET cc_start: 0.9284 (ptp) cc_final: 0.9065 (ptp) REVERT: L 230 MET cc_start: 0.7285 (tpt) cc_final: 0.6281 (tpp) REVERT: M 9 LYS cc_start: 0.8288 (mttt) cc_final: 0.7809 (ttmt) REVERT: N 51 HIS cc_start: 0.9226 (m90) cc_final: 0.8766 (m-70) REVERT: N 167 MET cc_start: 0.7936 (tpt) cc_final: 0.6809 (tpt) REVERT: N 329 LYS cc_start: 0.8521 (mttt) cc_final: 0.7851 (mmtt) REVERT: O 136 ASP cc_start: 0.8864 (t70) cc_final: 0.8282 (t0) REVERT: O 150 ILE cc_start: 0.9002 (mm) cc_final: 0.8792 (mm) REVERT: O 209 LEU cc_start: 0.9272 (pp) cc_final: 0.8979 (tt) REVERT: O 216 ASN cc_start: 0.9556 (p0) cc_final: 0.8302 (t0) REVERT: O 217 LEU cc_start: 0.9672 (tp) cc_final: 0.9381 (tp) REVERT: O 241 ASP cc_start: 0.9125 (t70) cc_final: 0.8910 (t0) REVERT: U 325 ASP cc_start: 0.9175 (t70) cc_final: 0.8959 (t0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1256 time to fit residues: 37.0705 Evaluate side-chains 142 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 202 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 201 HIS U 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.072778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055903 restraints weight = 149091.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.055186 restraints weight = 100926.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.055452 restraints weight = 81747.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055664 restraints weight = 72497.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055713 restraints weight = 65070.952| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18986 Z= 0.130 Angle : 0.597 8.498 25910 Z= 0.311 Chirality : 0.040 0.217 2991 Planarity : 0.004 0.055 3026 Dihedral : 17.055 62.107 2939 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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 (0.19), residues: 2078 helix: 1.68 (0.14), residues: 1272 sheet: 0.25 (0.32), residues: 261 loop : -0.50 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 148 TYR 0.012 0.001 TYR N 269 PHE 0.013 0.001 PHE N 334 TRP 0.007 0.001 TRP H 148 HIS 0.005 0.001 HIS M 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (18986) covalent geometry : angle 0.59709 / 0.31 (25910) hydrogen bonds : bond 0.04137 / 2.75 ( 1169) hydrogen bonds : angle 4.45557 / 3.26 ( 3453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 432 PHE cc_start: 0.8456 (m-80) cc_final: 0.7846 (m-80) REVERT: I 474 LEU cc_start: 0.9337 (tp) cc_final: 0.8980 (tp) REVERT: I 498 LYS cc_start: 0.9414 (pptt) cc_final: 0.9151 (pptt) REVERT: I 603 LEU cc_start: 0.9626 (mm) cc_final: 0.9194 (mm) REVERT: I 607 MET cc_start: 0.9486 (mpp) cc_final: 0.9171 (mmt) REVERT: K 130 ASP cc_start: 0.9210 (m-30) cc_final: 0.8698 (p0) REVERT: L 214 ASN cc_start: 0.8338 (p0) cc_final: 0.7895 (p0) REVERT: L 230 MET cc_start: 0.7176 (tpt) cc_final: 0.6263 (tpp) REVERT: N 51 HIS cc_start: 0.9183 (m90) cc_final: 0.8721 (m-70) REVERT: N 167 MET cc_start: 0.7966 (tpt) cc_final: 0.6807 (tpt) REVERT: O 136 ASP cc_start: 0.8813 (t70) cc_final: 0.8270 (t0) REVERT: O 209 LEU cc_start: 0.9268 (pp) cc_final: 0.8960 (tt) REVERT: O 216 ASN cc_start: 0.9529 (p0) cc_final: 0.8398 (t0) REVERT: O 217 LEU cc_start: 0.9660 (tp) cc_final: 0.9364 (tp) REVERT: O 239 TYR cc_start: 0.9150 (m-80) cc_final: 0.7970 (m-80) REVERT: O 241 ASP cc_start: 0.9141 (t70) cc_final: 0.8925 (t0) REVERT: U 309 MET cc_start: 0.9211 (mmp) cc_final: 0.8994 (mmm) REVERT: U 320 MET cc_start: 0.8675 (mmp) cc_final: 0.8447 (mmm) REVERT: U 325 ASP cc_start: 0.9169 (t70) cc_final: 0.8951 (t0) REVERT: U 342 ASP cc_start: 0.9194 (m-30) cc_final: 0.8878 (m-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1220 time to fit residues: 38.7041 Evaluate side-chains 150 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 204 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.073644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.056625 restraints weight = 149162.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.055947 restraints weight = 102124.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.056091 restraints weight = 87133.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056318 restraints weight = 77291.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056378 restraints weight = 67468.394| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18986 Z= 0.116 Angle : 0.597 7.696 25910 Z= 0.306 Chirality : 0.039 0.197 2991 Planarity : 0.004 0.058 3026 Dihedral : 16.960 62.787 2939 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.36 (0.19), residues: 2078 helix: 1.68 (0.14), residues: 1272 sheet: 0.22 (0.32), residues: 255 loop : -0.50 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 160 TYR 0.017 0.001 TYR L 288 PHE 0.024 0.001 PHE P 216 TRP 0.007 0.001 TRP I 391 HIS 0.004 0.001 HIS M 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (18986) covalent geometry : angle 0.59660 / 0.31 (25910) hydrogen bonds : bond 0.03945 / 2.60 ( 1169) hydrogen bonds : angle 4.30345 / 3.15 ( 3453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 432 PHE cc_start: 0.8344 (m-80) cc_final: 0.7776 (m-80) REVERT: I 474 LEU cc_start: 0.9320 (tp) cc_final: 0.8977 (tp) REVERT: I 498 LYS cc_start: 0.9394 (pptt) cc_final: 0.9140 (pptt) REVERT: I 607 MET cc_start: 0.9485 (mpp) cc_final: 0.9056 (mpp) REVERT: K 130 ASP cc_start: 0.9207 (m-30) cc_final: 0.8700 (p0) REVERT: K 136 MET cc_start: 0.8465 (mmp) cc_final: 0.8212 (mmm) REVERT: L 214 ASN cc_start: 0.8292 (p0) cc_final: 0.7752 (p0) REVERT: L 230 MET cc_start: 0.7130 (tpt) cc_final: 0.6238 (tpp) REVERT: M 9 LYS cc_start: 0.8096 (mttt) cc_final: 0.7617 (ttmt) REVERT: M 119 LYS cc_start: 0.9596 (tmtt) cc_final: 0.9244 (mmtm) REVERT: N 51 HIS cc_start: 0.9121 (m90) cc_final: 0.8682 (m-70) REVERT: N 167 MET cc_start: 0.7923 (tpt) cc_final: 0.6646 (tpt) REVERT: N 309 LEU cc_start: 0.9300 (mt) cc_final: 0.9093 (mt) REVERT: O 136 ASP cc_start: 0.8697 (t70) cc_final: 0.8203 (t0) REVERT: O 144 ILE cc_start: 0.7548 (pt) cc_final: 0.7214 (mt) REVERT: O 209 LEU cc_start: 0.9249 (pp) cc_final: 0.8939 (tt) REVERT: O 216 ASN cc_start: 0.9506 (p0) cc_final: 0.8386 (t0) REVERT: O 217 LEU cc_start: 0.9618 (tp) cc_final: 0.9329 (tp) REVERT: O 239 TYR cc_start: 0.9091 (m-80) cc_final: 0.7931 (m-80) REVERT: O 241 ASP cc_start: 0.9129 (t70) cc_final: 0.8925 (t0) REVERT: U 309 MET cc_start: 0.9187 (mmp) cc_final: 0.8954 (mmm) REVERT: U 320 MET cc_start: 0.8604 (mmp) cc_final: 0.8392 (mmm) REVERT: U 342 ASP cc_start: 0.9154 (m-30) cc_final: 0.8883 (m-30) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1194 time to fit residues: 38.3914 Evaluate side-chains 154 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 210 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 HIS ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.071598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054513 restraints weight = 150788.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053819 restraints weight = 105902.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053781 restraints weight = 89842.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.054168 restraints weight = 79322.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054181 restraints weight = 70398.935| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18986 Z= 0.211 Angle : 0.644 8.388 25910 Z= 0.339 Chirality : 0.040 0.214 2991 Planarity : 0.004 0.063 3026 Dihedral : 17.021 64.180 2939 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.21 (0.19), residues: 2078 helix: 1.56 (0.14), residues: 1272 sheet: 0.13 (0.32), residues: 257 loop : -0.55 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 148 TYR 0.015 0.002 TYR R 169 PHE 0.024 0.002 PHE O 139 TRP 0.040 0.002 TRP P 222 HIS 0.006 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (18986) covalent geometry : angle 0.64441 / 0.34 (25910) hydrogen bonds : bond 0.04410 / 2.97 ( 1169) hydrogen bonds : angle 4.51995 / 3.31 ( 3453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 432 PHE cc_start: 0.8470 (m-80) cc_final: 0.7858 (m-80) REVERT: L 214 ASN cc_start: 0.8378 (p0) cc_final: 0.7896 (p0) REVERT: L 221 MET cc_start: 0.9260 (ptp) cc_final: 0.8877 (ptp) REVERT: L 230 MET cc_start: 0.7282 (tpt) cc_final: 0.6282 (tpp) REVERT: L 285 ASP cc_start: 0.8862 (t0) cc_final: 0.8533 (t70) REVERT: M 9 LYS cc_start: 0.8241 (mttt) cc_final: 0.7740 (ttmt) REVERT: N 51 HIS cc_start: 0.9214 (m90) cc_final: 0.8781 (m-70) REVERT: N 167 MET cc_start: 0.8015 (tpt) cc_final: 0.6850 (tpt) REVERT: N 329 LYS cc_start: 0.8494 (mttt) cc_final: 0.7819 (mmtt) REVERT: O 136 ASP cc_start: 0.8808 (t70) cc_final: 0.8269 (t0) REVERT: O 144 ILE cc_start: 0.7590 (pt) cc_final: 0.7260 (mt) REVERT: O 209 LEU cc_start: 0.9264 (pp) cc_final: 0.8978 (tt) REVERT: O 216 ASN cc_start: 0.9540 (p0) cc_final: 0.8279 (t0) REVERT: O 217 LEU cc_start: 0.9649 (tp) cc_final: 0.9356 (tp) REVERT: O 241 ASP cc_start: 0.9163 (t70) cc_final: 0.8955 (t0) REVERT: Q 88 MET cc_start: -0.3118 (mtm) cc_final: -0.4018 (mmp) REVERT: U 309 MET cc_start: 0.9205 (mmp) cc_final: 0.8953 (mmm) REVERT: U 320 MET cc_start: 0.8714 (mmp) cc_final: 0.8493 (mmm) REVERT: U 325 ASP cc_start: 0.9222 (t70) cc_final: 0.9014 (t0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1254 time to fit residues: 36.2879 Evaluate side-chains 144 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 0.0170 chunk 156 optimal weight: 5.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN L 292 HIS ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 HIS U 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.073028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.055995 restraints weight = 149869.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.055300 restraints weight = 103980.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.055379 restraints weight = 86223.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.055838 restraints weight = 75781.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055784 restraints weight = 66814.056| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18986 Z= 0.128 Angle : 0.634 9.033 25910 Z= 0.327 Chirality : 0.041 0.306 2991 Planarity : 0.004 0.054 3026 Dihedral : 17.027 65.404 2939 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.26 (0.19), residues: 2078 helix: 1.58 (0.14), residues: 1272 sheet: 0.19 (0.32), residues: 255 loop : -0.49 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 47 TYR 0.021 0.001 TYR L 288 PHE 0.019 0.001 PHE P 216 TRP 0.023 0.001 TRP P 222 HIS 0.005 0.001 HIS Q 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (18986) covalent geometry : angle 0.63437 / 0.33 (25910) hydrogen bonds : bond 0.04023 / 2.66 ( 1169) hydrogen bonds : angle 4.43248 / 3.24 ( 3453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 432 PHE cc_start: 0.8405 (m-80) cc_final: 0.7813 (m-80) REVERT: I 474 LEU cc_start: 0.9323 (tp) cc_final: 0.8979 (tp) REVERT: I 498 LYS cc_start: 0.9440 (pptt) cc_final: 0.9170 (pptt) REVERT: K 130 ASP cc_start: 0.9297 (m-30) cc_final: 0.8948 (p0) REVERT: L 208 PHE cc_start: 0.7041 (p90) cc_final: 0.6818 (p90) REVERT: L 214 ASN cc_start: 0.8353 (p0) cc_final: 0.7882 (p0) REVERT: L 230 MET cc_start: 0.7208 (tpt) cc_final: 0.6324 (tpp) REVERT: M 9 LYS cc_start: 0.8098 (mttt) cc_final: 0.7607 (ttmt) REVERT: M 119 LYS cc_start: 0.9604 (tmtt) cc_final: 0.9240 (mmtm) REVERT: N 51 HIS cc_start: 0.9149 (m90) cc_final: 0.8720 (m-70) REVERT: N 167 MET cc_start: 0.7986 (tpt) cc_final: 0.6762 (tpt) REVERT: N 329 LYS cc_start: 0.8479 (mttt) cc_final: 0.7735 (mmtt) REVERT: O 136 ASP cc_start: 0.8738 (t70) cc_final: 0.8208 (t0) REVERT: O 144 ILE cc_start: 0.7543 (pt) cc_final: 0.7206 (mt) REVERT: O 209 LEU cc_start: 0.9263 (pp) cc_final: 0.8958 (tt) REVERT: O 216 ASN cc_start: 0.9493 (p0) cc_final: 0.8374 (t0) REVERT: O 217 LEU cc_start: 0.9616 (tp) cc_final: 0.9321 (tp) REVERT: O 239 TYR cc_start: 0.9114 (m-80) cc_final: 0.7919 (m-80) REVERT: P 165 MET cc_start: 0.9043 (ppp) cc_final: 0.8834 (ppp) REVERT: U 309 MET cc_start: 0.9190 (mmp) cc_final: 0.8938 (mmm) REVERT: U 342 ASP cc_start: 0.9162 (m-30) cc_final: 0.8859 (m-30) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1290 time to fit residues: 39.3156 Evaluate side-chains 156 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.072228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055273 restraints weight = 150481.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054329 restraints weight = 114184.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054547 restraints weight = 89347.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054909 restraints weight = 76823.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054962 restraints weight = 67841.476| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18986 Z= 0.155 Angle : 0.643 15.757 25910 Z= 0.334 Chirality : 0.040 0.191 2991 Planarity : 0.004 0.072 3026 Dihedral : 17.027 66.330 2939 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.22 (0.19), residues: 2078 helix: 1.57 (0.14), residues: 1271 sheet: 0.16 (0.32), residues: 257 loop : -0.55 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 35 TYR 0.010 0.001 TYR L 288 PHE 0.020 0.001 PHE M 92 TRP 0.020 0.001 TRP P 222 HIS 0.005 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (18986) covalent geometry : angle 0.64310 / 0.33 (25910) hydrogen bonds : bond 0.04104 / 2.73 ( 1169) hydrogen bonds : angle 4.49724 / 3.29 ( 3453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 432 PHE cc_start: 0.8387 (m-80) cc_final: 0.7789 (m-80) REVERT: I 474 LEU cc_start: 0.9334 (tp) cc_final: 0.9007 (tp) REVERT: I 498 LYS cc_start: 0.9439 (pptt) cc_final: 0.9189 (pptt) REVERT: K 130 ASP cc_start: 0.9314 (m-30) cc_final: 0.8955 (p0) REVERT: L 208 PHE cc_start: 0.7158 (p90) cc_final: 0.6902 (p90) REVERT: L 214 ASN cc_start: 0.8373 (p0) cc_final: 0.7927 (p0) REVERT: L 230 MET cc_start: 0.7201 (tpt) cc_final: 0.6232 (tpp) REVERT: M 9 LYS cc_start: 0.8123 (mttt) cc_final: 0.7624 (ttmt) REVERT: M 119 LYS cc_start: 0.9606 (tmtt) cc_final: 0.9261 (mmtm) REVERT: N 51 HIS cc_start: 0.9174 (m90) cc_final: 0.8753 (m-70) REVERT: N 329 LYS cc_start: 0.8480 (mttt) cc_final: 0.7753 (mmtt) REVERT: O 136 ASP cc_start: 0.8747 (t70) cc_final: 0.8205 (t0) REVERT: O 144 ILE cc_start: 0.7555 (pt) cc_final: 0.7235 (mt) REVERT: O 209 LEU cc_start: 0.9267 (pp) cc_final: 0.8972 (tt) REVERT: O 216 ASN cc_start: 0.9512 (p0) cc_final: 0.8267 (t0) REVERT: O 217 LEU cc_start: 0.9625 (tp) cc_final: 0.9340 (tp) REVERT: O 241 ASP cc_start: 0.9207 (t0) cc_final: 0.8945 (t0) REVERT: U 309 MET cc_start: 0.9205 (mmp) cc_final: 0.8948 (mmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1303 time to fit residues: 38.1590 Evaluate side-chains 145 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 173 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 211 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN K 39 GLN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 HIS U 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.073379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056443 restraints weight = 150219.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055880 restraints weight = 99604.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056045 restraints weight = 87507.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056056 restraints weight = 89006.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056205 restraints weight = 72270.266| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18986 Z= 0.120 Angle : 0.644 15.034 25910 Z= 0.330 Chirality : 0.040 0.205 2991 Planarity : 0.004 0.052 3026 Dihedral : 17.006 67.261 2939 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.19 (0.19), residues: 2078 helix: 1.50 (0.14), residues: 1276 sheet: 0.25 (0.32), residues: 255 loop : -0.51 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 35 TYR 0.019 0.001 TYR L 288 PHE 0.021 0.001 PHE O 287 TRP 0.021 0.001 TRP P 222 HIS 0.006 0.001 HIS Q 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (18986) covalent geometry : angle 0.64435 / 0.33 (25910) hydrogen bonds : bond 0.03946 / 2.60 ( 1169) hydrogen bonds : angle 4.40392 / 3.22 ( 3453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.58 seconds wall clock time: 51 minutes 22.79 seconds (3082.79 seconds total)