Starting phenix.real_space_refine on Tue Aug 26 16:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_0096_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_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 { model { file = "/net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_0096_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_0096_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_0096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gys_0096/08_2025/6gys_0096.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 8.26, per 1000 atoms: 0.21 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 4.16 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: 7.79 Time building geometry restraints manager: 3.63 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=" 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=" 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 bond pdb=" C PRO H 33 " pdb=" N TYR H 34 " ideal model delta sigma weight residual 1.331 1.242 0.089 2.07e-02 2.33e+03 1.85e+01 bond pdb=" C LEU C 58 " pdb=" N PRO C 59 " ideal model delta sigma weight residual 1.336 1.387 -0.051 1.20e-02 6.94e+03 1.82e+01 ... (remaining 40015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 53993 3.86 - 7.73: 570 7.73 - 11.59: 42 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=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA LEU H 24 " pdb=" CB LEU H 24 " pdb=" CG LEU H 24 " ideal model delta sigma weight residual 116.30 135.62 -19.32 3.50e+00 8.16e-02 3.05e+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: 5520 0.098 - 0.196: 471 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 2.42 2.12 0.30 2.00e-01 2.50e+01 2.25e+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: 4.060 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: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 38.500 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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= 0.524 Angle : 1.122 19.322 54614 Z= 0.643 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 aren 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 covalent geometry : bond 0.00804 (40020) covalent geometry : angle 1.12199 (54610) SS BOND : bond 0.00444 ( 2) SS BOND : angle 2.83593 ( 4) hydrogen bonds : bond 0.18687 ( 1785) hydrogen bonds : angle 7.78685 ( 5116) metal coordination : bond 0.51786 ( 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: 0.8908 (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: 0.9506 (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: 0.2439 time to fit residues: 162.0357 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 : 1.572 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 439 HIS A 450 ASN B 66 GLN B 152 HIS B 259 GLN 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 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 296 ASN H 420 GLN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 ASN ** 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 86 HIS L 268 GLN L 408 ASN L 505 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.050047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.035354 restraints weight = 401063.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.036676 restraints weight = 249098.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036997 restraints weight = 174630.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.037390 restraints weight = 133583.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.037620 restraints weight = 110835.997| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40039 Z= 0.169 Angle : 0.735 14.177 54614 Z= 0.396 Chirality : 0.044 0.273 6020 Planarity : 0.006 0.179 6548 Dihedral : 18.146 167.089 6057 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Rotamer: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.95 (0.11), residues: 4385 helix: -1.25 (0.09), residues: 2553 sheet: -3.07 (0.44), residues: 112 loop : -2.89 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 19 TYR 0.028 0.002 TYR E 49 PHE 0.024 0.002 PHE L 117 TRP 0.023 0.002 TRP I 346 HIS 0.008 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00357 (40020) covalent geometry : angle 0.73495 (54610) SS BOND : bond 0.01731 ( 2) SS BOND : angle 2.20299 ( 4) hydrogen bonds : bond 0.05615 ( 1785) hydrogen bonds : angle 5.71892 ( 5116) metal coordination : bond 0.00687 ( 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 339 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 335 time to evaluate : 1.208 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: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9067 (pp) cc_final: 0.8675 (pt) REVERT: A 273 LEU cc_start: 0.9288 (tp) cc_final: 0.8957 (tt) REVERT: A 317 MET cc_start: 0.8909 (mpp) cc_final: 0.8359 (mpp) REVERT: A 441 LYS cc_start: 0.9201 (tttt) cc_final: 0.8942 (tttp) REVERT: B 100 MET cc_start: 0.9438 (mmp) cc_final: 0.9132 (mmm) REVERT: B 208 MET cc_start: 0.8564 (ptt) cc_final: 0.8272 (ptt) REVERT: B 259 GLN cc_start: 0.9323 (tp40) cc_final: 0.9122 (tp-100) REVERT: B 295 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: B 414 LEU cc_start: 0.9704 (tp) cc_final: 0.9298 (tp) REVERT: B 417 MET cc_start: 0.9008 (mtp) cc_final: 0.8701 (mtp) REVERT: B 458 MET cc_start: 0.8808 (ptt) cc_final: 0.8503 (ptt) REVERT: C 71 TRP cc_start: 0.8831 (m100) cc_final: 0.8612 (m-90) REVERT: C 358 TYR cc_start: 0.8196 (m-80) cc_final: 0.7538 (m-80) REVERT: E 51 LYS cc_start: 0.9666 (mmtm) cc_final: 0.9358 (mtmm) REVERT: E 117 PHE cc_start: 0.9494 (t80) cc_final: 0.9128 (t80) REVERT: E 152 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8726 (tm-30) REVERT: E 461 MET cc_start: 0.9392 (mmm) cc_final: 0.9175 (mmm) REVERT: H 137 MET cc_start: 0.8823 (ptm) cc_final: 0.8516 (tmm) REVERT: H 147 TYR cc_start: 0.9357 (t80) cc_final: 0.9072 (t80) REVERT: H 161 ASP cc_start: 0.9572 (t0) cc_final: 0.9116 (p0) REVERT: H 170 PHE cc_start: 0.8717 (t80) cc_final: 0.8183 (t80) REVERT: H 320 ILE cc_start: 0.9260 (pt) cc_final: 0.8875 (pt) REVERT: H 359 LEU cc_start: 0.9517 (tt) cc_final: 0.8847 (tp) REVERT: H 370 TRP cc_start: 0.8223 (m-90) cc_final: 0.7160 (m-10) REVERT: I 103 MET cc_start: 0.8397 (mmp) cc_final: 0.8154 (mmm) REVERT: I 119 MET cc_start: 0.9438 (tmm) cc_final: 0.9081 (tmm) REVERT: I 294 TYR cc_start: 0.9556 (m-80) cc_final: 0.9185 (m-80) REVERT: I 605 ASP cc_start: 0.8600 (m-30) cc_final: 0.8353 (t70) REVERT: J 208 MET cc_start: 0.7109 (mmt) cc_final: 0.6552 (mmt) REVERT: J 565 LEU cc_start: 0.9220 (mt) cc_final: 0.8971 (tt) REVERT: K 77 MET cc_start: 0.8417 (pmm) cc_final: 0.7987 (pmm) REVERT: K 108 ASP cc_start: 0.9439 (t0) cc_final: 0.9190 (p0) REVERT: K 142 ASN cc_start: 0.9238 (t0) cc_final: 0.9023 (t0) REVERT: L 346 PHE cc_start: 0.9489 (m-10) cc_final: 0.8916 (m-10) REVERT: L 407 MET cc_start: 0.9166 (mmt) cc_final: 0.8641 (mpp) outliers start: 4 outliers final: 0 residues processed: 337 average time/residue: 0.2432 time to fit residues: 128.6616 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 : 1.473 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 383 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 261 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN B 552 ASN D 31 ASN E 496 GLN H 23 HIS ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 444 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 211 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.050596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.035863 restraints weight = 395638.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036945 restraints weight = 236777.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.037715 restraints weight = 166893.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.038199 restraints weight = 131097.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.038544 restraints weight = 111291.720| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2655 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= 0.142 Angle : 0.668 13.147 54614 Z= 0.358 Chirality : 0.043 0.253 6020 Planarity : 0.005 0.106 6548 Dihedral : 17.803 167.632 6057 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.21 (0.12), residues: 4385 helix: -0.65 (0.10), residues: 2553 sheet: -2.85 (0.48), residues: 102 loop : -2.59 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 265 TYR 0.022 0.001 TYR J 126 PHE 0.022 0.002 PHE H 92 TRP 0.027 0.002 TRP H 87 HIS 0.008 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00297 (40020) covalent geometry : angle 0.66746 (54610) SS BOND : bond 0.01870 ( 2) SS BOND : angle 1.67619 ( 4) hydrogen bonds : bond 0.04832 ( 1785) hydrogen bonds : angle 5.24512 ( 5116) metal coordination : bond 0.00203 ( 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 299 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 1.525 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: A 123 LEU cc_start: 0.8863 (pp) cc_final: 0.8339 (pt) REVERT: A 267 MET cc_start: 0.9110 (ptp) cc_final: 0.8650 (ptt) REVERT: A 273 LEU cc_start: 0.9324 (tp) cc_final: 0.8856 (tt) REVERT: B 100 MET cc_start: 0.9472 (mmp) cc_final: 0.9141 (mmp) REVERT: B 169 MET cc_start: 0.8876 (ppp) cc_final: 0.8665 (ppp) REVERT: B 204 MET cc_start: 0.8746 (mpp) cc_final: 0.8352 (mpp) REVERT: B 208 MET cc_start: 0.8540 (ptt) cc_final: 0.8296 (ptt) REVERT: B 295 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8629 (mmm-85) REVERT: B 352 ASP cc_start: 0.8385 (t70) cc_final: 0.7100 (t70) REVERT: B 356 ASP cc_start: 0.8537 (m-30) cc_final: 0.8059 (m-30) REVERT: B 376 GLU cc_start: 0.9243 (mp0) cc_final: 0.9000 (mp0) REVERT: B 414 LEU cc_start: 0.9641 (tp) cc_final: 0.9295 (tp) REVERT: B 417 MET cc_start: 0.8880 (mtp) cc_final: 0.8620 (mtp) REVERT: C 100 MET cc_start: 0.9433 (tpt) cc_final: 0.8998 (tpp) REVERT: D 159 ARG cc_start: 0.9023 (ttp-110) cc_final: 0.8678 (ttm110) REVERT: E 51 LYS cc_start: 0.9638 (mmtm) cc_final: 0.9395 (mtmm) REVERT: E 117 PHE cc_start: 0.9396 (t80) cc_final: 0.9008 (t80) REVERT: E 320 ASP cc_start: 0.9202 (m-30) cc_final: 0.8969 (t0) REVERT: H 66 MET cc_start: 0.8885 (ptp) cc_final: 0.8511 (ptp) REVERT: H 74 LEU cc_start: 0.9320 (tp) cc_final: 0.9112 (tp) REVERT: H 137 MET cc_start: 0.8802 (ptm) cc_final: 0.8433 (ppp) REVERT: H 147 TYR cc_start: 0.9343 (t80) cc_final: 0.8936 (t80) REVERT: H 161 ASP cc_start: 0.9522 (t0) cc_final: 0.9053 (p0) REVERT: H 170 PHE cc_start: 0.8548 (t80) cc_final: 0.8311 (t80) REVERT: H 270 MET cc_start: 0.9432 (mpp) cc_final: 0.9049 (mpp) REVERT: H 273 LEU cc_start: 0.9265 (tp) cc_final: 0.8926 (tp) REVERT: H 287 LEU cc_start: 0.9022 (mm) cc_final: 0.8776 (mm) REVERT: H 359 LEU cc_start: 0.9387 (tt) cc_final: 0.8967 (tt) REVERT: H 361 MET cc_start: 0.9210 (pmm) cc_final: 0.8960 (pmm) REVERT: H 370 TRP cc_start: 0.8528 (m-90) cc_final: 0.8269 (m-10) REVERT: I 43 MET cc_start: 0.8435 (mmp) cc_final: 0.8129 (mmm) REVERT: I 100 MET cc_start: 0.9070 (mmp) cc_final: 0.8771 (mmm) REVERT: I 103 MET cc_start: 0.8189 (mmp) cc_final: 0.7934 (mmm) REVERT: I 119 MET cc_start: 0.9445 (tmm) cc_final: 0.9019 (tmm) REVERT: I 294 TYR cc_start: 0.9609 (m-80) cc_final: 0.9203 (m-80) REVERT: I 605 ASP cc_start: 0.8526 (m-30) cc_final: 0.8296 (t70) REVERT: J 208 MET cc_start: 0.6864 (mmt) cc_final: 0.6627 (mmt) REVERT: J 565 LEU cc_start: 0.9244 (mt) cc_final: 0.8982 (tt) REVERT: K 77 MET cc_start: 0.8195 (pmm) cc_final: 0.7830 (pmm) REVERT: K 142 ASN cc_start: 0.9203 (t0) cc_final: 0.8972 (t0) REVERT: L 346 PHE cc_start: 0.9488 (m-10) cc_final: 0.8907 (m-10) REVERT: L 407 MET cc_start: 0.9097 (mmt) cc_final: 0.8623 (mpp) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 0.2373 time to fit residues: 113.2289 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 : 1.322 ------------------------------------------------------------------------------- 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: 6.9990 chunk 306 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 167 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 384 optimal weight: 8.9990 chunk 329 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 443 GLN B 38 GLN B 259 GLN B 303 GLN C 211 ASN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN I 32 ASN ** I 259 GLN ** 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 L 529 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.049935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.035485 restraints weight = 400042.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.036828 restraints weight = 254257.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.037093 restraints weight = 178949.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.037471 restraints weight = 134918.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037677 restraints weight = 118025.139| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40039 Z= 0.171 Angle : 0.666 13.156 54614 Z= 0.356 Chirality : 0.043 0.253 6020 Planarity : 0.005 0.062 6548 Dihedral : 17.665 169.054 6057 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.39 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.82 (0.12), residues: 4385 helix: -0.33 (0.10), residues: 2566 sheet: -3.04 (0.47), residues: 99 loop : -2.42 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 20 TYR 0.022 0.002 TYR C 358 PHE 0.017 0.002 PHE I 500 TRP 0.050 0.002 TRP H 150 HIS 0.006 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00362 (40020) covalent geometry : angle 0.66618 (54610) SS BOND : bond 0.00780 ( 2) SS BOND : angle 2.18088 ( 4) hydrogen bonds : bond 0.04690 ( 1785) hydrogen bonds : angle 5.12586 ( 5116) metal coordination : bond 0.00227 ( 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 258 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.477 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 267 MET cc_start: 0.9187 (ptp) cc_final: 0.8767 (ptt) REVERT: A 273 LEU cc_start: 0.9325 (tp) cc_final: 0.9091 (tt) REVERT: B 100 MET cc_start: 0.9485 (mmp) cc_final: 0.9259 (mmp) REVERT: B 174 MET cc_start: 0.8418 (ttm) cc_final: 0.7857 (ttt) REVERT: B 204 MET cc_start: 0.8854 (mpp) cc_final: 0.8361 (mpp) REVERT: B 208 MET cc_start: 0.8596 (ptt) cc_final: 0.8273 (ptt) REVERT: B 237 TYR cc_start: 0.8813 (t80) cc_final: 0.8521 (t80) REVERT: B 259 GLN cc_start: 0.9308 (tp40) cc_final: 0.9056 (tp-100) REVERT: B 295 ARG cc_start: 0.9032 (tpp80) cc_final: 0.8624 (mmm-85) REVERT: B 352 ASP cc_start: 0.8428 (t70) cc_final: 0.8088 (t70) REVERT: B 414 LEU cc_start: 0.9660 (tp) cc_final: 0.9345 (tp) REVERT: B 417 MET cc_start: 0.8892 (mtp) cc_final: 0.8631 (mtp) REVERT: B 458 MET cc_start: 0.8976 (ptt) cc_final: 0.8629 (ptt) REVERT: C 100 MET cc_start: 0.9298 (tpt) cc_final: 0.8869 (tpp) REVERT: C 204 MET cc_start: 0.8524 (ttp) cc_final: 0.8190 (ttm) REVERT: D 142 ASN cc_start: 0.9423 (m-40) cc_final: 0.9089 (m-40) REVERT: D 144 LYS cc_start: 0.9292 (mptt) cc_final: 0.9048 (mmtm) REVERT: E 51 LYS cc_start: 0.9647 (mmtm) cc_final: 0.9420 (mtmm) REVERT: E 117 PHE cc_start: 0.9492 (t80) cc_final: 0.9108 (t80) REVERT: E 320 ASP cc_start: 0.9202 (m-30) cc_final: 0.8972 (t0) REVERT: H 66 MET cc_start: 0.8849 (ptp) cc_final: 0.8415 (ptp) REVERT: H 74 LEU cc_start: 0.9267 (tp) cc_final: 0.9051 (tp) REVERT: H 137 MET cc_start: 0.8741 (ptm) cc_final: 0.8368 (ppp) REVERT: H 147 TYR cc_start: 0.9279 (t80) cc_final: 0.8896 (t80) REVERT: H 161 ASP cc_start: 0.9446 (t0) cc_final: 0.9018 (p0) REVERT: H 170 PHE cc_start: 0.8618 (t80) cc_final: 0.8325 (t80) REVERT: H 273 LEU cc_start: 0.9258 (tp) cc_final: 0.9027 (tp) REVERT: H 287 LEU cc_start: 0.9007 (mm) cc_final: 0.8768 (mm) REVERT: H 361 MET cc_start: 0.9187 (pmm) cc_final: 0.8937 (pmm) REVERT: H 370 TRP cc_start: 0.8505 (m-90) cc_final: 0.8201 (m-10) REVERT: I 43 MET cc_start: 0.8343 (mmp) cc_final: 0.8049 (mmm) REVERT: I 100 MET cc_start: 0.9036 (mmp) cc_final: 0.8766 (mmm) REVERT: I 103 MET cc_start: 0.8211 (mmt) cc_final: 0.7979 (mmm) REVERT: I 119 MET cc_start: 0.9440 (tmm) cc_final: 0.8940 (tmm) REVERT: I 294 TYR cc_start: 0.9627 (m-80) cc_final: 0.9234 (m-80) REVERT: I 605 ASP cc_start: 0.8510 (m-30) cc_final: 0.8301 (t70) REVERT: J 204 MET cc_start: 0.5989 (tpp) cc_final: 0.5685 (tpp) REVERT: K 77 MET cc_start: 0.8309 (pmm) cc_final: 0.7918 (pmm) REVERT: K 142 ASN cc_start: 0.9181 (t0) cc_final: 0.8947 (t0) REVERT: L 37 LEU cc_start: 0.9413 (mt) cc_final: 0.9208 (mp) REVERT: L 346 PHE cc_start: 0.9523 (m-10) cc_final: 0.8921 (m-10) REVERT: L 407 MET cc_start: 0.9086 (mmt) cc_final: 0.8607 (mpp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2298 time to fit residues: 97.0255 Evaluate side-chains 207 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 9.9990 chunk 386 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 445 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 368 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 407 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN D 97 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.049096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.034771 restraints weight = 408718.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.036018 restraints weight = 261194.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.036105 restraints weight = 186023.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.036540 restraints weight = 150361.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.036674 restraints weight = 129830.060| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 40039 Z= 0.212 Angle : 0.694 13.648 54614 Z= 0.371 Chirality : 0.043 0.254 6020 Planarity : 0.005 0.065 6548 Dihedral : 17.608 170.715 6057 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.65 (0.12), residues: 4385 helix: -0.23 (0.10), residues: 2585 sheet: -3.07 (0.47), residues: 101 loop : -2.28 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 262 TYR 0.025 0.002 TYR B 335 PHE 0.020 0.002 PHE C 500 TRP 0.048 0.002 TRP D 119 HIS 0.018 0.002 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00441 (40020) covalent geometry : angle 0.69342 (54610) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.55034 ( 4) hydrogen bonds : bond 0.04862 ( 1785) hydrogen bonds : angle 5.11416 ( 5116) metal coordination : bond 0.00219 ( 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 238 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.640 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: 0.8749 (pt) cc_final: 0.8387 (pt) REVERT: A 267 MET cc_start: 0.9096 (ptp) cc_final: 0.8883 (ptt) REVERT: A 273 LEU cc_start: 0.9415 (tp) cc_final: 0.8915 (tt) REVERT: B 204 MET cc_start: 0.8927 (mpp) cc_final: 0.8229 (mpp) REVERT: B 237 TYR cc_start: 0.8835 (t80) cc_final: 0.8593 (t80) REVERT: B 295 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8658 (mmm-85) REVERT: B 352 ASP cc_start: 0.8397 (t70) cc_final: 0.8073 (t70) REVERT: B 458 MET cc_start: 0.9009 (ptt) cc_final: 0.8502 (ptt) REVERT: C 100 MET cc_start: 0.9259 (tpt) cc_final: 0.8796 (tpp) REVERT: C 204 MET cc_start: 0.8653 (ttp) cc_final: 0.8289 (ttm) REVERT: C 226 MET cc_start: 0.9381 (pmm) cc_final: 0.9118 (pmm) REVERT: C 458 MET cc_start: 0.9286 (ptt) cc_final: 0.8617 (ptt) REVERT: D 142 ASN cc_start: 0.9443 (m-40) cc_final: 0.9143 (m-40) REVERT: E 51 LYS cc_start: 0.9655 (mmtm) cc_final: 0.9452 (mtmm) REVERT: E 117 PHE cc_start: 0.9519 (t80) cc_final: 0.9135 (t80) REVERT: E 320 ASP cc_start: 0.9136 (m-30) cc_final: 0.8926 (t70) REVERT: H 66 MET cc_start: 0.8917 (ptp) cc_final: 0.8473 (ptp) REVERT: H 137 MET cc_start: 0.8575 (ptm) cc_final: 0.8297 (ppp) REVERT: H 147 TYR cc_start: 0.9343 (t80) cc_final: 0.8639 (t80) REVERT: H 161 ASP cc_start: 0.9442 (t0) cc_final: 0.9025 (p0) REVERT: H 170 PHE cc_start: 0.8651 (t80) cc_final: 0.8380 (t80) REVERT: H 273 LEU cc_start: 0.9305 (tp) cc_final: 0.9045 (tp) REVERT: H 359 LEU cc_start: 0.9458 (tt) cc_final: 0.8922 (tt) REVERT: H 361 MET cc_start: 0.9295 (pmm) cc_final: 0.8963 (pmm) REVERT: H 370 TRP cc_start: 0.8447 (m-90) cc_final: 0.8048 (m-10) REVERT: I 43 MET cc_start: 0.8450 (mmp) cc_final: 0.8203 (mmm) REVERT: I 100 MET cc_start: 0.9094 (mmp) cc_final: 0.8837 (mmm) REVERT: I 103 MET cc_start: 0.8249 (mmt) cc_final: 0.8034 (mmm) REVERT: I 119 MET cc_start: 0.9447 (tmm) cc_final: 0.8943 (tmm) REVERT: I 294 TYR cc_start: 0.9646 (m-80) cc_final: 0.9251 (m-80) REVERT: I 605 ASP cc_start: 0.8522 (m-30) cc_final: 0.8296 (t70) REVERT: J 100 MET cc_start: 0.9261 (mpp) cc_final: 0.9037 (ppp) REVERT: J 204 MET cc_start: 0.5927 (tpp) cc_final: 0.5644 (tpp) REVERT: J 565 LEU cc_start: 0.9227 (mt) cc_final: 0.8990 (tp) REVERT: K 77 MET cc_start: 0.8375 (pmm) cc_final: 0.7812 (pmm) REVERT: K 142 ASN cc_start: 0.9171 (t0) cc_final: 0.8940 (t0) REVERT: L 37 LEU cc_start: 0.9420 (mt) cc_final: 0.9207 (mp) REVERT: L 117 PHE cc_start: 0.9247 (m-80) cc_final: 0.8899 (m-80) REVERT: L 407 MET cc_start: 0.9067 (mmt) cc_final: 0.8641 (mpp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2378 time to fit residues: 94.0697 Evaluate side-chains 194 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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: 5.9990 chunk 408 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 418 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 335 GLN B 259 GLN B 399 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 439 HIS I 32 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS K 174 ASN L 86 HIS ** 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 = 0.3560 r_free = 0.3560 target = 0.050636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.035942 restraints weight = 396424.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036987 restraints weight = 239671.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.037662 restraints weight = 170463.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.038148 restraints weight = 135552.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.038471 restraints weight = 115909.427| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40039 Z= 0.126 Angle : 0.629 13.138 54614 Z= 0.335 Chirality : 0.043 0.241 6020 Planarity : 0.004 0.065 6548 Dihedral : 17.469 170.957 6057 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.07 % Favored : 91.88 % Rotamer: Outliers : 0.02 % Allowed : 1.82 % Favored : 98.15 % 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 aren not related in a simple way. whole: -1.44 (0.13), residues: 4385 helix: -0.03 (0.10), residues: 2595 sheet: -2.66 (0.46), residues: 115 loop : -2.28 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 375 TYR 0.020 0.001 TYR B 335 PHE 0.025 0.001 PHE E 346 TRP 0.032 0.002 TRP H 150 HIS 0.006 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00268 (40020) covalent geometry : angle 0.62920 (54610) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.95640 ( 4) hydrogen bonds : bond 0.04192 ( 1785) hydrogen bonds : angle 4.85420 ( 5116) metal coordination : bond 0.00297 ( 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 263 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.631 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: A 123 LEU cc_start: 0.8942 (pt) cc_final: 0.8570 (pt) REVERT: A 267 MET cc_start: 0.9132 (ptp) cc_final: 0.8912 (ptt) REVERT: A 273 LEU cc_start: 0.9327 (tp) cc_final: 0.8912 (tt) REVERT: A 288 ILE cc_start: 0.9546 (pt) cc_final: 0.9308 (tt) REVERT: B 169 MET cc_start: 0.8768 (ppp) cc_final: 0.8542 (ppp) REVERT: B 252 LEU cc_start: 0.9491 (tp) cc_final: 0.9186 (mt) REVERT: B 295 ARG cc_start: 0.8959 (tpp80) cc_final: 0.8553 (mmm-85) REVERT: B 302 LEU cc_start: 0.9530 (mm) cc_final: 0.9311 (mp) REVERT: B 352 ASP cc_start: 0.8270 (t70) cc_final: 0.7890 (t70) REVERT: B 399 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9099 (pp30) REVERT: B 458 MET cc_start: 0.9001 (ptt) cc_final: 0.8699 (ptt) REVERT: B 460 MET cc_start: 0.8910 (mmm) cc_final: 0.8377 (mmm) REVERT: C 100 MET cc_start: 0.9219 (tpt) cc_final: 0.8804 (tpp) REVERT: C 204 MET cc_start: 0.8588 (ttp) cc_final: 0.8092 (ttm) REVERT: C 458 MET cc_start: 0.9223 (ptt) cc_final: 0.8621 (ptt) REVERT: C 460 MET cc_start: 0.9338 (mmm) cc_final: 0.9089 (mmm) REVERT: D 142 ASN cc_start: 0.9409 (m-40) cc_final: 0.9122 (m-40) REVERT: E 51 LYS cc_start: 0.9657 (mmtm) cc_final: 0.9436 (mtmm) REVERT: E 117 PHE cc_start: 0.9411 (t80) cc_final: 0.9019 (t80) REVERT: E 230 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9144 (mt-10) REVERT: H 66 MET cc_start: 0.8883 (ptp) cc_final: 0.8373 (ptp) REVERT: H 137 MET cc_start: 0.8652 (ptm) cc_final: 0.8298 (ppp) REVERT: H 147 TYR cc_start: 0.9348 (t80) cc_final: 0.8865 (t80) REVERT: H 161 ASP cc_start: 0.9368 (t0) cc_final: 0.8966 (p0) REVERT: H 170 PHE cc_start: 0.8688 (t80) cc_final: 0.8407 (t80) REVERT: H 273 LEU cc_start: 0.9315 (tp) cc_final: 0.9032 (tp) REVERT: H 287 LEU cc_start: 0.9039 (mm) cc_final: 0.8820 (mm) REVERT: H 361 MET cc_start: 0.9248 (pmm) cc_final: 0.8974 (pmm) REVERT: H 370 TRP cc_start: 0.8448 (m-90) cc_final: 0.8044 (m-10) REVERT: I 43 MET cc_start: 0.8405 (mmp) cc_final: 0.8155 (mmm) REVERT: I 100 MET cc_start: 0.9012 (mmp) cc_final: 0.8786 (mmm) REVERT: I 119 MET cc_start: 0.9438 (tmm) cc_final: 0.8940 (tmm) REVERT: I 294 TYR cc_start: 0.9653 (m-80) cc_final: 0.9223 (m-80) REVERT: I 605 ASP cc_start: 0.8501 (m-30) cc_final: 0.8286 (t70) REVERT: J 460 MET cc_start: 0.7654 (ptp) cc_final: 0.7423 (ptm) REVERT: J 565 LEU cc_start: 0.9248 (mt) cc_final: 0.9001 (tp) REVERT: K 77 MET cc_start: 0.8268 (pmm) cc_final: 0.7775 (pmm) REVERT: K 142 ASN cc_start: 0.9143 (t0) cc_final: 0.8910 (t0) REVERT: L 37 LEU cc_start: 0.9386 (mt) cc_final: 0.9171 (mp) REVERT: L 117 PHE cc_start: 0.9285 (m-80) cc_final: 0.8854 (m-80) REVERT: L 346 PHE cc_start: 0.9518 (m-10) cc_final: 0.8896 (m-10) REVERT: L 407 MET cc_start: 0.9064 (mmt) cc_final: 0.8581 (mpp) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.2444 time to fit residues: 106.4966 Evaluate side-chains 213 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 0.4980 chunk 343 optimal weight: 3.9990 chunk 417 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 403 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 317 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 31 ASN D 97 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN I 32 ASN I 66 GLN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.050566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.035874 restraints weight = 395770.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036905 restraints weight = 240597.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.037616 restraints weight = 172183.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.038096 restraints weight = 137000.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.038391 restraints weight = 117478.945| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40039 Z= 0.130 Angle : 0.621 13.709 54614 Z= 0.331 Chirality : 0.042 0.242 6020 Planarity : 0.004 0.056 6548 Dihedral : 17.346 171.642 6057 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.82 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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 aren not related in a simple way. whole: -1.28 (0.13), residues: 4385 helix: 0.11 (0.10), residues: 2602 sheet: -2.68 (0.46), residues: 119 loop : -2.22 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 375 TYR 0.024 0.001 TYR B 68 PHE 0.031 0.001 PHE K 176 TRP 0.062 0.002 TRP H 150 HIS 0.006 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00279 (40020) covalent geometry : angle 0.62087 (54610) SS BOND : bond 0.00500 ( 2) SS BOND : angle 3.16646 ( 4) hydrogen bonds : bond 0.04101 ( 1785) hydrogen bonds : angle 4.81738 ( 5116) metal coordination : bond 0.00313 ( 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 256 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.618 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: A 123 LEU cc_start: 0.8909 (pt) cc_final: 0.8565 (pt) REVERT: A 267 MET cc_start: 0.9124 (ptp) cc_final: 0.8838 (ptt) REVERT: A 273 LEU cc_start: 0.9319 (tp) cc_final: 0.8961 (tt) REVERT: A 317 MET cc_start: 0.8796 (mpp) cc_final: 0.8052 (mpp) REVERT: B 169 MET cc_start: 0.8793 (ppp) cc_final: 0.8513 (ppp) REVERT: B 174 MET cc_start: 0.8873 (tpt) cc_final: 0.8290 (tpp) REVERT: B 249 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 259 GLN cc_start: 0.9256 (tp40) cc_final: 0.9051 (tp-100) REVERT: B 295 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8497 (mmm-85) REVERT: B 352 ASP cc_start: 0.8158 (t70) cc_final: 0.7758 (t70) REVERT: B 376 GLU cc_start: 0.9254 (mp0) cc_final: 0.9004 (mp0) REVERT: B 458 MET cc_start: 0.9003 (ptt) cc_final: 0.8514 (ptt) REVERT: C 100 MET cc_start: 0.9204 (tpt) cc_final: 0.8792 (tpp) REVERT: C 204 MET cc_start: 0.8554 (ttp) cc_final: 0.7586 (ttp) REVERT: C 458 MET cc_start: 0.9196 (ptt) cc_final: 0.8594 (ptt) REVERT: C 460 MET cc_start: 0.9150 (mmm) cc_final: 0.8933 (mmm) REVERT: D 142 ASN cc_start: 0.9364 (m-40) cc_final: 0.9118 (m-40) REVERT: E 51 LYS cc_start: 0.9657 (mmtm) cc_final: 0.9421 (mtmm) REVERT: E 117 PHE cc_start: 0.9438 (t80) cc_final: 0.9050 (t80) REVERT: E 230 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9144 (mt-10) REVERT: H 66 MET cc_start: 0.8911 (ptp) cc_final: 0.8398 (ptp) REVERT: H 147 TYR cc_start: 0.9284 (t80) cc_final: 0.8800 (t80) REVERT: H 161 ASP cc_start: 0.9349 (t0) cc_final: 0.8942 (p0) REVERT: H 170 PHE cc_start: 0.8737 (t80) cc_final: 0.8421 (t80) REVERT: H 273 LEU cc_start: 0.9289 (tp) cc_final: 0.8971 (tp) REVERT: H 287 LEU cc_start: 0.8929 (mm) cc_final: 0.8728 (mm) REVERT: H 361 MET cc_start: 0.9251 (pmm) cc_final: 0.8995 (pmm) REVERT: H 370 TRP cc_start: 0.8413 (m-90) cc_final: 0.7963 (m-10) REVERT: I 43 MET cc_start: 0.8316 (mmp) cc_final: 0.8078 (mmm) REVERT: I 294 TYR cc_start: 0.9658 (m-80) cc_final: 0.9190 (m-80) REVERT: I 458 MET cc_start: 0.9232 (ppp) cc_final: 0.8799 (ppp) REVERT: J 208 MET cc_start: 0.7538 (tpt) cc_final: 0.7207 (mmm) REVERT: J 460 MET cc_start: 0.7535 (ptp) cc_final: 0.7240 (ptm) REVERT: J 565 LEU cc_start: 0.9254 (mt) cc_final: 0.8999 (tp) REVERT: K 77 MET cc_start: 0.8216 (pmm) cc_final: 0.7660 (pmm) REVERT: L 37 LEU cc_start: 0.9450 (mt) cc_final: 0.9200 (mp) REVERT: L 117 PHE cc_start: 0.9271 (m-80) cc_final: 0.8825 (m-80) REVERT: L 346 PHE cc_start: 0.9534 (m-10) cc_final: 0.8903 (m-10) REVERT: L 407 MET cc_start: 0.9065 (mmt) cc_final: 0.8649 (mpp) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2498 time to fit residues: 105.7699 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 : 1.695 ------------------------------------------------------------------------------- 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: 9.9990 chunk 202 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 407 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN I 32 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** L 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.048448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.034178 restraints weight = 417509.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.035244 restraints weight = 270136.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.035495 restraints weight = 199124.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.035762 restraints weight = 160292.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.036025 restraints weight = 137554.453| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 40039 Z= 0.265 Angle : 0.738 13.882 54614 Z= 0.396 Chirality : 0.044 0.252 6020 Planarity : 0.005 0.050 6548 Dihedral : 17.432 172.804 6057 Min Nonbonded Distance : 1.403 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.47 (0.13), residues: 4385 helix: -0.08 (0.10), residues: 2608 sheet: -3.13 (0.41), residues: 141 loop : -2.18 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 455 TYR 0.021 0.002 TYR C 358 PHE 0.043 0.002 PHE I 500 TRP 0.052 0.003 TRP H 150 HIS 0.010 0.002 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00544 (40020) covalent geometry : angle 0.73791 (54610) SS BOND : bond 0.00261 ( 2) SS BOND : angle 2.63768 ( 4) hydrogen bonds : bond 0.05102 ( 1785) hydrogen bonds : angle 5.09827 ( 5116) metal coordination : bond 0.00492 ( 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 216 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8633 (mmp) cc_final: 0.8424 (mmm) REVERT: A 267 MET cc_start: 0.9097 (ptp) cc_final: 0.8893 (ptt) REVERT: A 273 LEU cc_start: 0.9300 (tp) cc_final: 0.8937 (tt) REVERT: B 174 MET cc_start: 0.8833 (tpt) cc_final: 0.8440 (tpp) REVERT: B 237 TYR cc_start: 0.8751 (t80) cc_final: 0.8531 (t80) REVERT: B 295 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8618 (tpt-90) REVERT: B 352 ASP cc_start: 0.8235 (t70) cc_final: 0.7913 (t70) REVERT: B 460 MET cc_start: 0.8936 (mmm) cc_final: 0.8569 (mmm) REVERT: B 507 LEU cc_start: 0.9440 (tt) cc_final: 0.9151 (mt) REVERT: C 100 MET cc_start: 0.9172 (tpt) cc_final: 0.8729 (tpp) REVERT: C 204 MET cc_start: 0.8702 (ttp) cc_final: 0.7768 (ttp) REVERT: C 458 MET cc_start: 0.9238 (ptt) cc_final: 0.8631 (ptt) REVERT: C 460 MET cc_start: 0.8980 (mmm) cc_final: 0.8670 (mmm) REVERT: E 51 LYS cc_start: 0.9616 (mmtm) cc_final: 0.9402 (mtmm) REVERT: E 117 PHE cc_start: 0.9516 (t80) cc_final: 0.9113 (t80) REVERT: H 66 MET cc_start: 0.8998 (ptp) cc_final: 0.8475 (ptp) REVERT: H 147 TYR cc_start: 0.9271 (t80) cc_final: 0.8571 (t80) REVERT: H 161 ASP cc_start: 0.9385 (t0) cc_final: 0.8991 (p0) REVERT: H 170 PHE cc_start: 0.8827 (t80) cc_final: 0.8445 (t80) REVERT: H 273 LEU cc_start: 0.9215 (tp) cc_final: 0.8897 (tp) REVERT: H 361 MET cc_start: 0.9163 (pmm) cc_final: 0.8854 (pmm) REVERT: H 370 TRP cc_start: 0.8390 (m-90) cc_final: 0.7846 (m-10) REVERT: I 43 MET cc_start: 0.8355 (mmp) cc_final: 0.8099 (mmm) REVERT: I 103 MET cc_start: 0.7725 (mmp) cc_final: 0.7494 (mmm) REVERT: I 294 TYR cc_start: 0.9667 (m-80) cc_final: 0.9250 (m-80) REVERT: I 458 MET cc_start: 0.9309 (ppp) cc_final: 0.8853 (ppp) REVERT: J 460 MET cc_start: 0.7528 (ptp) cc_final: 0.7268 (ptm) REVERT: J 565 LEU cc_start: 0.9234 (mt) cc_final: 0.9000 (tp) REVERT: L 117 PHE cc_start: 0.9289 (m-80) cc_final: 0.8910 (m-80) REVERT: L 239 LEU cc_start: 0.9719 (mt) cc_final: 0.9431 (mt) REVERT: L 407 MET cc_start: 0.9002 (mmt) cc_final: 0.8659 (mpp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2504 time to fit residues: 89.8643 Evaluate side-chains 173 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.0770 chunk 397 optimal weight: 0.9980 chunk 306 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 168 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 259 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN I 32 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.050480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.035940 restraints weight = 396755.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.037241 restraints weight = 251326.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.037467 restraints weight = 179099.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.037889 restraints weight = 142404.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.038133 restraints weight = 119297.994| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40039 Z= 0.125 Angle : 0.636 14.195 54614 Z= 0.336 Chirality : 0.042 0.248 6020 Planarity : 0.004 0.057 6548 Dihedral : 17.317 171.986 6057 Min Nonbonded Distance : 1.540 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 aren not related in a simple way. whole: -1.17 (0.13), residues: 4385 helix: 0.16 (0.10), residues: 2606 sheet: -2.82 (0.43), residues: 132 loop : -2.10 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.018 0.001 TYR B 335 PHE 0.023 0.001 PHE I 500 TRP 0.046 0.002 TRP H 150 HIS 0.010 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00270 (40020) covalent geometry : angle 0.63623 (54610) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.85348 ( 4) hydrogen bonds : bond 0.04053 ( 1785) hydrogen bonds : angle 4.80062 ( 5116) metal coordination : bond 0.00109 ( 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 250 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.700 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: A 123 LEU cc_start: 0.8946 (pt) cc_final: 0.8530 (pt) REVERT: A 267 MET cc_start: 0.8999 (ptp) cc_final: 0.8761 (ptt) REVERT: A 273 LEU cc_start: 0.9313 (tp) cc_final: 0.8844 (tt) REVERT: A 431 TRP cc_start: 0.9152 (m100) cc_final: 0.8736 (m100) REVERT: A 458 LEU cc_start: 0.9147 (tt) cc_final: 0.8511 (mt) REVERT: B 174 MET cc_start: 0.8574 (tpt) cc_final: 0.8224 (tpp) REVERT: B 295 ARG cc_start: 0.8878 (tpp80) cc_final: 0.8532 (mmm-85) REVERT: B 302 LEU cc_start: 0.9483 (mm) cc_final: 0.9237 (mt) REVERT: B 352 ASP cc_start: 0.7979 (t70) cc_final: 0.7230 (t0) REVERT: B 356 ASP cc_start: 0.8003 (m-30) cc_final: 0.7477 (m-30) REVERT: B 458 MET cc_start: 0.8972 (ptt) cc_final: 0.8501 (ptt) REVERT: B 460 MET cc_start: 0.8939 (mmm) cc_final: 0.8476 (mmm) REVERT: B 469 PHE cc_start: 0.9286 (t80) cc_final: 0.8998 (t80) REVERT: C 100 MET cc_start: 0.9176 (tpt) cc_final: 0.8744 (tpp) REVERT: C 204 MET cc_start: 0.8629 (ttp) cc_final: 0.7703 (ttp) REVERT: C 458 MET cc_start: 0.9066 (ptt) cc_final: 0.8441 (ptt) REVERT: C 460 MET cc_start: 0.8888 (mmm) cc_final: 0.8497 (mmm) REVERT: D 142 ASN cc_start: 0.9386 (m-40) cc_final: 0.8751 (m-40) REVERT: D 144 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8801 (mmtt) REVERT: E 51 LYS cc_start: 0.9630 (mmtm) cc_final: 0.9369 (mtmm) REVERT: E 117 PHE cc_start: 0.9481 (t80) cc_final: 0.9134 (t80) REVERT: E 230 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9112 (mt-10) REVERT: H 19 GLU cc_start: 0.9347 (mp0) cc_final: 0.9109 (mp0) REVERT: H 66 MET cc_start: 0.8871 (ptp) cc_final: 0.8541 (ptp) REVERT: H 116 ASP cc_start: 0.8924 (p0) cc_final: 0.8697 (p0) REVERT: H 147 TYR cc_start: 0.9254 (t80) cc_final: 0.8570 (t80) REVERT: H 161 ASP cc_start: 0.9335 (t0) cc_final: 0.8927 (p0) REVERT: H 170 PHE cc_start: 0.8796 (t80) cc_final: 0.8452 (t80) REVERT: H 267 MET cc_start: 0.8959 (ptt) cc_final: 0.8571 (ptt) REVERT: H 361 MET cc_start: 0.9253 (pmm) cc_final: 0.9018 (pmm) REVERT: H 370 TRP cc_start: 0.8403 (m-90) cc_final: 0.7948 (m-10) REVERT: I 43 MET cc_start: 0.8304 (mmp) cc_final: 0.7996 (mmm) REVERT: I 294 TYR cc_start: 0.9665 (m-80) cc_final: 0.9154 (m-80) REVERT: I 458 MET cc_start: 0.9281 (ppp) cc_final: 0.9009 (ppp) REVERT: I 460 MET cc_start: 0.9285 (mmt) cc_final: 0.9076 (mmm) REVERT: J 226 MET cc_start: 0.9141 (mtp) cc_final: 0.8507 (mtp) REVERT: J 460 MET cc_start: 0.7506 (ptp) cc_final: 0.7219 (ptm) REVERT: J 565 LEU cc_start: 0.9230 (mt) cc_final: 0.8972 (tp) REVERT: L 37 LEU cc_start: 0.9381 (mt) cc_final: 0.9139 (mp) REVERT: L 117 PHE cc_start: 0.9305 (m-80) cc_final: 0.8931 (m-80) REVERT: L 346 PHE cc_start: 0.9537 (m-10) cc_final: 0.8856 (m-10) REVERT: L 407 MET cc_start: 0.9054 (mmt) cc_final: 0.8688 (mpp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2457 time to fit residues: 102.7422 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 : 1.572 ------------------------------------------------------------------------------- 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: 7.9990 chunk 141 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 203 optimal weight: 0.0570 chunk 368 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 259 GLN D 31 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN I 32 ASN ** I 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 GLN K 174 ASN ** L 165 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 = 0.3563 r_free = 0.3563 target = 0.050676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.036180 restraints weight = 396258.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037433 restraints weight = 253995.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.037674 restraints weight = 180493.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.038098 restraints weight = 143445.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.038367 restraints weight = 118985.398| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 40039 Z= 0.125 Angle : 0.625 14.074 54614 Z= 0.330 Chirality : 0.042 0.239 6020 Planarity : 0.004 0.058 6548 Dihedral : 17.209 172.934 6057 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 aren not related in a simple way. whole: -1.10 (0.13), residues: 4385 helix: 0.28 (0.10), residues: 2593 sheet: -3.02 (0.39), residues: 148 loop : -2.13 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 265 TYR 0.019 0.001 TYR C 137 PHE 0.033 0.001 PHE I 469 TRP 0.046 0.002 TRP H 150 HIS 0.005 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00271 (40020) covalent geometry : angle 0.62461 (54610) SS BOND : bond 0.00243 ( 2) SS BOND : angle 1.53113 ( 4) hydrogen bonds : bond 0.03935 ( 1785) hydrogen bonds : angle 4.70511 ( 5116) metal coordination : bond 0.00106 ( 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 242 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.614 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: A 25 ASP cc_start: 0.7555 (p0) cc_final: 0.6904 (p0) REVERT: A 267 MET cc_start: 0.9032 (ptp) cc_final: 0.8742 (ptt) REVERT: A 273 LEU cc_start: 0.9234 (tp) cc_final: 0.8852 (tt) REVERT: A 431 TRP cc_start: 0.9172 (m100) cc_final: 0.8684 (m100) REVERT: A 458 LEU cc_start: 0.9114 (tt) cc_final: 0.8501 (mt) REVERT: B 174 MET cc_start: 0.8522 (tpt) cc_final: 0.8201 (tpp) REVERT: B 259 GLN cc_start: 0.9188 (tp40) cc_final: 0.8976 (tp-100) REVERT: B 295 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8600 (mmm-85) REVERT: B 352 ASP cc_start: 0.7982 (t70) cc_final: 0.7216 (t0) REVERT: B 356 ASP cc_start: 0.8064 (m-30) cc_final: 0.7579 (m-30) REVERT: B 458 MET cc_start: 0.8984 (ptt) cc_final: 0.8545 (ptt) REVERT: B 460 MET cc_start: 0.8923 (mmm) cc_final: 0.8512 (mmm) REVERT: B 469 PHE cc_start: 0.9315 (t80) cc_final: 0.8829 (t80) REVERT: C 100 MET cc_start: 0.9142 (tpt) cc_final: 0.8706 (tpp) REVERT: C 204 MET cc_start: 0.8597 (ttp) cc_final: 0.7625 (ttp) REVERT: C 460 MET cc_start: 0.8748 (mmm) cc_final: 0.8375 (mmm) REVERT: D 146 LEU cc_start: 0.9621 (tt) cc_final: 0.9409 (tt) REVERT: E 51 LYS cc_start: 0.9620 (mmtm) cc_final: 0.9378 (mtmm) REVERT: E 117 PHE cc_start: 0.9479 (t80) cc_final: 0.9147 (t80) REVERT: E 230 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9123 (mt-10) REVERT: E 493 SER cc_start: 0.9290 (m) cc_final: 0.9004 (p) REVERT: H 19 GLU cc_start: 0.9339 (mp0) cc_final: 0.9089 (mp0) REVERT: H 116 ASP cc_start: 0.8981 (p0) cc_final: 0.8774 (p0) REVERT: H 147 TYR cc_start: 0.9247 (t80) cc_final: 0.8565 (t80) REVERT: H 161 ASP cc_start: 0.9277 (t0) cc_final: 0.8861 (p0) REVERT: H 170 PHE cc_start: 0.8783 (t80) cc_final: 0.8457 (t80) REVERT: H 267 MET cc_start: 0.8957 (ptt) cc_final: 0.8539 (ptt) REVERT: H 361 MET cc_start: 0.9237 (pmm) cc_final: 0.8973 (pmm) REVERT: H 370 TRP cc_start: 0.8363 (m-90) cc_final: 0.7904 (m-10) REVERT: I 43 MET cc_start: 0.8254 (mmp) cc_final: 0.7926 (mmm) REVERT: I 294 TYR cc_start: 0.9667 (m-80) cc_final: 0.9131 (m-80) REVERT: I 458 MET cc_start: 0.9292 (ppp) cc_final: 0.9039 (ppp) REVERT: J 208 MET cc_start: 0.7415 (tpt) cc_final: 0.7196 (mmm) REVERT: J 226 MET cc_start: 0.9139 (mtp) cc_final: 0.8429 (mtp) REVERT: J 460 MET cc_start: 0.7522 (ptp) cc_final: 0.7242 (ptm) REVERT: J 565 LEU cc_start: 0.9246 (mt) cc_final: 0.8991 (tp) REVERT: L 37 LEU cc_start: 0.9396 (mt) cc_final: 0.9124 (mp) REVERT: L 117 PHE cc_start: 0.9343 (m-80) cc_final: 0.8925 (m-80) REVERT: L 346 PHE cc_start: 0.9547 (m-10) cc_final: 0.8891 (m-10) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2493 time to fit residues: 100.2680 Evaluate side-chains 194 residues out of total 4163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 220 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 318 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 311 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN I 32 ASN ** I 259 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.050881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.036382 restraints weight = 398675.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.037677 restraints weight = 255133.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.037934 restraints weight = 180891.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.038392 restraints weight = 139721.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.038613 restraints weight = 118033.149| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4220 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= 0.122 Angle : 0.621 14.039 54614 Z= 0.327 Chirality : 0.042 0.229 6020 Planarity : 0.004 0.068 6548 Dihedral : 17.136 174.055 6057 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.13), residues: 4385 helix: 0.34 (0.10), residues: 2606 sheet: -2.91 (0.40), residues: 148 loop : -2.11 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 265 TYR 0.021 0.001 TYR B 137 PHE 0.022 0.001 PHE E 338 TRP 0.055 0.002 TRP H 87 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00265 (40020) covalent geometry : angle 0.62074 (54610) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.34612 ( 4) hydrogen bonds : bond 0.03858 ( 1785) hydrogen bonds : angle 4.62551 ( 5116) metal coordination : bond 0.00103 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7205.32 seconds wall clock time: 125 minutes 42.79 seconds (7542.79 seconds total)