Starting phenix.real_space_refine on Mon Jul 6 19:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096.map" model { file = "/net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gys_0096/07_2026/6gys_0096_neut.cif" } resolution = 4.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 104 5.49 5 S 168 5.16 5 C 24769 2.51 5 N 6478 2.21 5 O 7363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38890 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3517 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4775 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 4691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4691 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 553} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4224 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1079 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "G" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1053 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "H" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3517 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4775 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4575 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 534} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4224 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3627 SG CYS B 14 203.383 54.661 134.869 1.00342.11 S ATOM 3646 SG CYS B 17 204.184 58.016 135.776 1.00356.26 S ATOM 3627 SG CYS B 14 203.383 54.661 134.869 1.00342.11 S ATOM 3772 SG CYS B 33 206.706 55.422 136.612 1.00348.22 S ATOM 3845 SG CYS B 42 206.064 52.122 135.186 1.00344.46 S ATOM 8382 SG CYS C 17 157.661 80.210 89.051 1.00413.84 S ATOM 8490 SG CYS C 30 159.575 78.373 85.270 1.00423.48 S ATOM 8363 SG CYS C 14 158.549 81.882 85.933 1.00422.58 S ATOM 8508 SG CYS C 33 156.440 79.722 83.166 1.00425.94 S ATOM 24211 SG CYS I 17 30.422 74.934 88.138 1.00485.92 S ATOM 24319 SG CYS I 30 28.898 75.374 84.976 1.00478.10 S ATOM 24337 SG CYS I 33 26.603 74.544 87.654 1.00502.51 S ATOM 24410 SG CYS I 42 28.353 78.053 87.310 1.00487.62 S ATOM 28899 SG CYS J 17 94.739 41.790 66.592 1.00742.31 S ATOM 29007 SG CYS J 30 94.178 45.346 66.397 1.00742.87 S ATOM 29007 SG CYS J 30 94.178 45.346 66.397 1.00742.87 S ATOM 29098 SG CYS J 42 96.956 46.476 64.436 1.00749.59 S Time building chain proxies: 9.20, per 1000 atoms: 0.24 Number of scatterers: 38890 At special positions: 0 Unit cell: (258.64, 144.16, 168.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 168 16.00 P 104 15.00 O 7363 8.00 N 6478 7.00 C 24769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.04 Simple disulfide: pdb=" SG CYS I 99 " - pdb=" SG CYS I 215 " 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: 3.53 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 30 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 14 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 30 " pdb=" ZN I 702 " pdb="ZN ZN I 702 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 702 " - pdb=" SG CYS I 33 " pdb=" ZN J 701 " pdb="ZN ZN J 701 " - pdb=" SG CYS J 30 " pdb="ZN ZN J 701 " - pdb=" SG CYS J 17 " pdb=" ZN J 702 " pdb="ZN ZN J 702 " - pdb=" SG CYS J 42 " pdb="ZN ZN J 702 " - pdb=" SG CYS J 30 " 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 14 sheets defined 60.5% alpha, 2.0% beta 47 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.535A pdb=" N PHE A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.645A pdb=" N GLU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.677A pdb=" N PHE A 70 " --> pdb=" O MET A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.995A pdb=" N GLU A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.895A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.536A pdb=" N TRP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.097A pdb=" N ILE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.856A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.973A pdb=" N SER A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.716A pdb=" N CYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.845A pdb=" N ASN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.832A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.133A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 174 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.541A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.651A pdb=" N GLN B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.761A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.544A pdb=" N GLY B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 removed outlier: 3.614A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.759A pdb=" N LEU B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.632A pdb=" N ALA B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.678A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.780A pdb=" N LEU B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 553 removed outlier: 3.668A pdb=" N ASN B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 589 through 601 removed outlier: 3.850A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.560A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 606 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 607' Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 32 through 37 removed outlier: 4.155A pdb=" N ARG C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 56 through 70 removed outlier: 3.870A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.729A pdb=" N LEU C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.857A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 removed outlier: 3.573A pdb=" N LEU C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 148 " --> pdb=" O TRP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 174 removed outlier: 3.560A pdb=" N TYR C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.043A pdb=" N LEU C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 224 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 249 through 265 Processing helix chain 'C' and resid 279 through 303 Processing helix chain 'C' and resid 319 through 327 removed outlier: 5.001A pdb=" N TYR C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 326 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 3.534A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 387 removed outlier: 4.526A pdb=" N ILE C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 423 removed outlier: 3.599A pdb=" N ILE C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 445 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 477 removed outlier: 4.146A pdb=" N MET C 460 " --> pdb=" O HIS C 456 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 464 " --> pdb=" O MET C 460 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 removed outlier: 4.044A pdb=" N ALA C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.683A pdb=" N SER C 515 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 523 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 553 removed outlier: 3.702A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.537A pdb=" N GLY C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 removed outlier: 4.357A pdb=" N VAL C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.813A pdb=" N VAL D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.858A pdb=" N LYS E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 139 removed outlier: 3.584A pdb=" N GLU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 168 removed outlier: 3.710A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 3.796A pdb=" N VAL E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 224 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 235 through 239 removed outlier: 3.742A pdb=" N SER E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 371 through 378 removed outlier: 3.762A pdb=" N PHE E 378 " --> pdb=" O PHE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 Processing helix chain 'E' and resid 400 through 406 Processing helix chain 'E' and resid 418 through 422 removed outlier: 4.306A pdb=" N LYS E 421 " --> pdb=" O THR E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 436 through 443 removed outlier: 4.333A pdb=" N ASP E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 526 through 534 removed outlier: 3.961A pdb=" N LEU E 534 " --> pdb=" O PHE E 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.546A pdb=" N PHE H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU H 12 " --> pdb=" O ARG H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 24 removed outlier: 3.836A pdb=" N GLU H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 20 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR H 21 " --> pdb=" O ARG H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.019A pdb=" N GLU H 78 " --> pdb=" O ASN H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 removed outlier: 3.586A pdb=" N ILE H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 111 Processing helix chain 'H' and resid 143 through 151 removed outlier: 3.865A pdb=" N VAL H 151 " --> pdb=" O TYR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 176 through 190 removed outlier: 4.003A pdb=" N LYS H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.593A pdb=" N SER H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU H 268 " --> pdb=" O ILE H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'H' and resid 302 through 309 removed outlier: 3.626A pdb=" N ILE H 309 " --> pdb=" O VAL H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.679A pdb=" N SER H 349 " --> pdb=" O ASP H 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE H 350 " --> pdb=" O LEU H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 371 through 380 removed outlier: 4.123A pdb=" N ASN H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU H 379 " --> pdb=" O ASN H 375 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU H 380 " --> pdb=" O ILE H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 389 Processing helix chain 'H' and resid 423 through 433 removed outlier: 3.615A pdb=" N SER H 433 " --> pdb=" O ILE H 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 460 Processing helix chain 'H' and resid 461 through 463 No H-bonds generated for 'chain 'H' and resid 461 through 463' Processing helix chain 'I' and resid 14 through 21 removed outlier: 3.518A pdb=" N THR I 18 " --> pdb=" O CYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 36 removed outlier: 3.613A pdb=" N ARG I 34 " --> pdb=" O CYS I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 56 through 72 removed outlier: 4.648A pdb=" N ASP I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 3.577A pdb=" N TYR I 78 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 106 removed outlier: 3.547A pdb=" N TRP I 102 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 122 removed outlier: 3.995A pdb=" N LEU I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU I 120 " --> pdb=" O ASN I 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 121 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 130 Processing helix chain 'I' and resid 133 through 144 Processing helix chain 'I' and resid 153 through 174 removed outlier: 3.524A pdb=" N ILE I 163 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 183 Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.258A pdb=" N HIS I 189 " --> pdb=" O VAL I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 202 Processing helix chain 'I' and resid 203 through 224 removed outlier: 3.821A pdb=" N VAL I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN I 219 " --> pdb=" O CYS I 215 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN I 222 " --> pdb=" O PHE I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 242 removed outlier: 4.124A pdb=" N VAL I 234 " --> pdb=" O ASP I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 249 Processing helix chain 'I' and resid 249 through 268 removed outlier: 4.035A pdb=" N ALA I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE I 267 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS I 268 " --> pdb=" O PHE I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 303 removed outlier: 3.884A pdb=" N ARG I 291 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN I 303 " --> pdb=" O CYS I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 356 removed outlier: 3.568A pdb=" N ILE I 349 " --> pdb=" O TYR I 345 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP I 352 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 355 " --> pdb=" O LEU I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 382 removed outlier: 4.155A pdb=" N ASP I 378 " --> pdb=" O ARG I 374 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE I 379 " --> pdb=" O ARG I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 422 removed outlier: 3.687A pdb=" N ARG I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 Processing helix chain 'I' and resid 450 through 454 Processing helix chain 'I' and resid 456 through 477 removed outlier: 3.942A pdb=" N MET I 460 " --> pdb=" O HIS I 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER I 471 " --> pdb=" O VAL I 467 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE I 476 " --> pdb=" O PHE I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 3.638A pdb=" N ASP I 488 " --> pdb=" O GLN I 484 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA I 494 " --> pdb=" O THR I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 501 through 524 Processing helix chain 'I' and resid 535 through 553 removed outlier: 3.738A pdb=" N LEU I 541 " --> pdb=" O VAL I 537 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 545 " --> pdb=" O LEU I 541 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 546 " --> pdb=" O GLN I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 555 through 560 removed outlier: 4.098A pdb=" N LYS I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 593 Processing helix chain 'I' and resid 593 through 601 removed outlier: 4.582A pdb=" N SER I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.956A pdb=" N ASP I 605 " --> pdb=" O ASN I 602 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 607 " --> pdb=" O SER I 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 72 removed outlier: 3.908A pdb=" N GLN J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 106 removed outlier: 4.009A pdb=" N TRP J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 106 " --> pdb=" O TRP J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 122 removed outlier: 4.754A pdb=" N LEU J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 130 removed outlier: 3.913A pdb=" N TYR J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.542A pdb=" N LEU J 136 " --> pdb=" O ASP J 132 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP J 144 " --> pdb=" O VAL J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 173 removed outlier: 3.533A pdb=" N VAL J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR J 172 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR J 173 " --> pdb=" O MET J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 183 removed outlier: 3.864A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 193 removed outlier: 3.944A pdb=" N LEU J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 230 through 241 removed outlier: 4.163A pdb=" N VAL J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J 239 " --> pdb=" O GLN J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 249 Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 279 through 303 removed outlier: 3.984A pdb=" N VAL J 287 " --> pdb=" O SER J 283 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE J 292 " --> pdb=" O THR J 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN J 303 " --> pdb=" O CYS J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 354 removed outlier: 3.732A pdb=" N TRP J 346 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 348 " --> pdb=" O LEU J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 383 removed outlier: 4.617A pdb=" N TYR J 382 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS J 383 " --> pdb=" O ILE J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 420 removed outlier: 4.413A pdb=" N ALA J 403 " --> pdb=" O GLN J 399 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER J 408 " --> pdb=" O LEU J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 444 removed outlier: 3.580A pdb=" N ASN J 444 " --> pdb=" O SER J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 455 Processing helix chain 'J' and resid 456 through 477 removed outlier: 3.584A pdb=" N THR J 464 " --> pdb=" O MET J 460 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 471 " --> pdb=" O VAL J 467 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 496 removed outlier: 3.567A pdb=" N LYS J 483 " --> pdb=" O SER J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 500 removed outlier: 4.169A pdb=" N PHE J 500 " --> pdb=" O PRO J 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 497 through 500' Processing helix chain 'J' and resid 501 through 524 removed outlier: 3.730A pdb=" N ASP J 505 " --> pdb=" O GLY J 501 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU J 507 " --> pdb=" O LYS J 503 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU J 514 " --> pdb=" O LEU J 510 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER J 515 " --> pdb=" O THR J 511 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL J 524 " --> pdb=" O LEU J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 552 removed outlier: 3.819A pdb=" N ILE J 545 " --> pdb=" O LEU J 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 548 " --> pdb=" O ASP J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 562 Processing helix chain 'J' and resid 592 through 601 Processing helix chain 'J' and resid 602 through 607 removed outlier: 3.878A pdb=" N ILE J 606 " --> pdb=" O ILE J 603 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 24 Processing helix chain 'K' and resid 26 through 33 Processing helix chain 'K' and resid 83 through 97 Processing helix chain 'K' and resid 117 through 124 Processing helix chain 'K' and resid 127 through 141 Processing helix chain 'K' and resid 143 through 159 Processing helix chain 'K' and resid 162 through 169 Processing helix chain 'K' and resid 177 through 188 Processing helix chain 'L' and resid 29 through 35 Processing helix chain 'L' and resid 38 through 59 removed outlier: 3.803A pdb=" N THR L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 93 Processing helix chain 'L' and resid 109 through 139 removed outlier: 3.734A pdb=" N VAL L 138 " --> pdb=" O LYS L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 169 removed outlier: 3.917A pdb=" N LEU L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 191 Processing helix chain 'L' and resid 207 through 224 Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 281 through 295 Processing helix chain 'L' and resid 334 through 349 removed outlier: 3.567A pdb=" N PHE L 338 " --> pdb=" O ARG L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 Processing helix chain 'L' and resid 400 through 408 Processing helix chain 'L' and resid 418 through 422 removed outlier: 3.800A pdb=" N LYS L 421 " --> pdb=" O THR L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 435 removed outlier: 3.587A pdb=" N ILE L 435 " --> pdb=" O LEU L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 445 removed outlier: 3.565A pdb=" N GLU L 441 " --> pdb=" O PRO L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 479 removed outlier: 3.523A pdb=" N ARG L 455 " --> pdb=" O SER L 451 " (cutoff:3.500A) Proline residue: L 473 - end of helix Processing helix chain 'L' and resid 487 through 491 Processing helix chain 'L' and resid 492 through 503 Processing helix chain 'L' and resid 504 through 509 removed outlier: 4.635A pdb=" N LYS L 507 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 534 removed outlier: 3.741A pdb=" N LEU L 534 " --> pdb=" O PHE L 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 removed outlier: 7.120A pdb=" N TYR A 131 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 118 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.622A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 337 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 removed outlier: 5.784A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.845A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 77 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AA8, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.630A pdb=" N VAL L 73 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 118 through 120 removed outlier: 4.297A pdb=" N VAL H 140 " --> pdb=" O TYR H 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 276 through 278 removed outlier: 6.352A pdb=" N ILE H 276 " --> pdb=" O ARG H 313 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER H 315 " --> pdb=" O ILE H 276 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL H 278 " --> pdb=" O SER H 315 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET H 317 " --> pdb=" O VAL H 278 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 312 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER H 340 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU H 314 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL H 342 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG H 316 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 337 " --> pdb=" O SER H 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 344 through 345 Processing sheet with id=AB3, first strand: chain 'H' and resid 410 through 411 removed outlier: 5.557A pdb=" N ILE H 452 " --> pdb=" O LEU H 476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 16 through 19 removed outlier: 7.821A pdb=" N VAL K 79 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL K 9 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 240 through 241 1682 hydrogen bonds defined for protein. 4914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9666 1.33 - 1.45: 10131 1.45 - 1.58: 19766 1.58 - 1.70: 207 1.70 - 1.83: 250 Bond restraints: 40020 Sorted by residual: bond pdb=" N9 DA F 47 " pdb=" C4 DA F 47 " ideal model delta sigma weight residual 1.374 1.341 0.033 6.00e-03 2.78e+04 3.08e+01 bond pdb=" C LYS B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 1.336 1.288 0.048 9.80e-03 1.04e+04 2.40e+01 bond pdb=" N9 DA F 33 " pdb=" C4 DA F 33 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.10e+01 bond pdb=" C LEU L 37 " pdb=" N LYS L 38 " ideal model delta sigma weight residual 1.330 1.265 0.065 1.47e-02 4.63e+03 1.95e+01 bond pdb=" C TYR J 186 " pdb=" N PRO J 187 " ideal model delta sigma weight residual 1.337 1.385 -0.049 1.11e-02 8.12e+03 1.91e+01 ... (remaining 40015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 53984 3.86 - 7.73: 578 7.73 - 11.59: 43 11.59 - 15.46: 4 15.46 - 19.32: 1 Bond angle restraints: 54610 Sorted by residual: angle pdb=" C LEU A 286 " pdb=" N LEU A 287 " pdb=" CA LEU A 287 " ideal model delta sigma weight residual 122.36 109.17 13.19 1.72e+00 3.38e-01 5.88e+01 angle pdb=" C LEU H 286 " pdb=" N LEU H 287 " pdb=" CA LEU H 287 " ideal model delta sigma weight residual 122.36 109.92 12.44 1.72e+00 3.38e-01 5.23e+01 angle pdb=" N LYS E 260 " pdb=" CA LYS E 260 " pdb=" C LYS E 260 " ideal model delta sigma weight residual 114.09 103.28 10.81 1.55e+00 4.16e-01 4.87e+01 angle pdb=" C3' DA G 35 " pdb=" C2' DA G 35 " pdb=" C1' DA G 35 " ideal model delta sigma weight residual 102.50 94.72 7.78 1.20e+00 6.94e-01 4.21e+01 angle pdb=" O4' DT G 49 " pdb=" C4' DT G 49 " pdb=" C3' DT G 49 " ideal model delta sigma weight residual 106.00 102.30 3.70 6.00e-01 2.78e+00 3.81e+01 ... (remaining 54605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 23066 34.44 - 68.89: 765 68.89 - 103.33: 52 103.33 - 137.77: 0 137.77 - 172.22: 1 Dihedral angle restraints: 23884 sinusoidal: 10617 harmonic: 13267 Sorted by residual: dihedral pdb=" CA THR L 263 " pdb=" C THR L 263 " pdb=" N PRO L 264 " pdb=" CA PRO L 264 " ideal model delta harmonic sigma weight residual -180.00 -142.92 -37.08 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" CA ASP A 116 " pdb=" C ASP A 116 " pdb=" N ALA A 117 " pdb=" CA ALA A 117 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 dihedral pdb=" CA ARG H 274 " pdb=" C ARG H 274 " pdb=" N LYS H 275 " pdb=" CA LYS H 275 " ideal model delta harmonic sigma weight residual 180.00 143.35 36.65 0 5.00e+00 4.00e-02 5.37e+01 ... (remaining 23881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5508 0.098 - 0.196: 483 0.196 - 0.294: 26 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 6020 Sorted by residual: chirality pdb=" CB ILE H 301 " pdb=" CA ILE H 301 " pdb=" CG1 ILE H 301 " pdb=" CG2 ILE H 301 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1' DA G 35 " pdb=" O4' DA G 35 " pdb=" C2' DA G 35 " pdb=" N9 DA G 35 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 6017 not shown) Planarity restraints: 6548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 328 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C PHE H 328 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE H 328 " -0.025 2.00e-02 2.50e+03 pdb=" N THR H 329 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 328 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE A 328 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE A 328 " -0.021 2.00e-02 2.50e+03 pdb=" N THR A 329 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 443 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLN H 443 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN H 443 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN H 444 " 0.018 2.00e-02 2.50e+03 ... (remaining 6545 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.68: 2 1.68 - 2.48: 431 2.48 - 3.29: 46948 3.29 - 4.09: 106265 4.09 - 4.90: 184481 Warning: very small nonbonded interaction distances. Nonbonded interactions: 338127 Sorted by model distance: nonbonded pdb=" CD1 ILE I 28 " pdb=" CG2 ILE I 49 " model vdw 0.873 3.880 nonbonded pdb=" CG1 ILE I 28 " pdb=" CG2 ILE I 49 " model vdw 1.306 3.860 nonbonded pdb=" OP2 DA F 34 " pdb=" NH1 ARG L 334 " model vdw 1.808 3.120 nonbonded pdb=" OD2 ASP A 97 " pdb=" NH2 ARG D 161 " model vdw 1.864 3.120 nonbonded pdb=" CD1 ILE I 28 " pdb=" CB ILE I 49 " model vdw 1.865 3.890 ... (remaining 338122 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 'H' } ncs_group { reference = (chain 'B' and (resid 12 through 46 or resid 49 through 315 or resid 339 or (res \ id 340 and (name N or name CA or name C or name O or name CB )) or resid 341 thr \ ough 702)) selection = (chain 'C' and (resid 12 through 315 or resid 339 through 702)) selection = (chain 'I' and (resid 12 through 46 or resid 49 through 315 or resid 339 or (res \ id 340 and (name N or name CA or name C or name O or name CB )) or resid 341 thr \ ough 702)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } 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=0.99 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: 5.680 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 43.370 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.013 1.429 40039 Z= 0.572 Angle : 1.136 19.322 54614 Z= 0.693 Chirality : 0.058 0.490 6020 Planarity : 0.007 0.076 6548 Dihedral : 15.417 172.218 15236 Min Nonbonded Distance : 0.873 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.81 % Favored : 89.10 % Rotamer: Outliers : 0.56 % Allowed : 3.74 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.52 % 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: -4.13 (0.10), residues: 4385 helix: -2.34 (0.08), residues: 2435 sheet: -3.92 (0.33), residues: 170 loop : -3.07 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG I 232 TYR 0.039 0.004 TYR I 418 PHE 0.033 0.004 PHE C 112 TRP 0.043 0.005 TRP L 87 HIS 0.018 0.003 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.45 (40020) covalent geometry : angle 1.13582 / 0.69 (54610) SS BOND : bond 0.00444 / 0.23 ( 2) SS BOND : angle 2.83593 / 1.65 ( 4) hydrogen bonds : bond 0.18687 / 11.88 ( 1785) hydrogen bonds : angle 7.78685 / 5.33 ( 5116) metal coordination : bond 0.51786 / 25.17 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 403 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.9382 (p0) cc_final: 0.9087 (p0) REVERT: A 137 MET cc_start: 0.9105 (ttp) cc_final: 0.8834 (tmm) REVERT: A 270 MET cc_start: 0.9361 (mmt) cc_final: 0.9151 (mmm) REVERT: A 441 LYS cc_start: 0.9349 (tttt) cc_final: 0.9112 (tttp) REVERT: B 36 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7669 (mtm-85) REVERT: B 169 MET cc_start: 0.9610 (ttp) cc_final: 0.9404 (ptm) REVERT: B 174 MET cc_start: 0.8585 (ttm) cc_final: 0.8068 (ttm) REVERT: B 249 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8916 (mm-30) REVERT: B 292 ILE cc_start: 0.9782 (mt) cc_final: 0.9536 (mm) REVERT: B 295 ARG cc_start: 0.9461 (tpp80) cc_final: 0.9135 (mmm-85) REVERT: B 299 CYS cc_start: 0.9646 (m) cc_final: 0.9334 (t) REVERT: B 303 GLN cc_start: 0.8931 (mt0) cc_final: 0.8431 (tt0) REVERT: B 352 ASP cc_start: 0.9177 (t0) cc_final: 0.8817 (t0) REVERT: B 413 LYS cc_start: 0.9577 (mttt) cc_final: 0.9320 (mtpp) REVERT: B 414 LEU cc_start: 0.9777 (tp) cc_final: 0.9490 (tp) REVERT: B 417 MET cc_start: 0.9666 (mtp) cc_final: 0.9271 (mtt) REVERT: B 460 MET cc_start: 0.9595 (tpt) cc_final: 0.9327 (tpt) REVERT: B 469 PHE cc_start: 0.9685 (t80) cc_final: 0.9391 (t80) REVERT: C 68 TYR cc_start: 0.9471 (t80) cc_final: 0.9237 (t80) REVERT: C 71 TRP cc_start: 0.9362 (m100) cc_final: 0.8996 (m100) REVERT: C 100 MET cc_start: 0.9422 (mmp) cc_final: 0.8997 (mmm) REVERT: C 358 TYR cc_start: 0.8565 (m-80) cc_final: 0.7884 (m-80) REVERT: D 81 ASN cc_start: 0.9030 (t0) cc_final: 0.8810 (t0) REVERT: D 105 GLU cc_start: 0.9439 (mt-10) cc_final: 0.8909 (tm-30) REVERT: D 146 LEU cc_start: 0.9807 (tp) cc_final: 0.9525 (tp) REVERT: D 157 MET cc_start: 0.9563 (mtp) cc_final: 0.9229 (mtp) REVERT: D 180 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9454 (mt-10) REVERT: E 51 LYS cc_start: 0.9677 (mmtm) cc_final: 0.9421 (mtmm) REVERT: E 117 PHE cc_start: 0.9523 (t80) cc_final: 0.9301 (t80) REVERT: E 461 MET cc_start: 0.9677 (mmm) cc_final: 0.9247 (mmm) REVERT: H 147 TYR cc_start: 0.9670 (t80) cc_final: 0.9424 (t80) REVERT: H 170 PHE cc_start: 0.9082 (t80) cc_final: 0.8616 (t80) REVERT: H 175 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7427 (pp) REVERT: H 320 ILE cc_start: 0.8999 (pt) cc_final: 0.8764 (tt) REVERT: H 361 MET cc_start: 0.9535 (ptm) cc_final: 0.8824 (ttp) REVERT: H 370 TRP cc_start: 0.8640 (m-90) cc_final: 0.7787 (m-10) REVERT: I 119 MET cc_start: 0.9435 (tmm) cc_final: 0.9216 (tmm) REVERT: I 294 TYR cc_start: 0.9437 (m-80) cc_final: 0.8906 (m-80) REVERT: I 302 LEU cc_start: 0.9402 (mt) cc_final: 0.9192 (pp) REVERT: I 412 TRP cc_start: 0.9003 (t60) cc_final: 0.8687 (t60) REVERT: J 204 MET cc_start: 0.5618 (tpt) cc_final: 0.4829 (tpp) REVERT: J 226 MET cc_start: 0.8624 (mtp) cc_final: 0.8234 (mtt) REVERT: K 81 ASN cc_start: 0.9187 (t0) cc_final: 0.8869 (p0) REVERT: K 108 ASP cc_start: 0.9725 (t0) cc_final: 0.9386 (p0) REVERT: K 112 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8803 (mmmt) REVERT: K 142 ASN cc_start: 0.9481 (t0) cc_final: 0.9252 (t0) REVERT: L 44 GLN cc_start: 0.9624 (mt0) cc_final: 0.9411 (mm110) REVERT: L 180 VAL cc_start: 0.8059 (t) cc_final: 0.7772 (t) REVERT: L 346 PHE cc_start: 0.9507 (m-10) cc_final: 0.9086 (m-10) REVERT: L 407 MET cc_start: 0.9306 (mmt) cc_final: 0.8653 (mpp) outliers start: 23 outliers final: 3 residues processed: 424 average time/residue: 0.2673 time to fit residues: 178.0195 Evaluate side-chains 233 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 407 HIS A 439 HIS A 450 ASN B 66 GLN B 82 GLN B 152 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 543 ASN C 211 ASN C 259 GLN C 445 ASN C 461 GLN C 495 ASN C 598 GLN D 128 GLN D 174 ASN E 57 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS E 160 HIS ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 296 ASN H 420 GLN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 444 ASN H 450 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN I 104 ASN I 152 HIS ** I 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 HIS I 259 GLN I 303 GLN I 461 GLN I 543 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN L 57 GLN L 86 HIS L 268 GLN L 408 ASN L 505 HIS L 529 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.049890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.035243 restraints weight = 403214.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.036536 restraints weight = 250387.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.036909 restraints weight = 177134.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.037302 restraints weight = 131326.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.037654 restraints weight = 109307.980| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 40039 Z= 0.178 Angle : 0.791 14.828 54614 Z= 0.424 Chirality : 0.048 0.582 6020 Planarity : 0.007 0.329 6548 Dihedral : 18.354 162.125 6057 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.26 % Favored : 90.67 % Rotamer: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.11), residues: 4385 helix: -1.44 (0.09), residues: 2526 sheet: -3.44 (0.35), residues: 163 loop : -2.89 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 279 TYR 0.029 0.002 TYR E 49 PHE 0.025 0.002 PHE K 123 TRP 0.024 0.002 TRP B 346 HIS 0.008 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (40020) covalent geometry : angle 0.79099 / 0.42 (54610) SS BOND : bond 0.02939 / 1.55 ( 2) SS BOND : angle 2.14022 / 1.25 ( 4) hydrogen bonds : bond 0.06155 / 3.97 ( 1785) hydrogen bonds : angle 6.00195 / 4.10 ( 5116) metal coordination : bond 0.01173 / 0.52 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 322 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8636 (p0) cc_final: 0.8428 (p0) REVERT: A 123 LEU cc_start: 0.9001 (pp) cc_final: 0.8552 (pt) REVERT: A 273 LEU cc_start: 0.9214 (tp) cc_final: 0.8888 (tt) REVERT: A 317 MET cc_start: 0.9007 (mpp) cc_final: 0.8376 (mpp) REVERT: A 441 LYS cc_start: 0.9163 (tttt) cc_final: 0.8930 (tttp) REVERT: B 100 MET cc_start: 0.9392 (mmp) cc_final: 0.9015 (mmp) REVERT: B 174 MET cc_start: 0.8349 (ttm) cc_final: 0.7900 (ttm) REVERT: B 259 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8935 (tp-100) REVERT: B 295 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8670 (mmm-85) REVERT: B 352 ASP cc_start: 0.8466 (t0) cc_final: 0.8081 (t0) REVERT: B 414 LEU cc_start: 0.9707 (tp) cc_final: 0.9417 (tp) REVERT: B 417 MET cc_start: 0.8970 (mtp) cc_final: 0.8731 (mtt) REVERT: B 507 LEU cc_start: 0.9528 (tt) cc_final: 0.9133 (mt) REVERT: C 71 TRP cc_start: 0.8753 (m100) cc_final: 0.8446 (m-90) REVERT: C 204 MET cc_start: 0.8673 (tpt) cc_final: 0.8382 (ttt) REVERT: C 358 TYR cc_start: 0.8160 (m-80) cc_final: 0.7579 (m-80) REVERT: E 51 LYS cc_start: 0.9629 (mmtm) cc_final: 0.9317 (mtmm) REVERT: E 117 PHE cc_start: 0.9475 (t80) cc_final: 0.9236 (t80) REVERT: E 152 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 461 MET cc_start: 0.9359 (mmm) cc_final: 0.9149 (mmm) REVERT: E 464 LEU cc_start: 0.9568 (mt) cc_final: 0.9365 (mt) REVERT: H 137 MET cc_start: 0.8703 (ptm) cc_final: 0.8462 (tmm) REVERT: H 170 PHE cc_start: 0.8623 (t80) cc_final: 0.8107 (t80) REVERT: H 320 ILE cc_start: 0.9268 (pt) cc_final: 0.8899 (pt) REVERT: H 359 LEU cc_start: 0.9500 (tt) cc_final: 0.9207 (tp) REVERT: H 370 TRP cc_start: 0.8215 (m-90) cc_final: 0.7130 (m-10) REVERT: I 100 MET cc_start: 0.9055 (mmp) cc_final: 0.8705 (mmp) REVERT: I 103 MET cc_start: 0.8429 (mmp) cc_final: 0.8088 (mmm) REVERT: I 119 MET cc_start: 0.9447 (tmm) cc_final: 0.8790 (tmm) REVERT: I 294 TYR cc_start: 0.9531 (m-80) cc_final: 0.9167 (m-80) REVERT: I 605 ASP cc_start: 0.8607 (m-30) cc_final: 0.8355 (t70) REVERT: J 204 MET cc_start: 0.6733 (tpt) cc_final: 0.6493 (tpp) REVERT: J 208 MET cc_start: 0.7204 (mmt) cc_final: 0.6590 (mmt) REVERT: J 226 MET cc_start: 0.9138 (mtp) cc_final: 0.8430 (mtt) REVERT: J 565 LEU cc_start: 0.9276 (mt) cc_final: 0.9023 (tt) REVERT: K 77 MET cc_start: 0.8429 (pmm) cc_final: 0.7936 (pmm) REVERT: K 108 ASP cc_start: 0.9396 (t0) cc_final: 0.9123 (p0) REVERT: K 142 ASN cc_start: 0.9205 (t0) cc_final: 0.8987 (t0) REVERT: K 144 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9387 (ptmt) REVERT: L 346 PHE cc_start: 0.9476 (m-10) cc_final: 0.8898 (m-10) REVERT: L 407 MET cc_start: 0.9109 (mmt) cc_final: 0.8624 (mpp) outliers start: 6 outliers final: 1 residues processed: 326 average time/residue: 0.2720 time to fit residues: 140.2615 Evaluate side-chains 223 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 236 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 209 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 383 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 66 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN B 406 GLN C 211 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN E 453 ASN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 439 HIS ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 ASN J 116 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN K 174 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.050745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.036255 restraints weight = 397241.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.037559 restraints weight = 249267.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037848 restraints weight = 175971.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.038239 restraints weight = 134896.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.038546 restraints weight = 113620.338| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 40039 Z= 0.149 Angle : 0.721 13.761 54614 Z= 0.385 Chirality : 0.046 0.358 6020 Planarity : 0.005 0.069 6548 Dihedral : 18.033 161.688 6057 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.12), residues: 4385 helix: -0.99 (0.09), residues: 2564 sheet: -3.23 (0.44), residues: 118 loop : -2.68 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 375 TYR 0.070 0.002 TYR E 366 PHE 0.029 0.002 PHE L 117 TRP 0.023 0.002 TRP H 150 HIS 0.007 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (40020) covalent geometry : angle 0.72058 / 0.38 (54610) SS BOND : bond 0.00225 / 0.11 ( 2) SS BOND : angle 3.08484 / 1.78 ( 4) hydrogen bonds : bond 0.05304 / 3.41 ( 1785) hydrogen bonds : angle 5.56040 / 3.80 ( 5116) metal coordination : bond 0.00172 / 0.10 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 304 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8837 (pp) cc_final: 0.8320 (pt) REVERT: A 267 MET cc_start: 0.8905 (ptp) cc_final: 0.8680 (ptt) REVERT: A 273 LEU cc_start: 0.9297 (tp) cc_final: 0.8847 (tt) REVERT: A 441 LYS cc_start: 0.9131 (tttt) cc_final: 0.8917 (tttp) REVERT: B 100 MET cc_start: 0.9399 (mmp) cc_final: 0.9060 (mmp) REVERT: B 204 MET cc_start: 0.8701 (mpp) cc_final: 0.8336 (mpp) REVERT: B 208 MET cc_start: 0.8512 (ptt) cc_final: 0.8234 (ptt) REVERT: B 295 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8678 (mmm-85) REVERT: B 414 LEU cc_start: 0.9653 (tp) cc_final: 0.9379 (tp) REVERT: B 456 HIS cc_start: 0.9362 (t-90) cc_final: 0.9152 (t-90) REVERT: B 458 MET cc_start: 0.8870 (ptp) cc_final: 0.8456 (ptp) REVERT: C 100 MET cc_start: 0.9346 (tpt) cc_final: 0.8890 (tpp) REVERT: D 159 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8480 (ttm110) REVERT: E 51 LYS cc_start: 0.9624 (mmtm) cc_final: 0.9371 (mtmm) REVERT: E 117 PHE cc_start: 0.9447 (t80) cc_final: 0.9054 (t80) REVERT: E 152 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8612 (tm-30) REVERT: E 320 ASP cc_start: 0.9142 (m-30) cc_final: 0.8894 (t0) REVERT: H 74 LEU cc_start: 0.9311 (tp) cc_final: 0.9071 (tp) REVERT: H 137 MET cc_start: 0.8853 (ptm) cc_final: 0.8482 (ppp) REVERT: H 147 TYR cc_start: 0.9349 (t80) cc_final: 0.9044 (t80) REVERT: H 161 ASP cc_start: 0.9513 (t0) cc_final: 0.9033 (p0) REVERT: H 170 PHE cc_start: 0.8313 (t80) cc_final: 0.8111 (t80) REVERT: H 270 MET cc_start: 0.9381 (mpp) cc_final: 0.8636 (mpp) REVERT: H 273 LEU cc_start: 0.9196 (tp) cc_final: 0.8703 (tp) REVERT: H 361 MET cc_start: 0.9162 (pmm) cc_final: 0.8875 (pmm) REVERT: H 370 TRP cc_start: 0.8402 (m-90) cc_final: 0.8168 (m-10) REVERT: I 43 MET cc_start: 0.8394 (mmp) cc_final: 0.8144 (mmm) REVERT: I 100 MET cc_start: 0.9140 (mmp) cc_final: 0.8883 (mmp) REVERT: I 103 MET cc_start: 0.8297 (mmp) cc_final: 0.8004 (mmm) REVERT: I 119 MET cc_start: 0.9494 (tmm) cc_final: 0.9076 (tmm) REVERT: I 294 TYR cc_start: 0.9589 (m-80) cc_final: 0.9053 (m-80) REVERT: I 605 ASP cc_start: 0.8513 (m-30) cc_final: 0.8282 (t70) REVERT: J 208 MET cc_start: 0.7086 (mmt) cc_final: 0.6561 (mmt) REVERT: J 458 MET cc_start: 0.8178 (ptt) cc_final: 0.7835 (ptt) REVERT: J 565 LEU cc_start: 0.9223 (mt) cc_final: 0.8958 (tt) REVERT: K 77 MET cc_start: 0.8228 (pmm) cc_final: 0.7812 (pmm) REVERT: K 142 ASN cc_start: 0.9193 (t0) cc_final: 0.8958 (t0) REVERT: L 346 PHE cc_start: 0.9488 (m-10) cc_final: 0.8907 (m-10) REVERT: L 407 MET cc_start: 0.9076 (mmt) cc_final: 0.8606 (mpp) outliers start: 3 outliers final: 0 residues processed: 307 average time/residue: 0.2621 time to fit residues: 128.4720 Evaluate side-chains 220 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 217 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 368 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 288 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN B 303 GLN B 445 ASN B 569 ASN D 174 ASN E 31 GLN E 60 GLN E 340 ASN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.048646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034476 restraints weight = 413247.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.035745 restraints weight = 265476.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.035909 restraints weight = 185884.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.036292 restraints weight = 143483.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.036459 restraints weight = 126967.524| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 40039 Z= 0.270 Angle : 0.789 12.790 54614 Z= 0.420 Chirality : 0.046 0.329 6020 Planarity : 0.005 0.065 6548 Dihedral : 17.949 158.800 6057 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.90 % Favored : 90.03 % Rotamer: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 4385 helix: -0.73 (0.10), residues: 2547 sheet: -3.66 (0.41), residues: 120 loop : -2.49 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 20 TYR 0.049 0.002 TYR E 366 PHE 0.038 0.002 PHE E 401 TRP 0.048 0.003 TRP H 150 HIS 0.008 0.002 HIS C 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (40020) covalent geometry : angle 0.78858 / 0.42 (54610) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 1.67343 / 0.98 ( 4) hydrogen bonds : bond 0.05757 / 3.73 ( 1785) hydrogen bonds : angle 5.54100 / 3.78 ( 5116) metal coordination : bond 0.00303 / 0.16 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.9090 (ptp) cc_final: 0.8806 (ptt) REVERT: A 441 LYS cc_start: 0.9241 (tttt) cc_final: 0.9010 (tttp) REVERT: B 100 MET cc_start: 0.9457 (mmp) cc_final: 0.9180 (mmp) REVERT: B 115 MET cc_start: 0.7297 (tmm) cc_final: 0.6607 (tmm) REVERT: B 204 MET cc_start: 0.8842 (mpp) cc_final: 0.8412 (mpp) REVERT: B 208 MET cc_start: 0.8592 (ptt) cc_final: 0.8303 (ptt) REVERT: B 259 GLN cc_start: 0.9255 (tp-100) cc_final: 0.8981 (tp-100) REVERT: B 295 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8659 (mmm-85) REVERT: B 335 TYR cc_start: 0.5989 (t80) cc_final: 0.5783 (t80) REVERT: B 352 ASP cc_start: 0.8452 (t70) cc_final: 0.8133 (t0) REVERT: C 100 MET cc_start: 0.9317 (tpt) cc_final: 0.8928 (tpp) REVERT: C 174 MET cc_start: 0.8928 (mtp) cc_final: 0.8481 (mtt) REVERT: C 204 MET cc_start: 0.8572 (ttp) cc_final: 0.7990 (ttp) REVERT: C 226 MET cc_start: 0.9303 (pmm) cc_final: 0.9081 (pmm) REVERT: D 142 ASN cc_start: 0.9483 (m-40) cc_final: 0.9044 (m-40) REVERT: E 51 LYS cc_start: 0.9651 (mmtm) cc_final: 0.9420 (mtmm) REVERT: E 117 PHE cc_start: 0.9513 (t80) cc_final: 0.9142 (t80) REVERT: E 124 LYS cc_start: 0.9689 (mtpt) cc_final: 0.9455 (ttmm) REVERT: E 320 ASP cc_start: 0.9171 (m-30) cc_final: 0.8905 (t0) REVERT: H 137 MET cc_start: 0.8854 (ptm) cc_final: 0.8558 (tmm) REVERT: H 147 TYR cc_start: 0.9350 (t80) cc_final: 0.9000 (t80) REVERT: H 161 ASP cc_start: 0.9536 (t0) cc_final: 0.9093 (p0) REVERT: H 170 PHE cc_start: 0.8699 (t80) cc_final: 0.8319 (t80) REVERT: H 273 LEU cc_start: 0.9222 (tp) cc_final: 0.9021 (tp) REVERT: H 361 MET cc_start: 0.9240 (pmm) cc_final: 0.8951 (pmm) REVERT: I 43 MET cc_start: 0.8449 (mmp) cc_final: 0.8170 (mmm) REVERT: I 103 MET cc_start: 0.8353 (mmt) cc_final: 0.8115 (mmp) REVERT: I 119 MET cc_start: 0.9454 (tmm) cc_final: 0.8991 (tmm) REVERT: I 204 MET cc_start: 0.9103 (mmp) cc_final: 0.8870 (mmp) REVERT: I 294 TYR cc_start: 0.9614 (m-80) cc_final: 0.9264 (m-80) REVERT: I 605 ASP cc_start: 0.8562 (m-30) cc_final: 0.8339 (t70) REVERT: K 77 MET cc_start: 0.8395 (pmm) cc_final: 0.7968 (pmm) REVERT: K 142 ASN cc_start: 0.9207 (t0) cc_final: 0.8998 (t0) REVERT: L 117 PHE cc_start: 0.9278 (m-80) cc_final: 0.8923 (m-80) REVERT: L 407 MET cc_start: 0.9046 (mmt) cc_final: 0.8721 (mmm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2494 time to fit residues: 102.9346 Evaluate side-chains 198 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 249 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 445 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN E 44 GLN E 60 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 348 ASN H 371 ASN H 474 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS J 104 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.048619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034440 restraints weight = 412258.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.035548 restraints weight = 264701.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.035834 restraints weight = 193463.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.036171 restraints weight = 148056.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.036437 restraints weight = 127509.147| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 40039 Z= 0.229 Angle : 0.737 13.346 54614 Z= 0.395 Chirality : 0.046 0.323 6020 Planarity : 0.005 0.067 6548 Dihedral : 17.894 158.854 6057 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.12), residues: 4385 helix: -0.58 (0.10), residues: 2565 sheet: -3.57 (0.44), residues: 108 loop : -2.37 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 262 TYR 0.020 0.002 TYR A 67 PHE 0.022 0.002 PHE H 356 TRP 0.034 0.002 TRP H 150 HIS 0.007 0.001 HIS C 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 (40020) covalent geometry : angle 0.73606 / 0.39 (54610) SS BOND : bond 0.00210 / 0.10 ( 2) SS BOND : angle 3.54749 / 2.02 ( 4) hydrogen bonds : bond 0.05330 / 3.44 ( 1785) hydrogen bonds : angle 5.42586 / 3.72 ( 5116) metal coordination : bond 0.00701 / 0.40 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.607 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 123 LEU cc_start: 0.8778 (pt) cc_final: 0.8461 (pt) REVERT: A 267 MET cc_start: 0.8914 (ptp) cc_final: 0.8687 (ptt) REVERT: A 273 LEU cc_start: 0.9112 (tt) cc_final: 0.8911 (tt) REVERT: A 317 MET cc_start: 0.8955 (mpp) cc_final: 0.8201 (mpp) REVERT: B 100 MET cc_start: 0.9469 (mmp) cc_final: 0.9253 (mmp) REVERT: B 115 MET cc_start: 0.7497 (tmm) cc_final: 0.6797 (tmm) REVERT: B 204 MET cc_start: 0.8867 (mpp) cc_final: 0.8415 (mpp) REVERT: B 208 MET cc_start: 0.8613 (ptt) cc_final: 0.8263 (ptt) REVERT: B 252 LEU cc_start: 0.9474 (tp) cc_final: 0.9203 (mt) REVERT: B 259 GLN cc_start: 0.9154 (tp-100) cc_final: 0.8921 (tp-100) REVERT: B 295 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8602 (mmm-85) REVERT: B 352 ASP cc_start: 0.8355 (t70) cc_final: 0.7972 (t0) REVERT: B 417 MET cc_start: 0.8978 (mtm) cc_final: 0.8720 (mtt) REVERT: B 458 MET cc_start: 0.9127 (ptt) cc_final: 0.8676 (ptt) REVERT: C 100 MET cc_start: 0.9222 (tpt) cc_final: 0.8857 (tpp) REVERT: C 204 MET cc_start: 0.8587 (ttp) cc_final: 0.7878 (ttp) REVERT: C 458 MET cc_start: 0.9441 (ptt) cc_final: 0.9177 (ptm) REVERT: D 142 ASN cc_start: 0.9355 (m-40) cc_final: 0.9053 (m-40) REVERT: E 51 LYS cc_start: 0.9636 (mmtm) cc_final: 0.9407 (mtmm) REVERT: E 117 PHE cc_start: 0.9464 (t80) cc_final: 0.9079 (t80) REVERT: E 124 LYS cc_start: 0.9683 (mtpt) cc_final: 0.9401 (ttmm) REVERT: E 320 ASP cc_start: 0.9126 (m-30) cc_final: 0.8892 (t0) REVERT: H 74 LEU cc_start: 0.9242 (tp) cc_final: 0.9015 (tp) REVERT: H 137 MET cc_start: 0.8660 (ptm) cc_final: 0.8224 (ppp) REVERT: H 147 TYR cc_start: 0.9320 (t80) cc_final: 0.8654 (t80) REVERT: H 161 ASP cc_start: 0.9483 (t0) cc_final: 0.9028 (p0) REVERT: H 170 PHE cc_start: 0.8576 (t80) cc_final: 0.8287 (t80) REVERT: H 273 LEU cc_start: 0.9200 (tp) cc_final: 0.8965 (tp) REVERT: H 359 LEU cc_start: 0.9441 (tt) cc_final: 0.8998 (tt) REVERT: I 43 MET cc_start: 0.8433 (mmp) cc_final: 0.8165 (mmm) REVERT: I 100 MET cc_start: 0.9006 (mmp) cc_final: 0.8679 (mmm) REVERT: I 103 MET cc_start: 0.8230 (mmt) cc_final: 0.7994 (mmm) REVERT: I 119 MET cc_start: 0.9447 (tmm) cc_final: 0.8968 (tmm) REVERT: I 294 TYR cc_start: 0.9632 (m-80) cc_final: 0.9264 (m-80) REVERT: I 605 ASP cc_start: 0.8502 (m-30) cc_final: 0.8301 (t70) REVERT: J 204 MET cc_start: 0.6494 (tpt) cc_final: 0.6286 (tpp) REVERT: K 77 MET cc_start: 0.8417 (pmm) cc_final: 0.7912 (pmm) REVERT: K 142 ASN cc_start: 0.9199 (t0) cc_final: 0.8979 (t0) REVERT: L 117 PHE cc_start: 0.9263 (m-80) cc_final: 0.8885 (m-80) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.2419 time to fit residues: 97.5965 Evaluate side-chains 195 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 431 optimal weight: 0.0040 chunk 408 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 418 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 335 GLN A 443 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN E 496 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 348 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN L 44 GLN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 ASN L 256 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.050183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.035688 restraints weight = 399303.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.036985 restraints weight = 254988.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.037172 restraints weight = 178078.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037653 restraints weight = 140114.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.037920 restraints weight = 118416.513| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40039 Z= 0.135 Angle : 0.681 13.521 54614 Z= 0.359 Chirality : 0.045 0.326 6020 Planarity : 0.005 0.075 6548 Dihedral : 17.741 156.820 6057 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.67 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.12), residues: 4385 helix: -0.33 (0.10), residues: 2570 sheet: -3.02 (0.46), residues: 105 loop : -2.36 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 26 TYR 0.030 0.001 TYR B 335 PHE 0.024 0.002 PHE B 225 TRP 0.029 0.002 TRP H 150 HIS 0.007 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (40020) covalent geometry : angle 0.68052 / 0.36 (54610) SS BOND : bond 0.00214 / 0.10 ( 2) SS BOND : angle 2.27237 / 1.32 ( 4) hydrogen bonds : bond 0.04626 / 2.98 ( 1785) hydrogen bonds : angle 5.17369 / 3.53 ( 5116) metal coordination : bond 0.00171 / 0.08 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.368 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 123 LEU cc_start: 0.8884 (pt) cc_final: 0.8564 (pt) REVERT: A 317 MET cc_start: 0.8798 (mpp) cc_final: 0.8059 (mpp) REVERT: B 100 MET cc_start: 0.9469 (mmp) cc_final: 0.9201 (mmp) REVERT: B 115 MET cc_start: 0.7363 (tmm) cc_final: 0.6780 (tmm) REVERT: B 174 MET cc_start: 0.8426 (ttm) cc_final: 0.8075 (ttt) REVERT: B 204 MET cc_start: 0.8852 (mpp) cc_final: 0.8365 (mpp) REVERT: B 208 MET cc_start: 0.8622 (ptt) cc_final: 0.8293 (ptt) REVERT: B 237 TYR cc_start: 0.8763 (t80) cc_final: 0.8562 (t80) REVERT: B 259 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8963 (tp-100) REVERT: B 295 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8574 (mmm-85) REVERT: B 302 LEU cc_start: 0.9555 (mm) cc_final: 0.9292 (mt) REVERT: B 352 ASP cc_start: 0.8221 (t70) cc_final: 0.7929 (t70) REVERT: B 404 LEU cc_start: 0.9632 (mp) cc_final: 0.9398 (pp) REVERT: B 414 LEU cc_start: 0.9692 (tp) cc_final: 0.9385 (tp) REVERT: B 458 MET cc_start: 0.9131 (ptt) cc_final: 0.8803 (ptt) REVERT: C 100 MET cc_start: 0.9188 (tpt) cc_final: 0.8792 (tpp) REVERT: C 204 MET cc_start: 0.8526 (ttp) cc_final: 0.8053 (ttm) REVERT: D 142 ASN cc_start: 0.9454 (m-40) cc_final: 0.8886 (m-40) REVERT: E 51 LYS cc_start: 0.9669 (mmtm) cc_final: 0.9391 (mtmm) REVERT: E 117 PHE cc_start: 0.9435 (t80) cc_final: 0.9096 (t80) REVERT: E 124 LYS cc_start: 0.9685 (mtpt) cc_final: 0.9452 (ttmm) REVERT: E 320 ASP cc_start: 0.9166 (m-30) cc_final: 0.8913 (t0) REVERT: H 74 LEU cc_start: 0.9290 (tp) cc_final: 0.9053 (tp) REVERT: H 137 MET cc_start: 0.8707 (ptm) cc_final: 0.8283 (ppp) REVERT: H 161 ASP cc_start: 0.9434 (t0) cc_final: 0.9003 (p0) REVERT: H 170 PHE cc_start: 0.8677 (t80) cc_final: 0.8321 (t80) REVERT: H 273 LEU cc_start: 0.9263 (tp) cc_final: 0.8992 (tp) REVERT: H 317 MET cc_start: 0.7487 (mmp) cc_final: 0.7284 (mmp) REVERT: H 359 LEU cc_start: 0.9438 (tt) cc_final: 0.8892 (tt) REVERT: H 361 MET cc_start: 0.9281 (pmm) cc_final: 0.8668 (pmm) REVERT: I 43 MET cc_start: 0.8440 (mmp) cc_final: 0.8176 (mmm) REVERT: I 100 MET cc_start: 0.9049 (mmp) cc_final: 0.8764 (mmm) REVERT: I 103 MET cc_start: 0.8225 (mmt) cc_final: 0.8005 (mmm) REVERT: I 119 MET cc_start: 0.9432 (tmm) cc_final: 0.8936 (tmm) REVERT: I 294 TYR cc_start: 0.9627 (m-80) cc_final: 0.9234 (m-80) REVERT: I 605 ASP cc_start: 0.8470 (m-30) cc_final: 0.8266 (t70) REVERT: J 460 MET cc_start: 0.7604 (ptp) cc_final: 0.7361 (ptm) REVERT: J 565 LEU cc_start: 0.9231 (mt) cc_final: 0.8993 (tp) REVERT: K 77 MET cc_start: 0.8370 (pmm) cc_final: 0.7913 (pmm) REVERT: K 142 ASN cc_start: 0.9148 (t0) cc_final: 0.8919 (t0) REVERT: L 117 PHE cc_start: 0.9311 (m-80) cc_final: 0.8919 (m-80) REVERT: L 346 PHE cc_start: 0.9515 (m-10) cc_final: 0.8852 (m-10) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2255 time to fit residues: 96.6885 Evaluate side-chains 197 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 417 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 403 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 317 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN E 60 GLN H 23 HIS ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.049194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.034929 restraints weight = 405828.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.036107 restraints weight = 262963.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.036341 restraints weight = 181771.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.036710 restraints weight = 143223.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036961 restraints weight = 125075.872| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 40039 Z= 0.189 Angle : 0.687 13.860 54614 Z= 0.367 Chirality : 0.044 0.311 6020 Planarity : 0.005 0.055 6548 Dihedral : 17.663 155.020 6057 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.99 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 4385 helix: -0.22 (0.10), residues: 2579 sheet: -3.22 (0.39), residues: 145 loop : -2.26 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 265 TYR 0.022 0.002 TYR B 294 PHE 0.018 0.002 PHE B 225 TRP 0.060 0.002 TRP H 150 HIS 0.007 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (40020) covalent geometry : angle 0.68705 / 0.37 (54610) SS BOND : bond 0.00190 / 0.09 ( 2) SS BOND : angle 1.38346 / 0.81 ( 4) hydrogen bonds : bond 0.04823 / 3.11 ( 1785) hydrogen bonds : angle 5.15961 / 3.52 ( 5116) metal coordination : bond 0.00196 / 0.12 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.522 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: A 123 LEU cc_start: 0.8827 (pt) cc_final: 0.8451 (pt) REVERT: A 267 MET cc_start: 0.8937 (ptp) cc_final: 0.8643 (ptt) REVERT: B 100 MET cc_start: 0.9502 (mmp) cc_final: 0.9241 (mmp) REVERT: B 115 MET cc_start: 0.7556 (tmm) cc_final: 0.7075 (tmm) REVERT: B 174 MET cc_start: 0.8443 (ttm) cc_final: 0.8136 (ttt) REVERT: B 208 MET cc_start: 0.8684 (ptt) cc_final: 0.8334 (ptt) REVERT: B 259 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8880 (tp-100) REVERT: B 295 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8631 (mmm-85) REVERT: B 352 ASP cc_start: 0.8242 (t70) cc_final: 0.7925 (t70) REVERT: B 458 MET cc_start: 0.9183 (ptt) cc_final: 0.8699 (ptt) REVERT: C 100 MET cc_start: 0.9189 (tpt) cc_final: 0.8789 (tpp) REVERT: C 204 MET cc_start: 0.8525 (ttp) cc_final: 0.7638 (ttp) REVERT: D 142 ASN cc_start: 0.9336 (m-40) cc_final: 0.9020 (m-40) REVERT: E 51 LYS cc_start: 0.9672 (mmtm) cc_final: 0.9401 (mtmm) REVERT: E 117 PHE cc_start: 0.9454 (t80) cc_final: 0.9109 (t80) REVERT: E 320 ASP cc_start: 0.9205 (m-30) cc_final: 0.8975 (t0) REVERT: H 137 MET cc_start: 0.8426 (ptm) cc_final: 0.8160 (ppp) REVERT: H 147 TYR cc_start: 0.9289 (t80) cc_final: 0.8576 (t80) REVERT: H 161 ASP cc_start: 0.9420 (t0) cc_final: 0.8998 (p0) REVERT: H 170 PHE cc_start: 0.8729 (t80) cc_final: 0.8367 (t80) REVERT: H 287 LEU cc_start: 0.9048 (mm) cc_final: 0.8847 (mm) REVERT: H 361 MET cc_start: 0.9245 (pmm) cc_final: 0.8851 (pmm) REVERT: I 43 MET cc_start: 0.8456 (mmp) cc_final: 0.8187 (mmm) REVERT: I 100 MET cc_start: 0.9025 (mmp) cc_final: 0.8731 (mmm) REVERT: I 103 MET cc_start: 0.8189 (mmt) cc_final: 0.7969 (mmm) REVERT: I 119 MET cc_start: 0.9465 (tmm) cc_final: 0.8962 (tmm) REVERT: I 294 TYR cc_start: 0.9645 (m-80) cc_final: 0.9265 (m-80) REVERT: I 605 ASP cc_start: 0.8479 (m-30) cc_final: 0.8278 (t70) REVERT: J 460 MET cc_start: 0.7473 (ptp) cc_final: 0.7248 (ptm) REVERT: J 565 LEU cc_start: 0.9253 (mt) cc_final: 0.9020 (tp) REVERT: K 77 MET cc_start: 0.8387 (pmm) cc_final: 0.7859 (pmm) REVERT: K 142 ASN cc_start: 0.9163 (t0) cc_final: 0.8928 (t0) REVERT: L 117 PHE cc_start: 0.9316 (m-80) cc_final: 0.8938 (m-80) REVERT: L 407 MET cc_start: 0.9174 (mmm) cc_final: 0.8689 (mpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2321 time to fit residues: 89.4432 Evaluate side-chains 185 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 285 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.0570 chunk 276 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 158 optimal weight: 0.9990 chunk 327 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN E 453 ASN ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN J 104 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS ** L 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.048816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034519 restraints weight = 408340.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.035584 restraints weight = 263309.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.035906 restraints weight = 194522.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.036147 restraints weight = 157892.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.036558 restraints weight = 130048.858| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 40039 Z= 0.206 Angle : 0.710 16.129 54614 Z= 0.378 Chirality : 0.045 0.309 6020 Planarity : 0.005 0.050 6548 Dihedral : 17.629 154.638 6057 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.40 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 4385 helix: -0.21 (0.10), residues: 2582 sheet: -3.22 (0.41), residues: 137 loop : -2.20 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 265 TYR 0.035 0.002 TYR B 68 PHE 0.029 0.002 PHE E 346 TRP 0.048 0.002 TRP H 150 HIS 0.008 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (40020) covalent geometry : angle 0.70948 / 0.38 (54610) SS BOND : bond 0.00189 / 0.09 ( 2) SS BOND : angle 2.89754 / 1.70 ( 4) hydrogen bonds : bond 0.04882 / 3.15 ( 1785) hydrogen bonds : angle 5.18175 / 3.54 ( 5116) metal coordination : bond 0.00233 / 0.14 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.230 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: A 267 MET cc_start: 0.8837 (ptp) cc_final: 0.8552 (ptt) REVERT: A 273 LEU cc_start: 0.9146 (tt) cc_final: 0.8918 (tt) REVERT: A 288 ILE cc_start: 0.9564 (pt) cc_final: 0.9149 (tt) REVERT: A 317 MET cc_start: 0.8899 (mpp) cc_final: 0.8107 (mpp) REVERT: B 115 MET cc_start: 0.7502 (tmm) cc_final: 0.7066 (tmm) REVERT: B 174 MET cc_start: 0.8414 (ttm) cc_final: 0.8196 (tpp) REVERT: B 204 MET cc_start: 0.8861 (mpp) cc_final: 0.8392 (mpp) REVERT: B 208 MET cc_start: 0.8696 (ptt) cc_final: 0.8351 (ptt) REVERT: B 259 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8807 (tp-100) REVERT: B 295 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8610 (mmm-85) REVERT: B 352 ASP cc_start: 0.8083 (t70) cc_final: 0.7751 (t70) REVERT: B 414 LEU cc_start: 0.9654 (tp) cc_final: 0.9450 (tp) REVERT: B 458 MET cc_start: 0.9162 (ptt) cc_final: 0.8647 (ptt) REVERT: C 100 MET cc_start: 0.9174 (tpt) cc_final: 0.8783 (tpp) REVERT: C 204 MET cc_start: 0.8460 (ttp) cc_final: 0.7569 (ttp) REVERT: C 458 MET cc_start: 0.9255 (ppp) cc_final: 0.9027 (ppp) REVERT: D 142 ASN cc_start: 0.9217 (m-40) cc_final: 0.8927 (m-40) REVERT: E 51 LYS cc_start: 0.9631 (mmtm) cc_final: 0.9402 (mtmm) REVERT: E 117 PHE cc_start: 0.9474 (t80) cc_final: 0.9128 (t80) REVERT: H 147 TYR cc_start: 0.9220 (t80) cc_final: 0.8530 (t80) REVERT: H 161 ASP cc_start: 0.9381 (t0) cc_final: 0.8987 (p0) REVERT: H 170 PHE cc_start: 0.8617 (t80) cc_final: 0.8320 (t80) REVERT: H 270 MET cc_start: 0.9297 (mpp) cc_final: 0.8739 (mpp) REVERT: H 287 LEU cc_start: 0.9050 (mm) cc_final: 0.8843 (mm) REVERT: H 361 MET cc_start: 0.9181 (pmm) cc_final: 0.8792 (pmm) REVERT: I 43 MET cc_start: 0.8444 (mmp) cc_final: 0.8180 (mmm) REVERT: I 100 MET cc_start: 0.9002 (mmp) cc_final: 0.8668 (mmm) REVERT: I 103 MET cc_start: 0.8085 (mmt) cc_final: 0.7884 (mmm) REVERT: I 115 MET cc_start: 0.8756 (ptp) cc_final: 0.8367 (ptp) REVERT: I 119 MET cc_start: 0.9466 (tmm) cc_final: 0.8948 (tmm) REVERT: I 294 TYR cc_start: 0.9654 (m-80) cc_final: 0.9254 (m-80) REVERT: I 458 MET cc_start: 0.9296 (ptm) cc_final: 0.8952 (ppp) REVERT: I 605 ASP cc_start: 0.8468 (m-30) cc_final: 0.8255 (t70) REVERT: J 204 MET cc_start: 0.6496 (tpt) cc_final: 0.6286 (tpp) REVERT: J 208 MET cc_start: 0.7455 (tpt) cc_final: 0.7243 (mmm) REVERT: J 458 MET cc_start: 0.8190 (ptt) cc_final: 0.7741 (ptt) REVERT: J 460 MET cc_start: 0.7503 (ptp) cc_final: 0.7277 (ptm) REVERT: J 565 LEU cc_start: 0.9239 (mt) cc_final: 0.9007 (tp) REVERT: K 77 MET cc_start: 0.8284 (pmm) cc_final: 0.7699 (pmm) REVERT: K 142 ASN cc_start: 0.9124 (t0) cc_final: 0.8890 (t0) REVERT: L 117 PHE cc_start: 0.9294 (m-80) cc_final: 0.8909 (m-80) REVERT: L 407 MET cc_start: 0.9122 (mmm) cc_final: 0.8667 (mpp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2175 time to fit residues: 82.5206 Evaluate side-chains 183 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 321 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 397 optimal weight: 0.6980 chunk 306 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 chunk 353 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN H 289 ASN I 32 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.050220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.035734 restraints weight = 397856.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.037073 restraints weight = 252372.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.037298 restraints weight = 177534.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.037727 restraints weight = 138600.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.037933 restraints weight = 116951.208| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40039 Z= 0.129 Angle : 0.666 14.724 54614 Z= 0.351 Chirality : 0.044 0.325 6020 Planarity : 0.004 0.054 6548 Dihedral : 17.528 154.430 6057 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4385 helix: -0.08 (0.10), residues: 2574 sheet: -2.89 (0.44), residues: 122 loop : -2.25 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 265 TYR 0.020 0.002 TYR B 294 PHE 0.035 0.002 PHE C 500 TRP 0.046 0.002 TRP H 150 HIS 0.008 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (40020) covalent geometry : angle 0.66527 / 0.35 (54610) SS BOND : bond 0.00595 / 0.28 ( 2) SS BOND : angle 3.74439 / 2.14 ( 4) hydrogen bonds : bond 0.04387 / 2.82 ( 1785) hydrogen bonds : angle 4.99955 / 3.41 ( 5116) metal coordination : bond 0.00138 / 0.08 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.565 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 123 LEU cc_start: 0.8713 (pt) cc_final: 0.8261 (pt) REVERT: A 267 MET cc_start: 0.8849 (ptp) cc_final: 0.8602 (ptt) REVERT: A 288 ILE cc_start: 0.9626 (pt) cc_final: 0.9280 (tt) REVERT: B 115 MET cc_start: 0.7455 (tmm) cc_final: 0.7051 (tmm) REVERT: B 169 MET cc_start: 0.8747 (ppp) cc_final: 0.8534 (ppp) REVERT: B 174 MET cc_start: 0.8353 (ttm) cc_final: 0.7750 (ttt) REVERT: B 204 MET cc_start: 0.8868 (mpp) cc_final: 0.8334 (mpp) REVERT: B 208 MET cc_start: 0.8696 (ptt) cc_final: 0.8363 (ptt) REVERT: B 295 ARG cc_start: 0.8962 (tpp80) cc_final: 0.8443 (mmm-85) REVERT: B 352 ASP cc_start: 0.8085 (t70) cc_final: 0.7806 (t70) REVERT: B 458 MET cc_start: 0.9104 (ptt) cc_final: 0.8734 (ptt) REVERT: B 460 MET cc_start: 0.8763 (mmm) cc_final: 0.8348 (mmm) REVERT: C 100 MET cc_start: 0.9157 (tpt) cc_final: 0.8793 (tpp) REVERT: C 204 MET cc_start: 0.8459 (ttp) cc_final: 0.7458 (ttp) REVERT: C 226 MET cc_start: 0.9284 (pmm) cc_final: 0.8977 (pmm) REVERT: D 142 ASN cc_start: 0.9272 (m-40) cc_final: 0.8995 (m-40) REVERT: E 51 LYS cc_start: 0.9652 (mmtm) cc_final: 0.9388 (mtmm) REVERT: E 117 PHE cc_start: 0.9448 (t80) cc_final: 0.9117 (t80) REVERT: H 19 GLU cc_start: 0.9349 (mp0) cc_final: 0.9119 (mp0) REVERT: H 147 TYR cc_start: 0.9282 (t80) cc_final: 0.8588 (t80) REVERT: H 161 ASP cc_start: 0.9408 (t0) cc_final: 0.9008 (p0) REVERT: H 170 PHE cc_start: 0.8618 (t80) cc_final: 0.8285 (t80) REVERT: H 270 MET cc_start: 0.9178 (mpp) cc_final: 0.8686 (mpp) REVERT: H 287 LEU cc_start: 0.9055 (mm) cc_final: 0.8791 (mt) REVERT: H 361 MET cc_start: 0.9263 (pmm) cc_final: 0.8894 (pmm) REVERT: H 370 TRP cc_start: 0.8375 (m-90) cc_final: 0.7941 (m-10) REVERT: I 43 MET cc_start: 0.8413 (mmp) cc_final: 0.8165 (mmm) REVERT: I 100 MET cc_start: 0.8947 (mmp) cc_final: 0.8675 (mmm) REVERT: I 294 TYR cc_start: 0.9656 (m-80) cc_final: 0.9230 (m-80) REVERT: I 605 ASP cc_start: 0.8476 (m-30) cc_final: 0.8261 (t70) REVERT: J 204 MET cc_start: 0.6466 (tpt) cc_final: 0.6239 (tpp) REVERT: J 208 MET cc_start: 0.7566 (tpt) cc_final: 0.7316 (mmm) REVERT: J 458 MET cc_start: 0.8198 (ptt) cc_final: 0.7764 (ptt) REVERT: J 460 MET cc_start: 0.7384 (ptp) cc_final: 0.7144 (ptm) REVERT: J 565 LEU cc_start: 0.9233 (mt) cc_final: 0.8993 (tp) REVERT: K 77 MET cc_start: 0.8198 (pmm) cc_final: 0.7626 (pmm) REVERT: K 142 ASN cc_start: 0.9114 (t0) cc_final: 0.8877 (t0) REVERT: L 117 PHE cc_start: 0.9296 (m-80) cc_final: 0.8905 (m-80) REVERT: L 346 PHE cc_start: 0.9509 (m-10) cc_final: 0.8803 (m-10) REVERT: L 407 MET cc_start: 0.9193 (mmm) cc_final: 0.8650 (mpp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2292 time to fit residues: 91.1694 Evaluate side-chains 190 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 211 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 433 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 203 optimal weight: 0.0470 chunk 368 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN H 289 ASN I 32 ASN I 66 GLN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.049616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.035190 restraints weight = 401427.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036401 restraints weight = 256460.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.036621 restraints weight = 184165.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.036893 restraints weight = 153419.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.037342 restraints weight = 127037.151| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40039 Z= 0.153 Angle : 0.666 13.996 54614 Z= 0.354 Chirality : 0.044 0.308 6020 Planarity : 0.004 0.053 6548 Dihedral : 17.456 152.904 6057 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.76 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 4385 helix: 0.01 (0.10), residues: 2569 sheet: -3.30 (0.38), residues: 156 loop : -2.18 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 265 TYR 0.019 0.002 TYR L 48 PHE 0.035 0.002 PHE I 469 TRP 0.059 0.002 TRP H 87 HIS 0.005 0.001 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (40020) covalent geometry : angle 0.66588 / 0.35 (54610) SS BOND : bond 0.00247 / 0.12 ( 2) SS BOND : angle 3.39630 / 1.97 ( 4) hydrogen bonds : bond 0.04482 / 2.88 ( 1785) hydrogen bonds : angle 4.99796 / 3.41 ( 5116) metal coordination : bond 0.00136 / 0.08 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.693 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 123 LEU cc_start: 0.8754 (pt) cc_final: 0.8282 (pt) REVERT: A 267 MET cc_start: 0.8925 (ptp) cc_final: 0.8665 (ptt) REVERT: B 115 MET cc_start: 0.7474 (tmm) cc_final: 0.7095 (tmm) REVERT: B 174 MET cc_start: 0.8427 (ttm) cc_final: 0.7831 (ttt) REVERT: B 204 MET cc_start: 0.8915 (mpp) cc_final: 0.8371 (mpp) REVERT: B 208 MET cc_start: 0.8756 (ptt) cc_final: 0.8443 (ptt) REVERT: B 259 GLN cc_start: 0.9258 (tp-100) cc_final: 0.9029 (tp-100) REVERT: B 295 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8547 (mmm-85) REVERT: B 352 ASP cc_start: 0.8117 (t70) cc_final: 0.7147 (t70) REVERT: B 356 ASP cc_start: 0.7983 (m-30) cc_final: 0.7704 (m-30) REVERT: B 458 MET cc_start: 0.9213 (ptt) cc_final: 0.8741 (ptt) REVERT: B 460 MET cc_start: 0.8864 (mmm) cc_final: 0.8459 (mmm) REVERT: C 100 MET cc_start: 0.9173 (tpt) cc_final: 0.8799 (tpp) REVERT: C 204 MET cc_start: 0.8478 (ttp) cc_final: 0.7572 (ttp) REVERT: C 458 MET cc_start: 0.9257 (ppp) cc_final: 0.9046 (ppp) REVERT: D 142 ASN cc_start: 0.9259 (m-40) cc_final: 0.8968 (m-40) REVERT: E 51 LYS cc_start: 0.9660 (mmtm) cc_final: 0.9395 (mtmm) REVERT: E 117 PHE cc_start: 0.9466 (t80) cc_final: 0.9144 (t80) REVERT: H 19 GLU cc_start: 0.9401 (mp0) cc_final: 0.9182 (mp0) REVERT: H 147 TYR cc_start: 0.9322 (t80) cc_final: 0.8611 (t80) REVERT: H 161 ASP cc_start: 0.9419 (t0) cc_final: 0.9022 (p0) REVERT: H 170 PHE cc_start: 0.8699 (t80) cc_final: 0.8368 (t80) REVERT: H 270 MET cc_start: 0.9131 (mpp) cc_final: 0.8818 (mpp) REVERT: H 287 LEU cc_start: 0.9082 (mm) cc_final: 0.8871 (mm) REVERT: H 361 MET cc_start: 0.9291 (pmm) cc_final: 0.8928 (pmm) REVERT: H 370 TRP cc_start: 0.8394 (m-90) cc_final: 0.7966 (m-10) REVERT: I 27 MET cc_start: 0.4416 (ttp) cc_final: 0.4198 (tmm) REVERT: I 43 MET cc_start: 0.8368 (mmp) cc_final: 0.8124 (mmm) REVERT: I 100 MET cc_start: 0.9017 (mmp) cc_final: 0.8802 (mmm) REVERT: I 294 TYR cc_start: 0.9663 (m-80) cc_final: 0.9237 (m-80) REVERT: I 605 ASP cc_start: 0.8478 (m-30) cc_final: 0.8267 (t70) REVERT: J 204 MET cc_start: 0.6487 (tpt) cc_final: 0.6269 (tpp) REVERT: J 208 MET cc_start: 0.7463 (tpt) cc_final: 0.7223 (mmm) REVERT: J 458 MET cc_start: 0.8195 (ptt) cc_final: 0.7733 (ptt) REVERT: J 460 MET cc_start: 0.7446 (ptp) cc_final: 0.7196 (ptm) REVERT: J 565 LEU cc_start: 0.9226 (mt) cc_final: 0.8989 (tp) REVERT: K 77 MET cc_start: 0.8238 (pmm) cc_final: 0.7605 (pmm) REVERT: L 117 PHE cc_start: 0.9296 (m-80) cc_final: 0.8914 (m-80) REVERT: L 346 PHE cc_start: 0.9529 (m-10) cc_final: 0.8843 (m-10) REVERT: L 407 MET cc_start: 0.9204 (mmm) cc_final: 0.8661 (mpp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2306 time to fit residues: 87.7490 Evaluate side-chains 187 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3283 > 50: distance: 72 - 90: 23.230 distance: 78 - 102: 17.078 distance: 83 - 109: 27.487 distance: 86 - 90: 23.860 distance: 87 - 116: 16.691 distance: 90 - 91: 34.656 distance: 91 - 92: 23.107 distance: 91 - 94: 15.810 distance: 92 - 93: 8.833 distance: 92 - 102: 7.431 distance: 93 - 123: 28.294 distance: 94 - 95: 9.874 distance: 95 - 96: 13.554 distance: 95 - 97: 13.514 distance: 96 - 98: 11.304 distance: 97 - 99: 9.755 distance: 98 - 100: 4.775 distance: 99 - 100: 9.243 distance: 100 - 101: 11.431 distance: 102 - 103: 18.542 distance: 103 - 104: 31.212 distance: 103 - 106: 8.844 distance: 104 - 105: 27.473 distance: 104 - 109: 17.416 distance: 105 - 134: 38.264 distance: 106 - 107: 13.146 distance: 106 - 108: 7.656 distance: 109 - 110: 9.533 distance: 110 - 111: 13.749 distance: 110 - 113: 10.899 distance: 111 - 112: 11.611 distance: 111 - 116: 23.685 distance: 112 - 145: 29.699 distance: 113 - 114: 25.988 distance: 113 - 115: 34.174 distance: 116 - 117: 14.775 distance: 117 - 118: 7.361 distance: 117 - 120: 31.561 distance: 118 - 119: 15.990 distance: 118 - 123: 26.590 distance: 119 - 157: 63.328 distance: 120 - 121: 10.379 distance: 120 - 122: 6.519 distance: 123 - 124: 8.045 distance: 124 - 125: 16.315 distance: 124 - 127: 39.320 distance: 125 - 126: 48.391 distance: 125 - 134: 21.785 distance: 127 - 128: 10.910 distance: 128 - 129: 30.331 distance: 129 - 131: 18.550 distance: 130 - 132: 22.699 distance: 131 - 133: 19.882 distance: 132 - 133: 40.313 distance: 134 - 135: 17.462 distance: 135 - 136: 22.361 distance: 135 - 138: 22.887 distance: 136 - 137: 25.935 distance: 136 - 145: 17.964 distance: 138 - 139: 29.953 distance: 139 - 140: 13.851 distance: 140 - 141: 31.952 distance: 141 - 142: 18.351 distance: 142 - 143: 20.044 distance: 142 - 144: 17.046 distance: 145 - 146: 39.118 distance: 146 - 147: 5.027 distance: 146 - 149: 15.648 distance: 147 - 148: 33.347 distance: 147 - 157: 17.289 distance: 149 - 150: 25.049 distance: 150 - 151: 19.684 distance: 150 - 152: 15.208 distance: 151 - 153: 8.198 distance: 152 - 154: 21.909 distance: 153 - 155: 16.792 distance: 154 - 155: 10.988 distance: 155 - 156: 22.948 distance: 157 - 158: 36.681 distance: 158 - 159: 22.458 distance: 158 - 161: 28.165 distance: 159 - 160: 23.154 distance: 159 - 163: 23.581 distance: 161 - 162: 9.423 distance: 163 - 164: 5.629 distance: 164 - 165: 28.480 distance: 164 - 167: 48.555 distance: 165 - 166: 17.953 distance: 165 - 173: 11.081 distance: 167 - 168: 15.172 distance: 168 - 169: 21.636 distance: 168 - 170: 4.022 distance: 169 - 171: 9.561 distance: 170 - 172: 27.194 distance: 173 - 174: 44.538 distance: 174 - 175: 52.756 distance: 174 - 177: 42.066 distance: 175 - 176: 49.904 distance: 175 - 181: 26.868 distance: 177 - 178: 4.299 distance: 178 - 179: 6.868 distance: 178 - 180: 49.014