Starting phenix.real_space_refine on Mon Oct 26 09:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5p_55592/10_2026/9t5p_55592.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 12993 2.51 5 N 3198 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19782 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2669 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5778 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 673} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2678 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2669 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "E" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2516 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2495 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'EDO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 EDO B 901 " occ=0.00 ... (2 atoms not shown) pdb=" O2 EDO B 901 " occ=0.00 residue: pdb=" C1 EDO B 902 " occ=0.00 ... (2 atoms not shown) pdb=" O2 EDO B 902 " occ=0.00 Time building chain proxies: 3.85, per 1000 atoms: 0.19 Number of scatterers: 19782 At special positions: 0 Unit cell: (123.84, 118.08, 195.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3476 8.00 N 3198 7.00 C 12993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 354 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 354 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 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: 1.48 Conformation dependent library (CDL) restraints added in 759.2 milliseconds 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 10 sheets defined 66.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 4.794A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.584A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 314 through 346 removed outlier: 3.837A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.880A pdb=" N GLU A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.560A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 409 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.604A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.955A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 3.914A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.567A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.392A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 287 removed outlier: 4.510A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.215A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 584 through 589 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.735A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.772A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'B' and resid 787 through 794 removed outlier: 3.535A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.013A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.118A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.708A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 258 removed outlier: 3.594A pdb=" N GLY C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 257 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 314 through 343 Processing helix chain 'C' and resid 353 through 360 removed outlier: 4.023A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.558A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.505A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.174A pdb=" N LEU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.581A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.004A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.337A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 3.744A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 3.835A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 287 removed outlier: 4.500A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.157A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 409 removed outlier: 3.885A pdb=" N ARG D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN D 404 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 143 through 157 removed outlier: 4.070A pdb=" N GLN E 151 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.702A pdb=" N LYS E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 186 removed outlier: 3.531A pdb=" N LEU E 176 " --> pdb=" O HIS E 172 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN E 181 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 205 removed outlier: 4.933A pdb=" N LYS E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 282 through 298 removed outlier: 3.915A pdb=" N GLU E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 331 removed outlier: 3.523A pdb=" N VAL E 310 " --> pdb=" O LYS E 306 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 315 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN E 328 " --> pdb=" O CYS E 324 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE E 329 " --> pdb=" O TYR E 325 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 387 removed outlier: 4.439A pdb=" N LYS E 364 " --> pdb=" O TYR E 360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 373 " --> pdb=" O TYR E 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU E 384 " --> pdb=" O CYS E 380 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'E' and resid 419 through 427 removed outlier: 3.771A pdb=" N VAL E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 425 " --> pdb=" O HIS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 439 removed outlier: 4.395A pdb=" N SER E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 455 Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.556A pdb=" N LYS F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.755A pdb=" N VAL F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 164 through 186 removed outlier: 3.551A pdb=" N LEU F 176 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN F 181 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TRP F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 206 removed outlier: 5.134A pdb=" N LYS F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 removed outlier: 3.559A pdb=" N THR F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 298 removed outlier: 3.888A pdb=" N LYS F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 331 removed outlier: 4.255A pdb=" N VAL F 310 " --> pdb=" O LYS F 306 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS F 315 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR F 325 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN F 328 " --> pdb=" O CYS F 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 348 Processing helix chain 'F' and resid 358 through 387 removed outlier: 3.615A pdb=" N SER F 368 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR F 369 " --> pdb=" O LEU F 365 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 378 " --> pdb=" O CYS F 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU F 384 " --> pdb=" O CYS F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 removed outlier: 4.144A pdb=" N LYS F 399 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 428 through 439 removed outlier: 3.788A pdb=" N VAL F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 454 Processing helix chain 'J' and resid 27 through 31 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 108 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56 removed outlier: 8.282A pdb=" N ARG C 306 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 297 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 292 through 296 Processing sheet with id=AA6, first strand: chain 'E' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'F' and resid 336 through 339 removed outlier: 3.528A pdb=" N HIS F 337 " --> pdb=" O CYS F 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.744A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.744A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6000 1.34 - 1.46: 5310 1.46 - 1.58: 8828 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 20302 Sorted by residual: bond pdb=" CA THR F 326 " pdb=" C THR F 326 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.43e-02 4.89e+03 7.19e+00 bond pdb=" CA TRP F 183 " pdb=" C TRP F 183 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.38e-02 5.25e+03 3.82e+00 bond pdb=" C TYR F 325 " pdb=" N THR F 326 " ideal model delta sigma weight residual 1.335 1.312 0.022 1.33e-02 5.65e+03 2.78e+00 bond pdb=" CA LEU F 365 " pdb=" C LEU F 365 " ideal model delta sigma weight residual 1.522 1.502 0.021 1.38e-02 5.25e+03 2.23e+00 bond pdb=" C HIS E 337 " pdb=" N VAL E 338 " ideal model delta sigma weight residual 1.331 1.317 0.015 1.11e-02 8.12e+03 1.73e+00 ... (remaining 20297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 26357 1.24 - 2.47: 914 2.47 - 3.71: 187 3.71 - 4.94: 49 4.94 - 6.18: 5 Bond angle restraints: 27512 Sorted by residual: angle pdb=" CA TRP F 183 " pdb=" C TRP F 183 " pdb=" N PHE F 184 " ideal model delta sigma weight residual 118.43 112.25 6.18 1.33e+00 5.65e-01 2.16e+01 angle pdb=" N VAL B 715 " pdb=" CA VAL B 715 " pdb=" C VAL B 715 " ideal model delta sigma weight residual 111.88 107.78 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N PHE A 372 " pdb=" CA PHE A 372 " pdb=" C PHE A 372 " ideal model delta sigma weight residual 113.43 108.81 4.62 1.26e+00 6.30e-01 1.35e+01 angle pdb=" N ALA B 481 " pdb=" CA ALA B 481 " pdb=" C ALA B 481 " ideal model delta sigma weight residual 112.93 108.15 4.78 1.33e+00 5.65e-01 1.29e+01 angle pdb=" N PHE E 388 " pdb=" CA PHE E 388 " pdb=" C PHE E 388 " ideal model delta sigma weight residual 114.56 110.22 4.34 1.27e+00 6.20e-01 1.17e+01 ... (remaining 27507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 11151 17.49 - 34.98: 713 34.98 - 52.47: 126 52.47 - 69.96: 29 69.96 - 87.45: 6 Dihedral angle restraints: 12025 sinusoidal: 4867 harmonic: 7158 Sorted by residual: dihedral pdb=" CA ALA F 332 " pdb=" C ALA F 332 " pdb=" N ILE F 333 " pdb=" CA ILE F 333 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER F 301 " pdb=" C SER F 301 " pdb=" N ASP F 302 " pdb=" CA ASP F 302 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual -86.00 -54.26 -31.74 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 12022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1894 0.029 - 0.059: 834 0.059 - 0.088: 249 0.088 - 0.117: 87 0.117 - 0.147: 15 Chirality restraints: 3079 Sorted by residual: chirality pdb=" CA ILE E 333 " pdb=" N ILE E 333 " pdb=" C ILE E 333 " pdb=" CB ILE E 333 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE F 333 " pdb=" N ILE F 333 " pdb=" C ILE F 333 " pdb=" CB ILE F 333 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ARG C 117 " pdb=" N ARG C 117 " pdb=" C ARG C 117 " pdb=" CB ARG C 117 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 3076 not shown) Planarity restraints: 3361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 124 " 0.026 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C SER J 124 " -0.090 2.00e-02 2.50e+03 pdb=" O SER J 124 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA J 125 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 21 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO C 22 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 22 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 22 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 27 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C PHE E 27 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE E 27 " -0.010 2.00e-02 2.50e+03 pdb=" N MET E 28 " -0.009 2.00e-02 2.50e+03 ... (remaining 3358 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6147 2.81 - 3.33: 23491 3.33 - 3.85: 34959 3.85 - 4.38: 40939 4.38 - 4.90: 65375 Nonbonded interactions: 170911 Sorted by model distance: nonbonded pdb=" O ALA B 481 " pdb=" O LYS B 482 " model vdw 2.282 3.040 nonbonded pdb=" O ASP A 371 " pdb=" OD1 ASP A 371 " model vdw 2.383 3.040 nonbonded pdb=" O ASN E 140 " pdb=" OD1 ASN E 140 " model vdw 2.386 3.040 nonbonded pdb=" O VAL B 459 " pdb=" O ALA B 481 " model vdw 2.410 3.040 nonbonded pdb=" O LYS F 138 " pdb=" OG1 THR F 139 " model vdw 2.411 3.040 ... (remaining 170906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 15 through 409) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 15 through 454) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 0.038 20317 Z= 0.201 Angle : 0.571 6.178 27542 Z= 0.333 Chirality : 0.038 0.147 3079 Planarity : 0.003 0.052 3361 Dihedral : 11.936 87.446 7342 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 65.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 6.83 % Allowed : 11.64 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2355 helix: 1.34 (0.15), residues: 1401 sheet: -1.33 (0.32), residues: 240 loop : -1.13 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 433 TYR 0.015 0.001 TYR A 30 PHE 0.009 0.001 PHE F 352 TRP 0.012 0.001 TRP F 24 HIS 0.004 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (20302) covalent geometry : angle 0.57013 / 0.33 (27512) SS BOND : bond 0.00220 / 0.14 ( 15) SS BOND : angle 0.85053 / 0.52 ( 30) hydrogen bonds : bond 0.16220 / 10.69 ( 1172) hydrogen bonds : angle 6.95248 / 4.97 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 273 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.9172 (OUTLIER) cc_final: 0.8115 (t70) REVERT: A 265 MET cc_start: 0.8413 (ttp) cc_final: 0.7965 (ttm) REVERT: B 35 MET cc_start: 0.8549 (mtt) cc_final: 0.8248 (mtt) REVERT: B 41 PHE cc_start: 0.9140 (t80) cc_final: 0.8827 (t80) REVERT: B 49 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: B 162 LYS cc_start: 0.9742 (mmtp) cc_final: 0.9517 (mtmt) REVERT: B 396 GLU cc_start: 0.9256 (tp30) cc_final: 0.8908 (mm-30) REVERT: B 418 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: B 476 LEU cc_start: 0.9584 (mt) cc_final: 0.9275 (tp) REVERT: B 510 LEU cc_start: 0.9035 (mt) cc_final: 0.8790 (pt) REVERT: C 155 HIS cc_start: 0.8751 (t70) cc_final: 0.8488 (t70) REVERT: C 233 ASP cc_start: 0.8438 (t0) cc_final: 0.8147 (t0) REVERT: C 324 PHE cc_start: 0.8394 (t80) cc_final: 0.8137 (t80) REVERT: D 35 MET cc_start: 0.8922 (mtt) cc_final: 0.8676 (mtp) REVERT: D 283 VAL cc_start: 0.8969 (t) cc_final: 0.8727 (m) REVERT: D 390 PHE cc_start: 0.9236 (t80) cc_final: 0.8826 (t80) REVERT: E 28 MET cc_start: 0.7659 (mtt) cc_final: 0.7434 (mtt) REVERT: E 295 ARG cc_start: 0.9348 (ttt90) cc_final: 0.9013 (tpt90) REVERT: E 329 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7544 (p90) REVERT: E 345 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7684 (p-80) REVERT: E 361 MET cc_start: 0.8777 (tpp) cc_final: 0.8135 (tmm) REVERT: F 19 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (mp) REVERT: F 37 MET cc_start: 0.9164 (ttp) cc_final: 0.8532 (tmm) REVERT: F 155 HIS cc_start: 0.7924 (t-90) cc_final: 0.7554 (t-170) REVERT: F 358 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8621 (pmm) REVERT: F 420 LEU cc_start: 0.8606 (tp) cc_final: 0.8313 (tt) outliers start: 149 outliers final: 83 residues processed: 405 average time/residue: 0.1538 time to fit residues: 93.4923 Evaluate side-chains 261 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 345 HIS Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 433 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN A 267 GLN B 46 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS B 694 HIS B 696 ASN B 758 GLN C 105 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS D 377 HIS E 145 GLN E 283 GLN E 337 HIS E 345 HIS E 428 GLN F 145 GLN F 283 GLN J 13 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.079818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060086 restraints weight = 127239.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.061589 restraints weight = 62920.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062569 restraints weight = 40035.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063160 restraints weight = 30357.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063403 restraints weight = 25942.260| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20317 Z= 0.166 Angle : 0.717 12.538 27542 Z= 0.365 Chirality : 0.044 0.285 3079 Planarity : 0.004 0.037 3361 Dihedral : 7.881 72.474 2792 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 5.04 % Allowed : 16.12 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2355 helix: 1.11 (0.14), residues: 1421 sheet: -0.92 (0.31), residues: 245 loop : -0.83 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.018 0.002 TYR F 349 PHE 0.020 0.002 PHE E 406 TRP 0.020 0.002 TRP B 475 HIS 0.008 0.001 HIS E 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (20302) covalent geometry : angle 0.71673 / 0.36 (27512) SS BOND : bond 0.00293 / 0.20 ( 15) SS BOND : angle 0.92596 / 0.54 ( 30) hydrogen bonds : bond 0.04378 / 2.92 ( 1172) hydrogen bonds : angle 4.90790 / 3.54 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8947 (mtp) cc_final: 0.8619 (mtt) REVERT: A 297 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7774 (m) REVERT: A 325 TYR cc_start: 0.8630 (t80) cc_final: 0.8013 (t80) REVERT: B 41 PHE cc_start: 0.8986 (t80) cc_final: 0.8746 (t80) REVERT: B 153 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8944 (pp) REVERT: B 162 LYS cc_start: 0.9792 (mmtp) cc_final: 0.9491 (mttt) REVERT: B 235 LYS cc_start: 0.9399 (tptp) cc_final: 0.9164 (tptp) REVERT: B 243 LEU cc_start: 0.9579 (mt) cc_final: 0.9099 (mp) REVERT: B 418 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: B 510 LEU cc_start: 0.9187 (mt) cc_final: 0.8858 (pt) REVERT: C 35 MET cc_start: 0.8970 (mtm) cc_final: 0.8729 (mtm) REVERT: C 162 LYS cc_start: 0.9134 (mttt) cc_final: 0.8877 (ptpt) REVERT: C 375 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8483 (mpp) REVERT: D 35 MET cc_start: 0.8996 (mtt) cc_final: 0.8769 (mpp) REVERT: D 248 LYS cc_start: 0.8822 (tptt) cc_final: 0.8438 (mmtm) REVERT: D 283 VAL cc_start: 0.8806 (t) cc_final: 0.8606 (m) REVERT: D 390 PHE cc_start: 0.9102 (t80) cc_final: 0.8764 (t80) REVERT: D 404 GLN cc_start: 0.7505 (pp30) cc_final: 0.6969 (pm20) REVERT: E 329 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7478 (p90) REVERT: F 37 MET cc_start: 0.9072 (ttp) cc_final: 0.8536 (tmm) REVERT: F 177 MET cc_start: 0.9183 (tmm) cc_final: 0.8975 (tmm) REVERT: F 293 LYS cc_start: 0.9663 (tptp) cc_final: 0.9381 (ptmm) REVERT: F 361 MET cc_start: 0.8744 (tmm) cc_final: 0.8525 (tmm) REVERT: F 420 LEU cc_start: 0.9081 (tp) cc_final: 0.8800 (tp) REVERT: F 422 MET cc_start: 0.9153 (tmm) cc_final: 0.8248 (mtt) REVERT: J 62 ASP cc_start: 0.9325 (p0) cc_final: 0.9070 (m-30) outliers start: 110 outliers final: 54 residues processed: 314 average time/residue: 0.1488 time to fit residues: 70.9372 Evaluate side-chains 230 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 421 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [226, 225, 90, 39, 103, 122, 54, 201, 5, 212, 119] chunk 226 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 201 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 212 optimal weight: 0.0170 chunk 119 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS B 46 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.080505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061418 restraints weight = 127991.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062933 restraints weight = 67611.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063283 restraints weight = 41980.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.063865 restraints weight = 33595.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.063775 restraints weight = 29697.371| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20317 Z= 0.126 Angle : 0.631 11.556 27542 Z= 0.321 Chirality : 0.041 0.204 3079 Planarity : 0.004 0.046 3361 Dihedral : 6.214 59.864 2688 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 4.26 % Allowed : 16.99 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2355 helix: 1.13 (0.14), residues: 1421 sheet: -0.75 (0.31), residues: 246 loop : -0.61 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 251 TYR 0.012 0.001 TYR B 305 PHE 0.019 0.001 PHE E 406 TRP 0.023 0.001 TRP A 168 HIS 0.008 0.001 HIS F 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (20302) covalent geometry : angle 0.63134 / 0.32 (27512) SS BOND : bond 0.00196 / 0.14 ( 15) SS BOND : angle 0.70522 / 0.43 ( 30) hydrogen bonds : bond 0.03818 / 2.58 ( 1172) hydrogen bonds : angle 4.56859 / 3.31 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 207 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8949 (mtp) cc_final: 0.8725 (mtt) REVERT: A 104 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.7700 (t70) REVERT: A 239 GLN cc_start: 0.8885 (pp30) cc_final: 0.8513 (pp30) REVERT: A 297 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7600 (m) REVERT: A 325 TYR cc_start: 0.8407 (t80) cc_final: 0.7605 (t80) REVERT: B 41 PHE cc_start: 0.9003 (t80) cc_final: 0.8796 (t80) REVERT: B 162 LYS cc_start: 0.9770 (mmtp) cc_final: 0.9492 (mttt) REVERT: B 375 MET cc_start: 0.8008 (ttp) cc_final: 0.7667 (ttm) REVERT: B 418 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8585 (pt0) REVERT: B 510 LEU cc_start: 0.9245 (mt) cc_final: 0.8932 (pt) REVERT: C 35 MET cc_start: 0.8942 (mtm) cc_final: 0.8677 (mtm) REVERT: C 288 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7735 (m110) REVERT: C 375 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8509 (mpp) REVERT: C 386 TYR cc_start: 0.8373 (m-80) cc_final: 0.8111 (m-80) REVERT: D 159 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6852 (mt) REVERT: D 248 LYS cc_start: 0.8905 (tptt) cc_final: 0.8675 (mmtt) REVERT: D 283 VAL cc_start: 0.8608 (t) cc_final: 0.8400 (m) REVERT: D 353 PHE cc_start: 0.4321 (OUTLIER) cc_final: 0.2600 (m-80) REVERT: D 390 PHE cc_start: 0.9086 (t80) cc_final: 0.8764 (t80) REVERT: D 404 GLN cc_start: 0.7352 (pp30) cc_final: 0.6806 (pm20) REVERT: E 28 MET cc_start: 0.7560 (mtt) cc_final: 0.7047 (mtt) REVERT: E 329 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7011 (p90) REVERT: E 358 MET cc_start: 0.7816 (mpp) cc_final: 0.7266 (mtm) REVERT: E 434 PHE cc_start: 0.9406 (t80) cc_final: 0.9201 (t80) REVERT: F 28 MET cc_start: 0.8325 (mmm) cc_final: 0.8107 (mmp) REVERT: F 37 MET cc_start: 0.9067 (ttp) cc_final: 0.8502 (tmm) REVERT: F 356 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8889 (t70) REVERT: F 358 MET cc_start: 0.8718 (pmm) cc_final: 0.8415 (pmm) REVERT: F 378 PHE cc_start: 0.8638 (m-80) cc_final: 0.7827 (m-80) REVERT: F 418 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.6586 (m-80) outliers start: 93 outliers final: 48 residues processed: 288 average time/residue: 0.1477 time to fit residues: 64.2278 Evaluate side-chains 231 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 453 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [204, 58, 9, 217, 212, 133, 64, 203, 98, 63, 55] chunk 204 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 212 optimal weight: 0.0070 chunk 133 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS C 404 GLN D 377 HIS ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061218 restraints weight = 128639.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.062694 restraints weight = 63045.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.063652 restraints weight = 40080.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.064234 restraints weight = 30551.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.064530 restraints weight = 26173.657| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20317 Z= 0.125 Angle : 0.622 13.091 27542 Z= 0.314 Chirality : 0.041 0.218 3079 Planarity : 0.004 0.044 3361 Dihedral : 5.848 59.326 2671 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 4.17 % Allowed : 18.09 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2355 helix: 1.14 (0.14), residues: 1416 sheet: -0.75 (0.31), residues: 244 loop : -0.61 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.017 0.001 TYR F 305 PHE 0.020 0.001 PHE E 406 TRP 0.017 0.001 TRP A 168 HIS 0.009 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20302) covalent geometry : angle 0.62232 / 0.31 (27512) SS BOND : bond 0.00251 / 0.18 ( 15) SS BOND : angle 0.76308 / 0.47 ( 30) hydrogen bonds : bond 0.03558 / 2.40 ( 1172) hydrogen bonds : angle 4.42254 / 3.20 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8994 (mtp) cc_final: 0.8705 (mtt) REVERT: A 238 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8290 (mm-30) REVERT: A 239 GLN cc_start: 0.8799 (pp30) cc_final: 0.8512 (pp30) REVERT: A 297 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7701 (m) REVERT: A 325 TYR cc_start: 0.8272 (t80) cc_final: 0.7498 (t80) REVERT: B 41 PHE cc_start: 0.9087 (t80) cc_final: 0.8864 (t80) REVERT: B 162 LYS cc_start: 0.9744 (mmtp) cc_final: 0.9508 (mttt) REVERT: B 375 MET cc_start: 0.7714 (ttp) cc_final: 0.7400 (ttm) REVERT: B 418 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: C 52 MET cc_start: 0.8196 (ptm) cc_final: 0.7908 (ptm) REVERT: C 104 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (m170) REVERT: C 375 MET cc_start: 0.9243 (mpp) cc_final: 0.8463 (mpp) REVERT: C 386 TYR cc_start: 0.8258 (m-80) cc_final: 0.7921 (m-80) REVERT: D 248 LYS cc_start: 0.8953 (tptt) cc_final: 0.8647 (mmtt) REVERT: D 283 VAL cc_start: 0.8677 (t) cc_final: 0.8452 (m) REVERT: D 375 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7357 (ptp) REVERT: D 390 PHE cc_start: 0.9122 (t80) cc_final: 0.8755 (t80) REVERT: D 404 GLN cc_start: 0.7347 (pp30) cc_final: 0.6813 (pm20) REVERT: E 28 MET cc_start: 0.7610 (mtt) cc_final: 0.7195 (mtt) REVERT: E 213 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8635 (mt) REVERT: E 329 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6738 (p90) REVERT: E 434 PHE cc_start: 0.9402 (t80) cc_final: 0.9166 (t80) REVERT: F 28 MET cc_start: 0.8277 (mmm) cc_final: 0.8041 (mmp) REVERT: F 37 MET cc_start: 0.9132 (ttp) cc_final: 0.8513 (tmm) REVERT: F 200 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8141 (mp) REVERT: F 292 ARG cc_start: 0.8973 (mmt-90) cc_final: 0.8258 (mmt180) REVERT: F 356 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8838 (t70) REVERT: F 378 PHE cc_start: 0.8669 (m-80) cc_final: 0.7939 (m-80) REVERT: F 418 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6876 (m-80) outliers start: 91 outliers final: 51 residues processed: 260 average time/residue: 0.1474 time to fit residues: 58.6071 Evaluate side-chains 229 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 453 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [133, 215, 223, 198, 211, 60, 52, 136, 41, 196, 179] chunk 133 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 179 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 400 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS C 404 GLN D 400 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.080634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061404 restraints weight = 127884.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062895 restraints weight = 63088.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.063851 restraints weight = 40083.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.064436 restraints weight = 30526.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.064675 restraints weight = 26176.571| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20317 Z= 0.121 Angle : 0.620 14.040 27542 Z= 0.309 Chirality : 0.040 0.164 3079 Planarity : 0.003 0.043 3361 Dihedral : 5.703 59.149 2664 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.35 % Allowed : 18.74 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2355 helix: 1.13 (0.14), residues: 1418 sheet: -0.61 (0.31), residues: 250 loop : -0.60 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 67 TYR 0.015 0.001 TYR F 305 PHE 0.041 0.001 PHE B 136 TRP 0.011 0.001 TRP D 168 HIS 0.012 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (20302) covalent geometry : angle 0.62042 / 0.31 (27512) SS BOND : bond 0.00229 / 0.16 ( 15) SS BOND : angle 0.64627 / 0.39 ( 30) hydrogen bonds : bond 0.03455 / 2.34 ( 1172) hydrogen bonds : angle 4.29820 / 3.12 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 183 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8810 (mtp) cc_final: 0.8548 (mtt) REVERT: A 104 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.7716 (t70) REVERT: A 238 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 239 GLN cc_start: 0.8963 (pp30) cc_final: 0.8667 (pp30) REVERT: A 297 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7869 (m) REVERT: A 325 TYR cc_start: 0.8233 (t80) cc_final: 0.7419 (t80) REVERT: A 343 MET cc_start: 0.8195 (ttm) cc_final: 0.7706 (ttm) REVERT: B 41 PHE cc_start: 0.9060 (t80) cc_final: 0.8819 (t80) REVERT: B 418 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: C 52 MET cc_start: 0.8183 (ptm) cc_final: 0.7796 (ptm) REVERT: C 162 LYS cc_start: 0.9055 (mttt) cc_final: 0.8850 (ptpt) REVERT: C 375 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8576 (mpp) REVERT: C 386 TYR cc_start: 0.8254 (m-80) cc_final: 0.7861 (m-80) REVERT: D 159 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7100 (mt) REVERT: D 248 LYS cc_start: 0.8740 (tptt) cc_final: 0.8461 (mmtt) REVERT: D 283 VAL cc_start: 0.8671 (t) cc_final: 0.8445 (m) REVERT: D 353 PHE cc_start: 0.4462 (OUTLIER) cc_final: 0.2745 (m-80) REVERT: D 390 PHE cc_start: 0.9133 (t80) cc_final: 0.8792 (t80) REVERT: D 404 GLN cc_start: 0.7275 (pp30) cc_final: 0.6734 (pm20) REVERT: E 28 MET cc_start: 0.7590 (mtt) cc_final: 0.7189 (mtt) REVERT: E 434 PHE cc_start: 0.9418 (t80) cc_final: 0.9163 (t80) REVERT: F 28 MET cc_start: 0.8249 (mmm) cc_final: 0.7996 (mmp) REVERT: F 37 MET cc_start: 0.9106 (ttp) cc_final: 0.8578 (tmm) REVERT: F 47 LEU cc_start: 0.9354 (tt) cc_final: 0.9044 (pp) REVERT: F 200 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8110 (mp) REVERT: F 292 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8143 (mmt180) REVERT: F 356 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8853 (t70) REVERT: F 378 PHE cc_start: 0.8665 (m-80) cc_final: 0.7919 (m-80) REVERT: F 418 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: F 442 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8732 (p) REVERT: J 73 ASP cc_start: 0.9026 (t0) cc_final: 0.8760 (t0) REVERT: J 83 MET cc_start: 0.6820 (ptp) cc_final: 0.6219 (mpp) outliers start: 95 outliers final: 60 residues processed: 261 average time/residue: 0.1399 time to fit residues: 56.2906 Evaluate side-chains 238 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 168 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [215, 212, 202, 56, 88, 148, 93, 142, 217, 201, 192] chunk 215 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 404 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.061260 restraints weight = 128009.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062745 restraints weight = 62627.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.063718 restraints weight = 39715.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064284 restraints weight = 30166.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064514 restraints weight = 25929.607| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20317 Z= 0.120 Angle : 0.625 15.557 27542 Z= 0.309 Chirality : 0.040 0.159 3079 Planarity : 0.003 0.043 3361 Dihedral : 5.557 59.315 2660 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.89 % Allowed : 19.70 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2355 helix: 1.14 (0.14), residues: 1422 sheet: -0.62 (0.31), residues: 250 loop : -0.61 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.013 0.001 TYR F 305 PHE 0.030 0.001 PHE B 136 TRP 0.030 0.001 TRP A 168 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (20302) covalent geometry : angle 0.62454 / 0.31 (27512) SS BOND : bond 0.00229 / 0.16 ( 15) SS BOND : angle 0.62765 / 0.38 ( 30) hydrogen bonds : bond 0.03385 / 2.30 ( 1172) hydrogen bonds : angle 4.24212 / 3.08 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 180 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8958 (mtp) cc_final: 0.8532 (mtt) REVERT: A 104 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.7726 (t70) REVERT: A 238 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 239 GLN cc_start: 0.9036 (pp30) cc_final: 0.8737 (pp30) REVERT: A 297 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7936 (m) REVERT: A 325 TYR cc_start: 0.8256 (t80) cc_final: 0.7585 (t80) REVERT: B 41 PHE cc_start: 0.9049 (t80) cc_final: 0.8825 (t80) REVERT: B 343 MET cc_start: 0.8552 (ttt) cc_final: 0.7995 (tmm) REVERT: B 418 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: C 52 MET cc_start: 0.8062 (ptm) cc_final: 0.7590 (ptm) REVERT: C 162 LYS cc_start: 0.9126 (mttt) cc_final: 0.8905 (mttt) REVERT: C 375 MET cc_start: 0.9251 (mpp) cc_final: 0.8576 (mpp) REVERT: C 386 TYR cc_start: 0.8370 (m-80) cc_final: 0.8031 (m-80) REVERT: D 35 MET cc_start: 0.9004 (mtp) cc_final: 0.8766 (ptp) REVERT: D 159 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7177 (mt) REVERT: D 248 LYS cc_start: 0.8761 (tptt) cc_final: 0.8482 (mmtt) REVERT: D 283 VAL cc_start: 0.8669 (t) cc_final: 0.8440 (m) REVERT: D 353 PHE cc_start: 0.4479 (OUTLIER) cc_final: 0.2775 (m-80) REVERT: D 390 PHE cc_start: 0.9134 (t80) cc_final: 0.8798 (t80) REVERT: D 404 GLN cc_start: 0.7278 (pp30) cc_final: 0.6740 (pm20) REVERT: E 28 MET cc_start: 0.7567 (mtt) cc_final: 0.7162 (mtt) REVERT: E 195 HIS cc_start: 0.9219 (t70) cc_final: 0.8923 (t-90) REVERT: E 434 PHE cc_start: 0.9427 (t80) cc_final: 0.9159 (t80) REVERT: F 28 MET cc_start: 0.8266 (mmm) cc_final: 0.7991 (mmp) REVERT: F 37 MET cc_start: 0.9150 (ttp) cc_final: 0.8502 (tmm) REVERT: F 199 ILE cc_start: 0.8910 (mm) cc_final: 0.8248 (mt) REVERT: F 200 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8117 (mp) REVERT: F 293 LYS cc_start: 0.9723 (tptp) cc_final: 0.9429 (pttt) REVERT: F 356 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8858 (t70) REVERT: F 378 PHE cc_start: 0.8475 (m-80) cc_final: 0.7746 (m-80) REVERT: F 418 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: F 442 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8673 (p) REVERT: J 83 MET cc_start: 0.6920 (ptp) cc_final: 0.6631 (ptp) outliers start: 85 outliers final: 62 residues processed: 250 average time/residue: 0.1428 time to fit residues: 55.3074 Evaluate side-chains 239 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [218, 119, 25, 41, 24, 59, 100, 2, 65, 74, 139] chunk 218 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 74 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.080780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061676 restraints weight = 128661.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063138 restraints weight = 62297.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.064108 restraints weight = 39510.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.064690 restraints weight = 30051.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.064938 restraints weight = 25757.709| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20317 Z= 0.115 Angle : 0.629 14.769 27542 Z= 0.310 Chirality : 0.040 0.161 3079 Planarity : 0.003 0.045 3361 Dihedral : 5.542 59.534 2660 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.89 % Allowed : 19.79 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2355 helix: 1.07 (0.14), residues: 1428 sheet: -0.44 (0.32), residues: 250 loop : -0.59 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 447 TYR 0.016 0.001 TYR D 325 PHE 0.026 0.001 PHE B 136 TRP 0.022 0.001 TRP B 143 HIS 0.006 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20302) covalent geometry : angle 0.62918 / 0.31 (27512) SS BOND : bond 0.00205 / 0.14 ( 15) SS BOND : angle 0.57205 / 0.35 ( 30) hydrogen bonds : bond 0.03380 / 2.30 ( 1172) hydrogen bonds : angle 4.21081 / 3.05 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8895 (mtp) cc_final: 0.8608 (mtt) REVERT: A 104 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.7680 (t70) REVERT: A 238 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 239 GLN cc_start: 0.9036 (pp30) cc_final: 0.8725 (pp30) REVERT: A 297 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7929 (m) REVERT: A 325 TYR cc_start: 0.8199 (t80) cc_final: 0.7493 (t80) REVERT: B 41 PHE cc_start: 0.9047 (t80) cc_final: 0.8823 (t80) REVERT: B 418 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: B 590 MET cc_start: 0.4490 (mmp) cc_final: 0.4019 (mmp) REVERT: C 52 MET cc_start: 0.7956 (ptm) cc_final: 0.7659 (ptt) REVERT: C 375 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8563 (mpp) REVERT: C 386 TYR cc_start: 0.8365 (m-80) cc_final: 0.7975 (m-80) REVERT: D 35 MET cc_start: 0.9021 (mtp) cc_final: 0.8183 (ptp) REVERT: D 159 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7098 (mt) REVERT: D 248 LYS cc_start: 0.8761 (tptt) cc_final: 0.8480 (mmtt) REVERT: D 283 VAL cc_start: 0.8587 (t) cc_final: 0.8365 (m) REVERT: D 353 PHE cc_start: 0.4406 (OUTLIER) cc_final: 0.2726 (m-80) REVERT: D 390 PHE cc_start: 0.9121 (t80) cc_final: 0.8795 (t80) REVERT: D 404 GLN cc_start: 0.7164 (pp30) cc_final: 0.6609 (pm20) REVERT: E 28 MET cc_start: 0.7590 (mtt) cc_final: 0.7199 (mtt) REVERT: E 195 HIS cc_start: 0.9226 (t70) cc_final: 0.8923 (t-90) REVERT: E 406 PHE cc_start: 0.7827 (p90) cc_final: 0.7340 (p90) REVERT: E 434 PHE cc_start: 0.9403 (t80) cc_final: 0.9166 (t80) REVERT: F 28 MET cc_start: 0.8260 (mmm) cc_final: 0.7971 (mmp) REVERT: F 37 MET cc_start: 0.9191 (ttp) cc_final: 0.8509 (tmm) REVERT: F 47 LEU cc_start: 0.9314 (tt) cc_final: 0.8810 (pp) REVERT: F 292 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8380 (mmp-170) REVERT: F 293 LYS cc_start: 0.9652 (tptp) cc_final: 0.9397 (pttt) REVERT: F 356 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8805 (t70) REVERT: F 378 PHE cc_start: 0.8467 (m-80) cc_final: 0.7706 (m-80) REVERT: F 418 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: F 442 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8632 (p) REVERT: J 83 MET cc_start: 0.6682 (ptp) cc_final: 0.6469 (mpp) outliers start: 85 outliers final: 63 residues processed: 253 average time/residue: 0.1469 time to fit residues: 57.3236 Evaluate side-chains 239 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 453 HIS Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [59, 11, 44, 65, 9, 54, 26, 183, 212, 217, 187] chunk 59 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.080869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.061796 restraints weight = 128109.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063319 restraints weight = 62494.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064300 restraints weight = 39679.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.064889 restraints weight = 30087.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065135 restraints weight = 25737.718| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20317 Z= 0.114 Angle : 0.636 14.925 27542 Z= 0.312 Chirality : 0.040 0.182 3079 Planarity : 0.003 0.046 3361 Dihedral : 5.499 59.695 2658 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.71 % Allowed : 20.38 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2355 helix: 1.09 (0.14), residues: 1428 sheet: -0.43 (0.31), residues: 250 loop : -0.56 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 447 TYR 0.019 0.001 TYR D 325 PHE 0.022 0.001 PHE B 136 TRP 0.016 0.001 TRP B 143 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20302) covalent geometry : angle 0.63657 / 0.31 (27512) SS BOND : bond 0.00211 / 0.15 ( 15) SS BOND : angle 0.54392 / 0.34 ( 30) hydrogen bonds : bond 0.03321 / 2.27 ( 1172) hydrogen bonds : angle 4.19717 / 3.05 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 180 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8931 (mtp) cc_final: 0.8479 (mtt) REVERT: A 104 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.7677 (t70) REVERT: A 238 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8464 (mm-30) REVERT: A 239 GLN cc_start: 0.9088 (pp30) cc_final: 0.8790 (pp30) REVERT: A 297 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7924 (m) REVERT: A 325 TYR cc_start: 0.8155 (t80) cc_final: 0.7435 (t80) REVERT: A 404 GLN cc_start: 0.8040 (tp40) cc_final: 0.7783 (tp-100) REVERT: B 41 PHE cc_start: 0.9049 (t80) cc_final: 0.8818 (t80) REVERT: B 343 MET cc_start: 0.8385 (ttt) cc_final: 0.7933 (tmm) REVERT: B 418 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: B 590 MET cc_start: 0.4719 (mmp) cc_final: 0.4322 (mmp) REVERT: C 52 MET cc_start: 0.7890 (ptm) cc_final: 0.7320 (ptm) REVERT: C 375 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8580 (mpp) REVERT: C 386 TYR cc_start: 0.8392 (m-80) cc_final: 0.7986 (m-80) REVERT: C 402 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8839 (mp) REVERT: D 159 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7296 (mt) REVERT: D 248 LYS cc_start: 0.8769 (tptt) cc_final: 0.8490 (mmtt) REVERT: D 265 MET cc_start: 0.7466 (mtp) cc_final: 0.7220 (mtm) REVERT: D 283 VAL cc_start: 0.8534 (t) cc_final: 0.8316 (m) REVERT: D 353 PHE cc_start: 0.4389 (OUTLIER) cc_final: 0.2731 (m-80) REVERT: D 390 PHE cc_start: 0.9120 (t80) cc_final: 0.8776 (t80) REVERT: D 404 GLN cc_start: 0.7159 (pp30) cc_final: 0.6608 (pm20) REVERT: E 28 MET cc_start: 0.7584 (mtt) cc_final: 0.7196 (mtt) REVERT: E 35 MET cc_start: 0.8616 (mmt) cc_final: 0.7941 (mmt) REVERT: E 195 HIS cc_start: 0.9244 (t70) cc_final: 0.8931 (t-90) REVERT: E 406 PHE cc_start: 0.7801 (p90) cc_final: 0.7316 (p90) REVERT: E 434 PHE cc_start: 0.9400 (t80) cc_final: 0.9157 (t80) REVERT: F 28 MET cc_start: 0.8251 (mmm) cc_final: 0.7991 (mmp) REVERT: F 37 MET cc_start: 0.9194 (ttp) cc_final: 0.8493 (tmm) REVERT: F 47 LEU cc_start: 0.9320 (tt) cc_final: 0.8852 (pp) REVERT: F 356 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8740 (t70) REVERT: F 378 PHE cc_start: 0.8470 (m-80) cc_final: 0.7700 (m-80) REVERT: F 418 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: F 442 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8623 (p) REVERT: J 83 MET cc_start: 0.6874 (ptp) cc_final: 0.6544 (mpp) outliers start: 81 outliers final: 60 residues processed: 246 average time/residue: 0.1441 time to fit residues: 54.7740 Evaluate side-chains 236 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [178, 30, 23, 62, 106, 69, 65, 83, 59, 227, 221] chunk 178 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.080409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061313 restraints weight = 127845.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062756 restraints weight = 62680.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063687 restraints weight = 39876.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064234 restraints weight = 30394.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064466 restraints weight = 26153.871| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20317 Z= 0.131 Angle : 0.646 16.441 27542 Z= 0.319 Chirality : 0.041 0.203 3079 Planarity : 0.003 0.045 3361 Dihedral : 5.485 59.685 2656 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.57 % Allowed : 20.52 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2355 helix: 1.09 (0.14), residues: 1431 sheet: -0.38 (0.32), residues: 250 loop : -0.58 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 447 TYR 0.016 0.001 TYR D 325 PHE 0.021 0.001 PHE E 406 TRP 0.036 0.001 TRP A 168 HIS 0.009 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20302) covalent geometry : angle 0.64560 / 0.32 (27512) SS BOND : bond 0.00266 / 0.18 ( 15) SS BOND : angle 0.58194 / 0.36 ( 30) hydrogen bonds : bond 0.03318 / 2.26 ( 1172) hydrogen bonds : angle 4.24058 / 3.07 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8930 (mtp) cc_final: 0.8473 (mtt) REVERT: A 104 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.7740 (t70) REVERT: A 238 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8467 (mm-30) REVERT: A 239 GLN cc_start: 0.9150 (pp30) cc_final: 0.8861 (pp30) REVERT: A 325 TYR cc_start: 0.8302 (t80) cc_final: 0.7578 (t80) REVERT: A 404 GLN cc_start: 0.8051 (tp40) cc_final: 0.7788 (tp-100) REVERT: B 343 MET cc_start: 0.8494 (ttt) cc_final: 0.7484 (tmm) REVERT: B 418 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: C 17 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: C 52 MET cc_start: 0.7907 (ptm) cc_final: 0.7430 (ptm) REVERT: C 243 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9064 (mm) REVERT: C 375 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8590 (mpp) REVERT: C 386 TYR cc_start: 0.8398 (m-80) cc_final: 0.7994 (m-80) REVERT: C 402 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 35 MET cc_start: 0.8807 (mtp) cc_final: 0.8426 (ptp) REVERT: D 159 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7173 (mt) REVERT: D 248 LYS cc_start: 0.8795 (tptt) cc_final: 0.8515 (mmtt) REVERT: D 353 PHE cc_start: 0.4473 (OUTLIER) cc_final: 0.2834 (m-80) REVERT: D 390 PHE cc_start: 0.9131 (t80) cc_final: 0.8784 (t80) REVERT: D 404 GLN cc_start: 0.7158 (pp30) cc_final: 0.6613 (pm20) REVERT: E 28 MET cc_start: 0.7503 (mtt) cc_final: 0.7170 (mtt) REVERT: E 195 HIS cc_start: 0.9265 (t70) cc_final: 0.8948 (t-90) REVERT: E 406 PHE cc_start: 0.8045 (p90) cc_final: 0.7552 (p90) REVERT: F 28 MET cc_start: 0.8457 (mmm) cc_final: 0.8189 (mmp) REVERT: F 37 MET cc_start: 0.9213 (ttp) cc_final: 0.8532 (tmm) REVERT: F 47 LEU cc_start: 0.9338 (tt) cc_final: 0.8818 (pp) REVERT: F 151 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7880 (tm-30) REVERT: F 200 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8237 (mp) REVERT: F 356 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (t70) REVERT: F 378 PHE cc_start: 0.8542 (m-80) cc_final: 0.7734 (m-80) REVERT: F 418 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: F 442 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8625 (p) REVERT: J 83 MET cc_start: 0.6831 (ptp) cc_final: 0.6601 (mpp) outliers start: 78 outliers final: 59 residues processed: 235 average time/residue: 0.1393 time to fit residues: 51.2574 Evaluate side-chains 233 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [104, 189, 120, 29, 224, 75, 112, 22, 97, 69, 152] chunk 104 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 224 optimal weight: 0.0010 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.080404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061348 restraints weight = 128101.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062787 restraints weight = 62444.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063696 restraints weight = 39570.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064279 restraints weight = 30224.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064503 restraints weight = 25889.159| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20317 Z= 0.130 Angle : 0.667 15.986 27542 Z= 0.329 Chirality : 0.041 0.230 3079 Planarity : 0.003 0.045 3361 Dihedral : 5.469 59.986 2654 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.57 % Allowed : 20.93 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2355 helix: 1.10 (0.14), residues: 1425 sheet: -0.35 (0.32), residues: 250 loop : -0.52 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 447 TYR 0.024 0.001 TYR D 325 PHE 0.021 0.001 PHE E 406 TRP 0.030 0.001 TRP A 168 HIS 0.010 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20302) covalent geometry : angle 0.66557 / 0.33 (27512) SS BOND : bond 0.00313 / 0.18 ( 15) SS BOND : angle 1.61534 / 1.15 ( 30) hydrogen bonds : bond 0.03355 / 2.27 ( 1172) hydrogen bonds : angle 4.21414 / 3.06 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 165 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8919 (mtp) cc_final: 0.8464 (mtt) REVERT: A 104 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7723 (t70) REVERT: A 238 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8461 (mm-30) REVERT: A 239 GLN cc_start: 0.9148 (pp30) cc_final: 0.8852 (pp30) REVERT: A 297 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.8014 (m) REVERT: A 325 TYR cc_start: 0.8309 (t80) cc_final: 0.7619 (t80) REVERT: A 404 GLN cc_start: 0.8302 (tp40) cc_final: 0.8034 (tp-100) REVERT: B 249 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8978 (ptmm) REVERT: B 343 MET cc_start: 0.8544 (ttt) cc_final: 0.7593 (tmm) REVERT: B 418 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: B 590 MET cc_start: 0.4892 (mmp) cc_final: 0.4361 (mmp) REVERT: C 17 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: C 52 MET cc_start: 0.7891 (ptm) cc_final: 0.7441 (ptm) REVERT: C 375 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8588 (mpp) REVERT: C 386 TYR cc_start: 0.8405 (m-80) cc_final: 0.8000 (m-80) REVERT: C 402 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8804 (mp) REVERT: D 35 MET cc_start: 0.8815 (mtp) cc_final: 0.8444 (ptp) REVERT: D 159 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7128 (mt) REVERT: D 248 LYS cc_start: 0.8768 (tptt) cc_final: 0.8477 (mmtt) REVERT: D 265 MET cc_start: 0.7415 (mtp) cc_final: 0.7172 (mtm) REVERT: D 390 PHE cc_start: 0.9131 (t80) cc_final: 0.8814 (t80) REVERT: D 404 GLN cc_start: 0.7160 (pp30) cc_final: 0.6613 (pm20) REVERT: E 28 MET cc_start: 0.7492 (mtt) cc_final: 0.7158 (mtt) REVERT: E 195 HIS cc_start: 0.9287 (t70) cc_final: 0.8974 (t-90) REVERT: E 406 PHE cc_start: 0.8020 (p90) cc_final: 0.7545 (p90) REVERT: F 28 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8227 (mmp) REVERT: F 37 MET cc_start: 0.9214 (ttp) cc_final: 0.8527 (tmm) REVERT: F 47 LEU cc_start: 0.9348 (tt) cc_final: 0.8817 (pp) REVERT: F 151 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7852 (tm-30) REVERT: F 200 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8239 (mp) REVERT: F 356 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (t70) REVERT: F 378 PHE cc_start: 0.8561 (m-80) cc_final: 0.7753 (m-80) REVERT: F 418 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: F 442 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8622 (p) outliers start: 78 outliers final: 61 residues processed: 229 average time/residue: 0.1331 time to fit residues: 48.5215 Evaluate side-chains 235 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 161 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 356 HIS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 418 PHE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 453 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [138, 87, 78, 171, 12, 100, 99, 30, 192, 61, 218] chunk 138 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 171 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.080267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.061228 restraints weight = 128410.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062690 restraints weight = 62738.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.063615 restraints weight = 39730.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064190 restraints weight = 30328.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064401 restraints weight = 25989.849| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20317 Z= 0.132 Angle : 0.676 15.964 27542 Z= 0.332 Chirality : 0.041 0.192 3079 Planarity : 0.003 0.044 3361 Dihedral : 5.470 59.783 2654 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.66 % Allowed : 20.80 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2355 helix: 1.09 (0.14), residues: 1425 sheet: -0.39 (0.32), residues: 250 loop : -0.53 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 447 TYR 0.021 0.001 TYR D 325 PHE 0.021 0.001 PHE E 406 TRP 0.029 0.001 TRP A 168 HIS 0.018 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (20302) covalent geometry : angle 0.67478 / 0.33 (27512) SS BOND : bond 0.00262 / 0.17 ( 15) SS BOND : angle 1.23534 / 0.85 ( 30) hydrogen bonds : bond 0.03372 / 2.28 ( 1172) hydrogen bonds : angle 4.23170 / 3.07 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3968.16 seconds wall clock time: 69 minutes 15.82 seconds (4155.82 seconds total)