Starting phenix.real_space_refine on Sun Jul 5 00:39:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxb_30903/07_2026/7dxb_30903.map" } resolution = 2.7 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= 0.006 sd= 0.181 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: 7 Type Number sf(0) Gaussians Ca 12 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 132 5.16 5 C 15904 2.51 5 N 3816 2.21 5 O 4372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24244 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5904 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 5904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5904 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 5904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5904 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 5904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5904 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 205 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 2, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 157 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 157 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Unusual residues: {' CA': 3, ' ZN': 1, '98R': 1, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1328 SG CYS A 182 86.749 24.297 78.722 1.00 37.00 S ATOM 1343 SG CYS A 184 89.052 24.024 75.713 1.00 46.93 S ATOM 1361 SG CYS A 187 87.589 27.391 76.683 1.00 57.76 S ATOM 7232 SG CYS B 182 24.298 36.561 78.718 1.00 37.00 S ATOM 7247 SG CYS B 184 24.026 34.257 75.709 1.00 46.93 S ATOM 7265 SG CYS B 187 27.393 35.721 76.679 1.00 57.76 S ATOM 13136 SG CYS C 182 36.562 99.011 78.713 1.00 37.00 S ATOM 13151 SG CYS C 184 34.259 99.283 75.704 1.00 46.93 S ATOM 13169 SG CYS C 187 35.723 95.916 76.675 1.00 57.76 S ATOM 19040 SG CYS D 182 99.013 86.747 78.717 1.00 37.00 S ATOM 19055 SG CYS D 184 99.285 89.050 75.708 1.00 46.93 S ATOM 19073 SG CYS D 187 95.918 87.587 76.678 1.00 57.76 S Time building chain proxies: 5.39, per 1000 atoms: 0.22 Number of scatterers: 24244 At special positions: 0 Unit cell: (124.355, 124.355, 168.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 12 19.99 S 132 16.00 P 4 15.00 O 4372 8.00 N 3816 7.00 C 15904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 758.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 178 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 182 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 187 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 184 " pdb=" ZN B1105 " pdb="ZN ZN B1105 " - pdb=" ND1 HIS B 178 " pdb="ZN ZN B1105 " - pdb=" SG CYS B 182 " pdb="ZN ZN B1105 " - pdb=" SG CYS B 187 " pdb="ZN ZN B1105 " - pdb=" SG CYS B 184 " pdb=" ZN C1105 " pdb="ZN ZN C1105 " - pdb=" ND1 HIS C 178 " pdb="ZN ZN C1105 " - pdb=" SG CYS C 182 " pdb="ZN ZN C1105 " - pdb=" SG CYS C 187 " pdb="ZN ZN C1105 " - pdb=" SG CYS C 184 " pdb=" ZN D1104 " pdb="ZN ZN D1104 " - pdb=" ND1 HIS D 178 " pdb="ZN ZN D1104 " - pdb=" SG CYS D 182 " pdb="ZN ZN D1104 " - pdb=" SG CYS D 187 " pdb="ZN ZN D1104 " - pdb=" SG CYS D 184 " Number of angles added : 12 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5648 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 39 through 50 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.651A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.563A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.846A pdb=" N GLN A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.077A pdb=" N LEU A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 removed outlier: 3.655A pdb=" N ASN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 263 removed outlier: 3.514A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.679A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.668A pdb=" N GLU A 331 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 358 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.833A pdb=" N ALA A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 removed outlier: 3.591A pdb=" N PHE A 396 " --> pdb=" O SER A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.511A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.563A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.564A pdb=" N TYR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.735A pdb=" N ILE A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.785A pdb=" N ILE A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 588 removed outlier: 4.170A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 628 through 663 Processing helix chain 'A' and resid 668 through 684 removed outlier: 3.876A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 788 through 824 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.650A pdb=" N LYS B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 removed outlier: 3.563A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.846A pdb=" N GLN B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.078A pdb=" N LEU B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.655A pdb=" N ASN B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 263 removed outlier: 3.514A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.680A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.668A pdb=" N GLU B 331 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 358 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 369 through 392 removed outlier: 3.834A pdb=" N ALA B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 396 removed outlier: 3.592A pdb=" N PHE B 396 " --> pdb=" O SER B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.511A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 448 Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.563A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.563A pdb=" N TYR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.735A pdb=" N ILE B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.785A pdb=" N ILE B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 551 through 588 removed outlier: 4.171A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 628 through 663 Processing helix chain 'B' and resid 668 through 684 removed outlier: 3.876A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 788 through 824 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 39 through 50 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.651A pdb=" N LYS C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.563A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.846A pdb=" N GLN C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.076A pdb=" N LEU C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 240 removed outlier: 3.655A pdb=" N ASN C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 263 removed outlier: 3.513A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.678A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.668A pdb=" N GLU C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 332 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 358 Proline residue: C 349 - end of helix Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 369 through 392 removed outlier: 3.834A pdb=" N ALA C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 396 removed outlier: 3.592A pdb=" N PHE C 396 " --> pdb=" O SER C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 393 through 396' Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.511A pdb=" N LYS C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 448 Processing helix chain 'C' and resid 448 through 454 removed outlier: 3.563A pdb=" N LEU C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.563A pdb=" N TYR C 509 " --> pdb=" O PRO C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 538 removed outlier: 3.735A pdb=" N ILE C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 545 removed outlier: 3.785A pdb=" N ILE C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 548 No H-bonds generated for 'chain 'C' and resid 546 through 548' Processing helix chain 'C' and resid 551 through 588 removed outlier: 4.170A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 628 through 663 Processing helix chain 'C' and resid 668 through 684 removed outlier: 3.876A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 761 through 783 Processing helix chain 'C' and resid 788 through 824 Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 39 through 50 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 84 removed outlier: 3.650A pdb=" N LYS D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.562A pdb=" N LEU D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 124 through 131 removed outlier: 3.846A pdb=" N GLN D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.076A pdb=" N LEU D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 removed outlier: 3.655A pdb=" N ASN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.514A pdb=" N VAL D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.679A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.668A pdb=" N GLU D 331 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 332 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 358 Proline residue: D 349 - end of helix Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 369 through 392 removed outlier: 3.834A pdb=" N ALA D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 removed outlier: 3.592A pdb=" N PHE D 396 " --> pdb=" O SER D 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 393 through 396' Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.510A pdb=" N LYS D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 448 Processing helix chain 'D' and resid 448 through 454 removed outlier: 3.563A pdb=" N LEU D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 Processing helix chain 'D' and resid 504 through 509 removed outlier: 3.563A pdb=" N TYR D 509 " --> pdb=" O PRO D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 538 removed outlier: 3.736A pdb=" N ILE D 532 " --> pdb=" O GLY D 528 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 removed outlier: 3.785A pdb=" N ILE D 544 " --> pdb=" O ARG D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 551 through 588 removed outlier: 4.170A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 628 through 663 Processing helix chain 'D' and resid 668 through 684 removed outlier: 3.876A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 Processing helix chain 'D' and resid 761 through 783 Processing helix chain 'D' and resid 788 through 824 1572 hydrogen bonds defined for protein. 4656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 2.87 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: 4569 1.33 - 1.45: 5811 1.45 - 1.57: 14164 1.57 - 1.69: 8 1.69 - 1.81: 216 Bond restraints: 24768 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.460 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C21 POV B1102 " pdb=" O21 POV B1102 " ideal model delta sigma weight residual 1.330 1.460 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C21 POV C1102 " pdb=" O21 POV C1102 " ideal model delta sigma weight residual 1.330 1.460 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C21 POV A 908 " pdb=" O21 POV A 908 " ideal model delta sigma weight residual 1.330 1.460 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C GLU C 440 " pdb=" N CYS C 441 " ideal model delta sigma weight residual 1.335 1.420 -0.085 1.31e-02 5.83e+03 4.25e+01 ... (remaining 24763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 32860 2.43 - 4.87: 492 4.87 - 7.30: 108 7.30 - 9.74: 44 9.74 - 12.17: 8 Bond angle restraints: 33512 Sorted by residual: angle pdb=" CA GLU B 786 " pdb=" C GLU B 786 " pdb=" N VAL B 787 " ideal model delta sigma weight residual 115.88 122.18 -6.30 1.28e+00 6.10e-01 2.43e+01 angle pdb=" CA GLU C 786 " pdb=" C GLU C 786 " pdb=" N VAL C 787 " ideal model delta sigma weight residual 115.88 122.17 -6.29 1.28e+00 6.10e-01 2.41e+01 angle pdb=" CA GLU A 786 " pdb=" C GLU A 786 " pdb=" N VAL A 787 " ideal model delta sigma weight residual 115.88 122.17 -6.29 1.28e+00 6.10e-01 2.41e+01 angle pdb=" CA GLU D 786 " pdb=" C GLU D 786 " pdb=" N VAL D 787 " ideal model delta sigma weight residual 115.88 122.17 -6.29 1.28e+00 6.10e-01 2.41e+01 angle pdb=" O GLU B 786 " pdb=" C GLU B 786 " pdb=" N VAL B 787 " ideal model delta sigma weight residual 122.89 117.23 5.66 1.22e+00 6.72e-01 2.15e+01 ... (remaining 33507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.03: 14328 26.03 - 52.05: 360 52.05 - 78.08: 108 78.08 - 104.11: 20 104.11 - 130.14: 36 Dihedral angle restraints: 14852 sinusoidal: 6140 harmonic: 8712 Sorted by residual: dihedral pdb=" C32 98R B1101 " pdb=" C33 98R B1101 " pdb=" C34 98R B1101 " pdb=" C35 98R B1101 " ideal model delta sinusoidal sigma weight residual 180.57 50.43 130.14 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C32 98R D1101 " pdb=" C33 98R D1101 " pdb=" C34 98R D1101 " pdb=" C35 98R D1101 " ideal model delta sinusoidal sigma weight residual 180.57 50.47 130.10 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C32 98R A 909 " pdb=" C33 98R A 909 " pdb=" C34 98R A 909 " pdb=" C35 98R A 909 " ideal model delta sinusoidal sigma weight residual 180.57 50.47 130.10 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 14849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3082 0.050 - 0.100: 622 0.100 - 0.150: 64 0.150 - 0.200: 20 0.200 - 0.250: 8 Chirality restraints: 3796 Sorted by residual: chirality pdb=" CBI Y01 C1104 " pdb=" CAU Y01 C1104 " pdb=" CBE Y01 C1104 " pdb=" CBG Y01 C1104 " both_signs ideal model delta sigma weight residual False 2.94 2.69 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CBI Y01 B1104 " pdb=" CAU Y01 B1104 " pdb=" CBE Y01 B1104 " pdb=" CBG Y01 B1104 " both_signs ideal model delta sigma weight residual False 2.94 2.69 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CBI Y01 A 903 " pdb=" CAU Y01 A 903 " pdb=" CBE Y01 A 903 " pdb=" CBG Y01 A 903 " both_signs ideal model delta sigma weight residual False 2.94 2.69 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3793 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 545 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.20e+00 pdb=" N PRO C 546 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 545 " -0.033 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO D 546 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 546 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 546 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 545 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 546 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 546 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 546 " 0.029 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 168 2.62 - 3.19: 21699 3.19 - 3.76: 37969 3.76 - 4.33: 52900 4.33 - 4.90: 86799 Nonbonded interactions: 199535 Sorted by model distance: nonbonded pdb=" O3 98R D1101 " pdb=" O3P 98R D1101 " model vdw 2.048 3.040 nonbonded pdb=" O3 98R C1101 " pdb=" O3P 98R C1101 " model vdw 2.048 3.040 nonbonded pdb=" O3 98R A 909 " pdb=" O3P 98R A 909 " model vdw 2.048 3.040 nonbonded pdb=" O3 98R B1101 " pdb=" O3P 98R B1101 " model vdw 2.048 3.040 nonbonded pdb=" OE2 GLU A 791 " pdb="CA CA A 906 " model vdw 2.282 2.510 ... (remaining 199530 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' and (resid 12 through 824 or resid 903 or resid 906 through 907)) selection = (chain 'B' and (resid 12 through 824 or resid 1103 or resid 1106 through 1107)) selection = (chain 'C' and (resid 12 through 824 or resid 1103 or resid 1106 through 1107)) selection = (chain 'D' and (resid 12 through 824 or resid 1103 or resid 1106 through 1107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.470 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.870 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.006 0.130 24784 Z= 0.309 Angle : 0.745 12.173 33524 Z= 0.353 Chirality : 0.041 0.250 3796 Planarity : 0.004 0.051 4140 Dihedral : 14.998 130.136 9204 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.34 % Allowed : 5.31 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 2920 helix: 1.30 (0.11), residues: 2136 sheet: None (None), residues: 0 loop : -0.64 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 89 TYR 0.014 0.001 TYR A 410 PHE 0.005 0.001 PHE C 17 TRP 0.008 0.001 TRP C 611 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.31 (24768) covalent geometry : angle 0.74352 / 0.35 (33512) hydrogen bonds : bond 0.21244 / 14.34 ( 1572) hydrogen bonds : angle 5.97100 / 4.26 ( 4656) metal coordination : bond 0.04749 / 3.01 ( 16) metal coordination : angle 2.85654 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 448 time to evaluate : 0.786 Fit side-chains REVERT: A 134 ASP cc_start: 0.7312 (m-30) cc_final: 0.7085 (m-30) REVERT: A 365 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7830 (mtpp) REVERT: A 432 TRP cc_start: 0.8621 (OUTLIER) cc_final: 0.8405 (t-100) REVERT: A 436 MET cc_start: 0.8712 (mtp) cc_final: 0.8220 (mtp) REVERT: A 438 TRP cc_start: 0.8344 (t-100) cc_final: 0.8058 (t-100) REVERT: A 524 ILE cc_start: 0.8723 (mt) cc_final: 0.8507 (mt) REVERT: A 563 LYS cc_start: 0.8638 (mttt) cc_final: 0.8219 (mptt) REVERT: A 566 PHE cc_start: 0.7928 (t80) cc_final: 0.7123 (m-10) REVERT: A 583 MET cc_start: 0.8679 (mtp) cc_final: 0.8331 (mtp) REVERT: A 619 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8604 (t) REVERT: B 134 ASP cc_start: 0.7308 (m-30) cc_final: 0.7065 (m-30) REVERT: B 365 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7819 (mtpp) REVERT: B 430 MET cc_start: 0.8728 (mtp) cc_final: 0.8523 (mtp) REVERT: B 432 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.8418 (t-100) REVERT: B 436 MET cc_start: 0.8711 (mtp) cc_final: 0.8233 (mtp) REVERT: B 438 TRP cc_start: 0.8339 (t-100) cc_final: 0.8046 (t-100) REVERT: B 524 ILE cc_start: 0.8727 (mt) cc_final: 0.8512 (mt) REVERT: B 563 LYS cc_start: 0.8638 (mttt) cc_final: 0.8221 (mptt) REVERT: B 566 PHE cc_start: 0.7936 (t80) cc_final: 0.7134 (m-10) REVERT: B 583 MET cc_start: 0.8686 (mtp) cc_final: 0.8332 (mtp) REVERT: C 134 ASP cc_start: 0.7284 (m-30) cc_final: 0.7045 (m-30) REVERT: C 365 LYS cc_start: 0.8383 (mtmt) cc_final: 0.7833 (mtpp) REVERT: C 432 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.8418 (t-100) REVERT: C 436 MET cc_start: 0.8712 (mtp) cc_final: 0.8235 (mtp) REVERT: C 438 TRP cc_start: 0.8337 (t-100) cc_final: 0.8047 (t-100) REVERT: C 563 LYS cc_start: 0.8638 (mttt) cc_final: 0.8216 (mptt) REVERT: C 566 PHE cc_start: 0.7931 (t80) cc_final: 0.7130 (m-10) REVERT: C 583 MET cc_start: 0.8691 (mtp) cc_final: 0.8337 (mtp) REVERT: D 134 ASP cc_start: 0.7299 (m-30) cc_final: 0.7064 (m-30) REVERT: D 365 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7832 (mtpp) REVERT: D 432 TRP cc_start: 0.8621 (OUTLIER) cc_final: 0.8403 (t-100) REVERT: D 436 MET cc_start: 0.8709 (mtp) cc_final: 0.8226 (mtp) REVERT: D 438 TRP cc_start: 0.8350 (t-100) cc_final: 0.8064 (t-100) REVERT: D 563 LYS cc_start: 0.8639 (mttt) cc_final: 0.8217 (mptt) REVERT: D 566 PHE cc_start: 0.7926 (t80) cc_final: 0.7119 (m-10) REVERT: D 583 MET cc_start: 0.8683 (mtp) cc_final: 0.8334 (mtp) REVERT: D 619 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8602 (t) outliers start: 60 outliers final: 4 residues processed: 492 average time/residue: 0.6296 time to fit residues: 354.6812 Evaluate side-chains 297 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 287 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 798 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.0470 chunk 111 optimal weight: 9.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 633 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107639 restraints weight = 27537.668| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.90 r_work: 0.3149 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24784 Z= 0.136 Angle : 0.560 6.565 33524 Z= 0.287 Chirality : 0.039 0.190 3796 Planarity : 0.004 0.047 4140 Dihedral : 13.852 179.649 3582 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 11.84 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.15), residues: 2920 helix: 2.15 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -0.85 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 560 TYR 0.019 0.001 TYR C 410 PHE 0.010 0.001 PHE D 576 TRP 0.009 0.001 TRP A 322 HIS 0.002 0.001 HIS B 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (24768) covalent geometry : angle 0.55968 / 0.29 (33512) hydrogen bonds : bond 0.05209 / 3.51 ( 1572) hydrogen bonds : angle 3.82096 / 2.71 ( 4656) metal coordination : bond 0.00565 / 0.43 ( 16) metal coordination : angle 1.57798 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 315 time to evaluate : 0.647 Fit side-chains REVERT: A 29 GLU cc_start: 0.7953 (tp30) cc_final: 0.7671 (tp30) REVERT: A 48 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 134 ASP cc_start: 0.6972 (m-30) cc_final: 0.6680 (m-30) REVERT: A 140 GLU cc_start: 0.7667 (pm20) cc_final: 0.7455 (pm20) REVERT: A 365 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7281 (mmtm) REVERT: A 405 ILE cc_start: 0.8362 (mt) cc_final: 0.8117 (mm) REVERT: A 432 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.8325 (m-90) REVERT: A 436 MET cc_start: 0.8417 (mtp) cc_final: 0.8059 (mtp) REVERT: A 438 TRP cc_start: 0.8031 (t-100) cc_final: 0.7642 (t-100) REVERT: A 461 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: A 525 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 560 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7658 (ttm-80) REVERT: A 563 LYS cc_start: 0.8410 (mttt) cc_final: 0.7658 (mptt) REVERT: B 29 GLU cc_start: 0.7959 (tp30) cc_final: 0.7683 (tp30) REVERT: B 48 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 134 ASP cc_start: 0.6963 (m-30) cc_final: 0.6672 (m-30) REVERT: B 140 GLU cc_start: 0.7674 (pm20) cc_final: 0.7410 (pm20) REVERT: B 365 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7317 (mmtm) REVERT: B 405 ILE cc_start: 0.8361 (mt) cc_final: 0.8119 (mm) REVERT: B 430 MET cc_start: 0.8565 (mtp) cc_final: 0.8310 (mtp) REVERT: B 432 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8342 (m-90) REVERT: B 436 MET cc_start: 0.8454 (mtp) cc_final: 0.8109 (mtp) REVERT: B 438 TRP cc_start: 0.8034 (t-100) cc_final: 0.7641 (t-100) REVERT: B 461 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: B 525 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 560 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: B 563 LYS cc_start: 0.8414 (mttt) cc_final: 0.7662 (mptt) REVERT: C 29 GLU cc_start: 0.7962 (tp30) cc_final: 0.7679 (tp30) REVERT: C 48 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: C 134 ASP cc_start: 0.6944 (m-30) cc_final: 0.6645 (m-30) REVERT: C 365 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7323 (mmtm) REVERT: C 405 ILE cc_start: 0.8342 (mt) cc_final: 0.8094 (mm) REVERT: C 430 MET cc_start: 0.8929 (mtm) cc_final: 0.8555 (mtp) REVERT: C 432 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.8334 (m-90) REVERT: C 436 MET cc_start: 0.8430 (mtp) cc_final: 0.8082 (mtp) REVERT: C 438 TRP cc_start: 0.8030 (t-100) cc_final: 0.7636 (t-100) REVERT: C 461 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: C 525 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8159 (mp) REVERT: C 560 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: C 563 LYS cc_start: 0.8410 (mttt) cc_final: 0.7657 (mptt) REVERT: D 29 GLU cc_start: 0.7946 (tp30) cc_final: 0.7664 (tp30) REVERT: D 48 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: D 134 ASP cc_start: 0.6967 (m-30) cc_final: 0.6671 (m-30) REVERT: D 140 GLU cc_start: 0.7665 (pm20) cc_final: 0.7448 (pm20) REVERT: D 365 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7296 (mmtm) REVERT: D 432 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.8325 (m-90) REVERT: D 436 MET cc_start: 0.8413 (mtp) cc_final: 0.8055 (mtp) REVERT: D 438 TRP cc_start: 0.8031 (t-100) cc_final: 0.7645 (t-100) REVERT: D 461 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: D 524 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8035 (mt) REVERT: D 560 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: D 563 LYS cc_start: 0.8408 (mttt) cc_final: 0.7656 (mptt) outliers start: 76 outliers final: 16 residues processed: 365 average time/residue: 0.5788 time to fit residues: 245.5956 Evaluate side-chains 319 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 798 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 287 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 111 optimal weight: 0.0770 chunk 88 optimal weight: 0.0020 chunk 283 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110410 restraints weight = 27250.982| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.88 r_work: 0.3182 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24784 Z= 0.110 Angle : 0.504 9.402 33524 Z= 0.254 Chirality : 0.038 0.219 3796 Planarity : 0.004 0.047 4140 Dihedral : 12.165 153.192 3580 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.02 % Allowed : 11.33 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.15), residues: 2920 helix: 2.35 (0.11), residues: 2156 sheet: None (None), residues: 0 loop : -0.87 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.021 0.001 TYR C 410 PHE 0.010 0.001 PHE B 576 TRP 0.010 0.001 TRP B 322 HIS 0.001 0.000 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24768) covalent geometry : angle 0.50380 / 0.25 (33512) hydrogen bonds : bond 0.04334 / 2.91 ( 1572) hydrogen bonds : angle 3.51741 / 2.50 ( 4656) metal coordination : bond 0.00549 / 0.42 ( 16) metal coordination : angle 1.36051 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 292 time to evaluate : 0.905 Fit side-chains REVERT: A 27 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 29 GLU cc_start: 0.7895 (tp30) cc_final: 0.7610 (tp30) REVERT: A 48 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 134 ASP cc_start: 0.6925 (m-30) cc_final: 0.6675 (m-30) REVERT: A 140 GLU cc_start: 0.7544 (pm20) cc_final: 0.7282 (pm20) REVERT: A 365 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7310 (mmtm) REVERT: A 405 ILE cc_start: 0.8322 (mt) cc_final: 0.8111 (mm) REVERT: A 436 MET cc_start: 0.8379 (mtp) cc_final: 0.8140 (mtp) REVERT: A 438 TRP cc_start: 0.8034 (t-100) cc_final: 0.7659 (t-100) REVERT: A 563 LYS cc_start: 0.8309 (mttt) cc_final: 0.7600 (mptt) REVERT: A 564 ASP cc_start: 0.7364 (m-30) cc_final: 0.7134 (m-30) REVERT: A 573 ILE cc_start: 0.8526 (mt) cc_final: 0.8310 (mt) REVERT: B 27 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: B 29 GLU cc_start: 0.7895 (tp30) cc_final: 0.7609 (tp30) REVERT: B 48 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: B 134 ASP cc_start: 0.6922 (m-30) cc_final: 0.6672 (m-30) REVERT: B 140 GLU cc_start: 0.7539 (pm20) cc_final: 0.7267 (pm20) REVERT: B 365 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7305 (mmtm) REVERT: B 367 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8105 (mm) REVERT: B 405 ILE cc_start: 0.8350 (mt) cc_final: 0.8146 (mm) REVERT: B 430 MET cc_start: 0.8619 (mtp) cc_final: 0.8325 (mtp) REVERT: B 436 MET cc_start: 0.8377 (mtp) cc_final: 0.8149 (mtp) REVERT: B 438 TRP cc_start: 0.8030 (t-100) cc_final: 0.7654 (t-100) REVERT: B 563 LYS cc_start: 0.8318 (mttt) cc_final: 0.7609 (mptt) REVERT: B 564 ASP cc_start: 0.7421 (m-30) cc_final: 0.7188 (m-30) REVERT: B 573 ILE cc_start: 0.8520 (mt) cc_final: 0.8302 (mt) REVERT: B 627 ASP cc_start: 0.8655 (t0) cc_final: 0.8406 (t0) REVERT: C 27 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: C 29 GLU cc_start: 0.7927 (tp30) cc_final: 0.7640 (tp30) REVERT: C 48 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 140 GLU cc_start: 0.7548 (pm20) cc_final: 0.7323 (pm20) REVERT: C 365 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7302 (mmtm) REVERT: C 367 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8106 (mm) REVERT: C 405 ILE cc_start: 0.8314 (mt) cc_final: 0.8102 (mm) REVERT: C 436 MET cc_start: 0.8376 (mtp) cc_final: 0.8140 (mtp) REVERT: C 438 TRP cc_start: 0.8031 (t-100) cc_final: 0.7654 (t-100) REVERT: C 563 LYS cc_start: 0.8316 (mttt) cc_final: 0.7606 (mptt) REVERT: C 573 ILE cc_start: 0.8533 (mt) cc_final: 0.8318 (mt) REVERT: C 627 ASP cc_start: 0.8665 (t0) cc_final: 0.8429 (t0) REVERT: D 27 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: D 29 GLU cc_start: 0.7915 (tp30) cc_final: 0.7631 (tp30) REVERT: D 48 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: D 134 ASP cc_start: 0.6914 (m-30) cc_final: 0.6669 (m-30) REVERT: D 140 GLU cc_start: 0.7549 (pm20) cc_final: 0.7338 (pm20) REVERT: D 365 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7314 (mmtm) REVERT: D 367 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8113 (mm) REVERT: D 436 MET cc_start: 0.8379 (mtp) cc_final: 0.8136 (mtp) REVERT: D 438 TRP cc_start: 0.8036 (t-100) cc_final: 0.7661 (t-100) REVERT: D 524 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7993 (mt) REVERT: D 563 LYS cc_start: 0.8309 (mttt) cc_final: 0.7599 (mptt) REVERT: D 564 ASP cc_start: 0.7419 (m-30) cc_final: 0.7185 (m-30) REVERT: D 573 ILE cc_start: 0.8525 (mt) cc_final: 0.8308 (mt) REVERT: D 627 ASP cc_start: 0.8632 (t0) cc_final: 0.8379 (t0) outliers start: 103 outliers final: 33 residues processed: 356 average time/residue: 0.5548 time to fit residues: 231.3650 Evaluate side-chains 322 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 819 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 798 ASP Chi-restraints excluded: chain D residue 819 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 115 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 659 ASN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104914 restraints weight = 27321.149| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.83 r_work: 0.3090 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24784 Z= 0.220 Angle : 0.613 9.109 33524 Z= 0.304 Chirality : 0.042 0.212 3796 Planarity : 0.004 0.047 4140 Dihedral : 12.224 156.660 3572 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.55 % Allowed : 12.85 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 2920 helix: 2.09 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -0.83 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 395 TYR 0.023 0.002 TYR C 138 PHE 0.014 0.002 PHE B 572 TRP 0.014 0.002 TRP B 322 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (24768) covalent geometry : angle 0.61231 / 0.30 (33512) hydrogen bonds : bond 0.05323 / 3.56 ( 1572) hydrogen bonds : angle 3.60823 / 2.56 ( 4656) metal coordination : bond 0.01266 / 0.97 ( 16) metal coordination : angle 2.00319 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 281 time to evaluate : 0.871 Fit side-chains REVERT: A 27 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: A 29 GLU cc_start: 0.7949 (tp30) cc_final: 0.7659 (tp30) REVERT: A 48 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 134 ASP cc_start: 0.7086 (m-30) cc_final: 0.6880 (m-30) REVERT: A 140 GLU cc_start: 0.7665 (pm20) cc_final: 0.7418 (pm20) REVERT: A 365 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7539 (mmtm) REVERT: A 436 MET cc_start: 0.8529 (mtp) cc_final: 0.8154 (mtp) REVERT: A 438 TRP cc_start: 0.8080 (t-100) cc_final: 0.7696 (t-100) REVERT: A 563 LYS cc_start: 0.8413 (mttt) cc_final: 0.7690 (mptt) REVERT: B 27 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: B 29 GLU cc_start: 0.7937 (tp30) cc_final: 0.7646 (tp30) REVERT: B 48 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 134 ASP cc_start: 0.7097 (m-30) cc_final: 0.6892 (m-30) REVERT: B 140 GLU cc_start: 0.7660 (pm20) cc_final: 0.7413 (pm20) REVERT: B 365 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7654 (mmtm) REVERT: B 430 MET cc_start: 0.8724 (mtp) cc_final: 0.8440 (mtp) REVERT: B 436 MET cc_start: 0.8531 (mtp) cc_final: 0.8164 (mtp) REVERT: B 438 TRP cc_start: 0.8079 (t-100) cc_final: 0.7709 (t-100) REVERT: B 563 LYS cc_start: 0.8419 (mttt) cc_final: 0.7708 (mptt) REVERT: C 27 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 29 GLU cc_start: 0.8003 (tp30) cc_final: 0.7693 (tp30) REVERT: C 48 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 119 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7186 (mmmm) REVERT: C 134 ASP cc_start: 0.7077 (m-30) cc_final: 0.6872 (m-30) REVERT: C 140 GLU cc_start: 0.7666 (pm20) cc_final: 0.7405 (pm20) REVERT: C 236 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 365 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7645 (mmtm) REVERT: C 436 MET cc_start: 0.8548 (mtp) cc_final: 0.8171 (mtp) REVERT: C 438 TRP cc_start: 0.8075 (t-100) cc_final: 0.7707 (t-100) REVERT: C 563 LYS cc_start: 0.8363 (mttt) cc_final: 0.7643 (mptt) REVERT: D 27 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: D 29 GLU cc_start: 0.8008 (tp30) cc_final: 0.7696 (tp30) REVERT: D 48 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: D 134 ASP cc_start: 0.7085 (m-30) cc_final: 0.6879 (m-30) REVERT: D 140 GLU cc_start: 0.7691 (pm20) cc_final: 0.7460 (pm20) REVERT: D 236 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8453 (mt) REVERT: D 365 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7665 (mmtm) REVERT: D 436 MET cc_start: 0.8581 (mtp) cc_final: 0.8204 (mtp) REVERT: D 438 TRP cc_start: 0.8082 (t-100) cc_final: 0.7705 (t-100) REVERT: D 521 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7523 (p0) REVERT: D 524 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8233 (mt) REVERT: D 563 LYS cc_start: 0.8417 (mttt) cc_final: 0.7703 (mptt) outliers start: 91 outliers final: 42 residues processed: 339 average time/residue: 0.6048 time to fit residues: 238.2793 Evaluate side-chains 321 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 819 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 798 ASP Chi-restraints excluded: chain D residue 819 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 219 optimal weight: 0.0980 chunk 77 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109891 restraints weight = 27069.410| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.86 r_work: 0.3166 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24784 Z= 0.109 Angle : 0.503 7.378 33524 Z= 0.254 Chirality : 0.038 0.175 3796 Planarity : 0.004 0.045 4140 Dihedral : 11.470 141.130 3572 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.05 % Allowed : 13.71 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.15), residues: 2920 helix: 2.38 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -0.78 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 560 TYR 0.020 0.001 TYR D 410 PHE 0.009 0.001 PHE B 576 TRP 0.012 0.001 TRP C 322 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (24768) covalent geometry : angle 0.50256 / 0.25 (33512) hydrogen bonds : bond 0.04066 / 2.74 ( 1572) hydrogen bonds : angle 3.40033 / 2.41 ( 4656) metal coordination : bond 0.00644 / 0.49 ( 16) metal coordination : angle 1.40809 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 289 time to evaluate : 0.968 Fit side-chains REVERT: A 27 GLU cc_start: 0.7978 (tp30) cc_final: 0.7726 (tt0) REVERT: A 29 GLU cc_start: 0.7960 (tp30) cc_final: 0.7631 (tp30) REVERT: A 48 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 134 ASP cc_start: 0.6978 (m-30) cc_final: 0.6747 (m-30) REVERT: A 365 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7394 (mmtm) REVERT: A 430 MET cc_start: 0.8991 (mtm) cc_final: 0.8768 (mtm) REVERT: A 436 MET cc_start: 0.8348 (mtp) cc_final: 0.8093 (mtp) REVERT: A 438 TRP cc_start: 0.8006 (t-100) cc_final: 0.7631 (t-100) REVERT: A 563 LYS cc_start: 0.8225 (mttt) cc_final: 0.7491 (mptt) REVERT: B 27 GLU cc_start: 0.7973 (tp30) cc_final: 0.7725 (tt0) REVERT: B 29 GLU cc_start: 0.7949 (tp30) cc_final: 0.7622 (tp30) REVERT: B 48 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 365 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7492 (mmtm) REVERT: B 430 MET cc_start: 0.8565 (mtp) cc_final: 0.8297 (mtp) REVERT: B 436 MET cc_start: 0.8347 (mtp) cc_final: 0.8105 (mtp) REVERT: B 438 TRP cc_start: 0.8008 (t-100) cc_final: 0.7628 (t-100) REVERT: B 563 LYS cc_start: 0.8233 (mttt) cc_final: 0.7495 (mptt) REVERT: C 27 GLU cc_start: 0.7974 (tp30) cc_final: 0.7731 (tt0) REVERT: C 29 GLU cc_start: 0.7962 (tp30) cc_final: 0.7632 (tp30) REVERT: C 48 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 119 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7109 (mmmm) REVERT: C 140 GLU cc_start: 0.7644 (pm20) cc_final: 0.7415 (pm20) REVERT: C 365 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7494 (mmtm) REVERT: C 430 MET cc_start: 0.9004 (mtm) cc_final: 0.8786 (mtm) REVERT: C 436 MET cc_start: 0.8340 (mtp) cc_final: 0.8083 (mtp) REVERT: C 438 TRP cc_start: 0.8001 (t-100) cc_final: 0.7628 (t-100) REVERT: C 563 LYS cc_start: 0.8211 (mttt) cc_final: 0.7469 (mptt) REVERT: D 27 GLU cc_start: 0.7975 (tp30) cc_final: 0.7725 (tt0) REVERT: D 29 GLU cc_start: 0.7956 (tp30) cc_final: 0.7626 (tp30) REVERT: D 48 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: D 119 LYS cc_start: 0.7368 (mmmt) cc_final: 0.7004 (mmmm) REVERT: D 140 GLU cc_start: 0.7678 (pm20) cc_final: 0.7469 (pm20) REVERT: D 365 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7496 (mmtm) REVERT: D 367 LEU cc_start: 0.8390 (tp) cc_final: 0.8189 (mm) REVERT: D 430 MET cc_start: 0.8989 (mtm) cc_final: 0.8766 (mtm) REVERT: D 436 MET cc_start: 0.8342 (mtp) cc_final: 0.8087 (mtp) REVERT: D 438 TRP cc_start: 0.8006 (t-100) cc_final: 0.7631 (t-100) REVERT: D 441 CYS cc_start: 0.7847 (m) cc_final: 0.7397 (m) REVERT: D 521 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6894 (p0) REVERT: D 524 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7826 (mt) REVERT: D 563 LYS cc_start: 0.8230 (mttt) cc_final: 0.7493 (mptt) outliers start: 78 outliers final: 24 residues processed: 328 average time/residue: 0.6096 time to fit residues: 232.1647 Evaluate side-chains 306 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 819 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 786 GLU Chi-restraints excluded: chain D residue 819 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 183 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 280 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105469 restraints weight = 27329.533| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.86 r_work: 0.3103 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24784 Z= 0.181 Angle : 0.576 8.773 33524 Z= 0.286 Chirality : 0.041 0.230 3796 Planarity : 0.004 0.046 4140 Dihedral : 11.175 130.651 3564 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.73 % Allowed : 13.98 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.15), residues: 2920 helix: 2.15 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.020 0.001 TYR A 410 PHE 0.012 0.001 PHE A 576 TRP 0.013 0.001 TRP C 322 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (24768) covalent geometry : angle 0.57487 / 0.29 (33512) hydrogen bonds : bond 0.04877 / 3.27 ( 1572) hydrogen bonds : angle 3.49168 / 2.48 ( 4656) metal coordination : bond 0.01176 / 0.91 ( 16) metal coordination : angle 1.80945 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 0.980 Fit side-chains REVERT: A 27 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 29 GLU cc_start: 0.7944 (tp30) cc_final: 0.7600 (tp30) REVERT: A 48 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 134 ASP cc_start: 0.6984 (m-30) cc_final: 0.6766 (m-30) REVERT: A 365 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7525 (mmtm) REVERT: A 430 MET cc_start: 0.8985 (mtm) cc_final: 0.8773 (mtm) REVERT: A 436 MET cc_start: 0.8393 (mtp) cc_final: 0.8091 (mtp) REVERT: A 438 TRP cc_start: 0.8010 (t-100) cc_final: 0.7641 (t-100) REVERT: A 441 CYS cc_start: 0.7805 (m) cc_final: 0.7268 (m) REVERT: A 563 LYS cc_start: 0.8229 (mttt) cc_final: 0.7467 (mptt) REVERT: B 27 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: B 29 GLU cc_start: 0.7938 (tp30) cc_final: 0.7599 (tp30) REVERT: B 48 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 119 LYS cc_start: 0.7430 (mmmt) cc_final: 0.7099 (mmmm) REVERT: B 134 ASP cc_start: 0.6979 (m-30) cc_final: 0.6771 (m-30) REVERT: B 365 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7527 (mmtm) REVERT: B 430 MET cc_start: 0.8686 (mtp) cc_final: 0.8413 (mtp) REVERT: B 436 MET cc_start: 0.8399 (mtp) cc_final: 0.8108 (mtp) REVERT: B 438 TRP cc_start: 0.8011 (t-100) cc_final: 0.7640 (t-100) REVERT: B 441 CYS cc_start: 0.7818 (m) cc_final: 0.7278 (m) REVERT: B 563 LYS cc_start: 0.8232 (mttt) cc_final: 0.7467 (mptt) REVERT: C 27 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: C 29 GLU cc_start: 0.7961 (tp30) cc_final: 0.7616 (tp30) REVERT: C 48 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: C 119 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7401 (mmmm) REVERT: C 134 ASP cc_start: 0.6963 (m-30) cc_final: 0.6756 (m-30) REVERT: C 140 GLU cc_start: 0.7669 (pm20) cc_final: 0.7437 (pm20) REVERT: C 365 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7534 (mmtm) REVERT: C 430 MET cc_start: 0.8985 (mtm) cc_final: 0.8777 (mtm) REVERT: C 436 MET cc_start: 0.8390 (mtp) cc_final: 0.8089 (mtp) REVERT: C 438 TRP cc_start: 0.8007 (t-100) cc_final: 0.7646 (t-100) REVERT: C 441 CYS cc_start: 0.7784 (m) cc_final: 0.7261 (m) REVERT: C 563 LYS cc_start: 0.8221 (mttt) cc_final: 0.7448 (mptt) REVERT: D 27 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: D 29 GLU cc_start: 0.7953 (tp30) cc_final: 0.7608 (tp30) REVERT: D 48 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 119 LYS cc_start: 0.7556 (mmmt) cc_final: 0.7224 (mmmm) REVERT: D 134 ASP cc_start: 0.6984 (m-30) cc_final: 0.6767 (m-30) REVERT: D 140 GLU cc_start: 0.7694 (pm20) cc_final: 0.7458 (pm20) REVERT: D 365 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7525 (mtpp) REVERT: D 430 MET cc_start: 0.8982 (mtm) cc_final: 0.8772 (mtm) REVERT: D 436 MET cc_start: 0.8390 (mtp) cc_final: 0.8105 (mtp) REVERT: D 438 TRP cc_start: 0.8006 (t-100) cc_final: 0.7646 (t-100) REVERT: D 441 CYS cc_start: 0.7811 (m) cc_final: 0.7282 (m) REVERT: D 521 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7374 (p0) REVERT: D 524 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7991 (mt) REVERT: D 563 LYS cc_start: 0.8226 (mttt) cc_final: 0.7481 (mptt) outliers start: 70 outliers final: 33 residues processed: 315 average time/residue: 0.6586 time to fit residues: 238.6488 Evaluate side-chains 319 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 819 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 786 GLU Chi-restraints excluded: chain D residue 819 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108743 restraints weight = 27301.225| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.87 r_work: 0.3153 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24784 Z= 0.122 Angle : 0.520 8.662 33524 Z= 0.260 Chirality : 0.039 0.205 3796 Planarity : 0.004 0.045 4140 Dihedral : 10.628 115.393 3564 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.81 % Allowed : 14.73 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.15), residues: 2920 helix: 2.28 (0.11), residues: 2180 sheet: None (None), residues: 0 loop : -0.72 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.020 0.001 TYR A 410 PHE 0.010 0.001 PHE C 576 TRP 0.011 0.001 TRP A 322 HIS 0.002 0.000 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (24768) covalent geometry : angle 0.51927 / 0.26 (33512) hydrogen bonds : bond 0.04169 / 2.80 ( 1572) hydrogen bonds : angle 3.37983 / 2.40 ( 4656) metal coordination : bond 0.00743 / 0.57 ( 16) metal coordination : angle 1.41586 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 0.768 Fit side-chains REVERT: A 27 GLU cc_start: 0.7973 (tp30) cc_final: 0.7746 (tt0) REVERT: A 29 GLU cc_start: 0.7895 (tp30) cc_final: 0.7572 (tp30) REVERT: A 48 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 134 ASP cc_start: 0.7056 (m-30) cc_final: 0.6834 (m-30) REVERT: A 365 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7520 (mtpp) REVERT: A 430 MET cc_start: 0.8982 (mtm) cc_final: 0.8755 (mtm) REVERT: A 436 MET cc_start: 0.8346 (mtp) cc_final: 0.8122 (mtp) REVERT: A 438 TRP cc_start: 0.8046 (t-100) cc_final: 0.7700 (t-100) REVERT: A 441 CYS cc_start: 0.7900 (m) cc_final: 0.7445 (m) REVERT: A 461 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: A 563 LYS cc_start: 0.8233 (mttt) cc_final: 0.7505 (mptt) REVERT: B 27 GLU cc_start: 0.7970 (tp30) cc_final: 0.7745 (tt0) REVERT: B 29 GLU cc_start: 0.7885 (tp30) cc_final: 0.7561 (tp30) REVERT: B 48 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 119 LYS cc_start: 0.7512 (mmmt) cc_final: 0.7099 (mmmm) REVERT: B 134 ASP cc_start: 0.7055 (m-30) cc_final: 0.6821 (m-30) REVERT: B 365 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7524 (mtpp) REVERT: B 430 MET cc_start: 0.8679 (mtp) cc_final: 0.8406 (mtp) REVERT: B 436 MET cc_start: 0.8359 (mtp) cc_final: 0.8142 (mtp) REVERT: B 438 TRP cc_start: 0.8047 (t-100) cc_final: 0.7698 (t-100) REVERT: B 441 CYS cc_start: 0.7900 (m) cc_final: 0.7439 (m) REVERT: B 461 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: B 563 LYS cc_start: 0.8217 (mttt) cc_final: 0.7484 (mptt) REVERT: C 27 GLU cc_start: 0.7973 (tp30) cc_final: 0.7756 (tt0) REVERT: C 29 GLU cc_start: 0.7907 (tp30) cc_final: 0.7585 (tp30) REVERT: C 48 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: C 119 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7425 (mmmm) REVERT: C 134 ASP cc_start: 0.7021 (m-30) cc_final: 0.6821 (m-30) REVERT: C 140 GLU cc_start: 0.7675 (pm20) cc_final: 0.7471 (pm20) REVERT: C 365 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7536 (mtpp) REVERT: C 430 MET cc_start: 0.8985 (mtm) cc_final: 0.8762 (mtm) REVERT: C 436 MET cc_start: 0.8356 (mtp) cc_final: 0.8135 (mtp) REVERT: C 438 TRP cc_start: 0.8042 (t-100) cc_final: 0.7707 (t-100) REVERT: C 441 CYS cc_start: 0.8055 (m) cc_final: 0.7670 (m) REVERT: C 461 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: C 525 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8223 (mp) REVERT: C 563 LYS cc_start: 0.8223 (mttt) cc_final: 0.7481 (mptt) REVERT: D 27 GLU cc_start: 0.7979 (tp30) cc_final: 0.7755 (tt0) REVERT: D 29 GLU cc_start: 0.7903 (tp30) cc_final: 0.7579 (tp30) REVERT: D 48 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: D 119 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7190 (mmmm) REVERT: D 134 ASP cc_start: 0.7054 (m-30) cc_final: 0.6841 (m-30) REVERT: D 365 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7530 (mmtm) REVERT: D 367 LEU cc_start: 0.8435 (tp) cc_final: 0.8232 (mm) REVERT: D 430 MET cc_start: 0.8973 (mtm) cc_final: 0.8767 (mtm) REVERT: D 436 MET cc_start: 0.8352 (mtp) cc_final: 0.8144 (mtp) REVERT: D 438 TRP cc_start: 0.8038 (t-100) cc_final: 0.7703 (t-100) REVERT: D 441 CYS cc_start: 0.8047 (m) cc_final: 0.7693 (m) REVERT: D 461 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: D 521 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7035 (p0) REVERT: D 524 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7877 (mt) REVERT: D 563 LYS cc_start: 0.8233 (mttt) cc_final: 0.7506 (mptt) outliers start: 72 outliers final: 29 residues processed: 327 average time/residue: 0.5528 time to fit residues: 211.0711 Evaluate side-chains 301 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 786 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 278 optimal weight: 1.9990 chunk 193 optimal weight: 0.0470 chunk 221 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 213 optimal weight: 0.0670 chunk 84 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.3628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 633 ASN ** 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 = 0.3830 r_free = 0.3830 target = 0.152173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113604 restraints weight = 27444.609| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.86 r_work: 0.3219 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24784 Z= 0.100 Angle : 0.492 8.622 33524 Z= 0.246 Chirality : 0.037 0.208 3796 Planarity : 0.003 0.045 4140 Dihedral : 9.711 89.807 3564 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.30 % Allowed : 15.78 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.15), residues: 2920 helix: 2.50 (0.11), residues: 2180 sheet: None (None), residues: 0 loop : -0.67 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 248 TYR 0.022 0.001 TYR A 410 PHE 0.009 0.001 PHE A 576 TRP 0.013 0.001 TRP D 611 HIS 0.001 0.000 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (24768) covalent geometry : angle 0.49158 / 0.25 (33512) hydrogen bonds : bond 0.03590 / 2.43 ( 1572) hydrogen bonds : angle 3.29674 / 2.35 ( 4656) metal coordination : bond 0.00639 / 0.49 ( 16) metal coordination : angle 1.42247 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.937 Fit side-chains REVERT: A 29 GLU cc_start: 0.7887 (tp30) cc_final: 0.7585 (tp30) REVERT: A 48 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 365 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7517 (mtpp) REVERT: A 430 MET cc_start: 0.8961 (mtm) cc_final: 0.8748 (mtm) REVERT: A 436 MET cc_start: 0.8224 (mtp) cc_final: 0.8018 (mtp) REVERT: A 438 TRP cc_start: 0.8060 (t-100) cc_final: 0.7731 (t-100) REVERT: A 441 CYS cc_start: 0.8110 (m) cc_final: 0.7738 (m) REVERT: A 563 LYS cc_start: 0.8183 (mttt) cc_final: 0.7470 (mptt) REVERT: A 786 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (pt0) REVERT: B 29 GLU cc_start: 0.7880 (tp30) cc_final: 0.7579 (tp30) REVERT: B 48 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: B 119 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7298 (mmmm) REVERT: B 365 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7515 (mtpp) REVERT: B 430 MET cc_start: 0.8671 (mtp) cc_final: 0.8387 (mtp) REVERT: B 436 MET cc_start: 0.8235 (mtp) cc_final: 0.8031 (mtp) REVERT: B 438 TRP cc_start: 0.8060 (t-100) cc_final: 0.7728 (t-100) REVERT: B 441 CYS cc_start: 0.8106 (m) cc_final: 0.7731 (m) REVERT: B 563 LYS cc_start: 0.8160 (mttt) cc_final: 0.7459 (mptt) REVERT: B 786 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: C 29 GLU cc_start: 0.7875 (tp30) cc_final: 0.7579 (tp30) REVERT: C 48 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: C 365 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7522 (mtpp) REVERT: C 430 MET cc_start: 0.8987 (mtm) cc_final: 0.8775 (mtm) REVERT: C 436 MET cc_start: 0.8238 (mtp) cc_final: 0.8023 (mtp) REVERT: C 438 TRP cc_start: 0.8054 (t-100) cc_final: 0.7742 (t-100) REVERT: C 441 CYS cc_start: 0.8116 (m) cc_final: 0.7727 (m) REVERT: C 525 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 563 LYS cc_start: 0.8173 (mttt) cc_final: 0.7462 (mptt) REVERT: C 786 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: D 29 GLU cc_start: 0.7883 (tp30) cc_final: 0.7581 (tp30) REVERT: D 48 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: D 119 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7352 (mmmm) REVERT: D 365 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7505 (mtpp) REVERT: D 430 MET cc_start: 0.8995 (mtm) cc_final: 0.8786 (mtm) REVERT: D 436 MET cc_start: 0.8238 (mtp) cc_final: 0.8021 (mtp) REVERT: D 438 TRP cc_start: 0.8054 (t-100) cc_final: 0.7741 (t-100) REVERT: D 441 CYS cc_start: 0.8110 (m) cc_final: 0.7739 (m) REVERT: D 521 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6694 (p0) REVERT: D 524 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7873 (mt) REVERT: D 563 LYS cc_start: 0.8169 (mttt) cc_final: 0.7458 (mptt) REVERT: D 786 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7679 (pt0) outliers start: 59 outliers final: 16 residues processed: 319 average time/residue: 0.6229 time to fit residues: 230.4271 Evaluate side-chains 293 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 786 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 11 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107923 restraints weight = 27320.876| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.85 r_work: 0.3139 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24784 Z= 0.160 Angle : 0.560 8.290 33524 Z= 0.280 Chirality : 0.041 0.281 3796 Planarity : 0.004 0.045 4140 Dihedral : 9.843 89.369 3564 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.46 % Allowed : 16.13 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.15), residues: 2920 helix: 2.31 (0.11), residues: 2180 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 248 TYR 0.022 0.001 TYR D 410 PHE 0.016 0.001 PHE B 572 TRP 0.010 0.001 TRP C 432 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (24768) covalent geometry : angle 0.55961 / 0.28 (33512) hydrogen bonds : bond 0.04458 / 2.99 ( 1572) hydrogen bonds : angle 3.37035 / 2.40 ( 4656) metal coordination : bond 0.01049 / 0.81 ( 16) metal coordination : angle 1.59999 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.973 Fit side-chains REVERT: A 29 GLU cc_start: 0.7925 (tp30) cc_final: 0.7589 (tp30) REVERT: A 48 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 365 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7485 (mtpp) REVERT: A 436 MET cc_start: 0.8338 (mtp) cc_final: 0.8118 (mtp) REVERT: A 438 TRP cc_start: 0.8021 (t-100) cc_final: 0.7689 (t-100) REVERT: A 441 CYS cc_start: 0.8037 (m) cc_final: 0.7656 (m) REVERT: A 460 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5759 (tt) REVERT: A 563 LYS cc_start: 0.8216 (mttt) cc_final: 0.7483 (mptt) REVERT: B 29 GLU cc_start: 0.7917 (tp30) cc_final: 0.7579 (tp30) REVERT: B 48 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 119 LYS cc_start: 0.7700 (mmmt) cc_final: 0.7364 (mmmm) REVERT: B 365 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7492 (mtpp) REVERT: B 430 MET cc_start: 0.8679 (mtp) cc_final: 0.8393 (mtp) REVERT: B 436 MET cc_start: 0.8346 (mtp) cc_final: 0.8126 (mtp) REVERT: B 438 TRP cc_start: 0.8012 (t-100) cc_final: 0.7680 (t-100) REVERT: B 441 CYS cc_start: 0.8046 (m) cc_final: 0.7661 (m) REVERT: B 460 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5784 (tt) REVERT: B 563 LYS cc_start: 0.8218 (mttt) cc_final: 0.7485 (mptt) REVERT: C 29 GLU cc_start: 0.7924 (tp30) cc_final: 0.7587 (tp30) REVERT: C 48 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: C 365 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7493 (mtpp) REVERT: C 436 MET cc_start: 0.8338 (mtp) cc_final: 0.8117 (mtp) REVERT: C 438 TRP cc_start: 0.8023 (t-100) cc_final: 0.7715 (t-100) REVERT: C 441 CYS cc_start: 0.8034 (m) cc_final: 0.7651 (m) REVERT: C 460 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5782 (tt) REVERT: C 563 LYS cc_start: 0.8229 (mttt) cc_final: 0.7493 (mptt) REVERT: D 29 GLU cc_start: 0.7939 (tp30) cc_final: 0.7601 (tp30) REVERT: D 48 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: D 119 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7472 (mmmm) REVERT: D 365 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7497 (mtpp) REVERT: D 436 MET cc_start: 0.8340 (mtp) cc_final: 0.8118 (mtp) REVERT: D 438 TRP cc_start: 0.8029 (t-100) cc_final: 0.7718 (t-100) REVERT: D 441 CYS cc_start: 0.8044 (m) cc_final: 0.7669 (m) REVERT: D 460 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5783 (tt) REVERT: D 521 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7115 (p0) REVERT: D 524 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7984 (mt) REVERT: D 563 LYS cc_start: 0.8225 (mttt) cc_final: 0.7492 (mptt) outliers start: 63 outliers final: 23 residues processed: 310 average time/residue: 0.6058 time to fit residues: 217.8394 Evaluate side-chains 301 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 207 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 812 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108571 restraints weight = 27270.526| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.85 r_work: 0.3142 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24784 Z= 0.140 Angle : 0.548 9.220 33524 Z= 0.273 Chirality : 0.040 0.260 3796 Planarity : 0.004 0.044 4140 Dihedral : 9.601 89.417 3564 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.52 % Allowed : 17.11 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.15), residues: 2920 helix: 2.31 (0.11), residues: 2180 sheet: None (None), residues: 0 loop : -0.69 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 248 TYR 0.023 0.001 TYR D 410 PHE 0.017 0.001 PHE A 572 TRP 0.010 0.001 TRP A 322 HIS 0.003 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (24768) covalent geometry : angle 0.54722 / 0.27 (33512) hydrogen bonds : bond 0.04277 / 2.87 ( 1572) hydrogen bonds : angle 3.37601 / 2.41 ( 4656) metal coordination : bond 0.00923 / 0.71 ( 16) metal coordination : angle 1.44543 / 1.16 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.955 Fit side-chains REVERT: A 29 GLU cc_start: 0.7949 (tp30) cc_final: 0.7589 (tp30) REVERT: A 48 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 365 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7481 (mtpp) REVERT: A 430 MET cc_start: 0.8890 (mtm) cc_final: 0.8686 (mtp) REVERT: A 438 TRP cc_start: 0.7997 (t-100) cc_final: 0.7664 (t-100) REVERT: A 441 CYS cc_start: 0.8076 (m) cc_final: 0.7684 (m) REVERT: A 460 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5756 (tt) REVERT: A 563 LYS cc_start: 0.8182 (mttt) cc_final: 0.7463 (mptt) REVERT: B 29 GLU cc_start: 0.7945 (tp30) cc_final: 0.7586 (tp30) REVERT: B 48 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 119 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7307 (mmmm) REVERT: B 362 ARG cc_start: 0.7017 (tpp-160) cc_final: 0.6363 (ttm170) REVERT: B 365 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7425 (mtpp) REVERT: B 430 MET cc_start: 0.8676 (mtp) cc_final: 0.8393 (mtp) REVERT: B 436 MET cc_start: 0.8334 (mtp) cc_final: 0.8131 (mtp) REVERT: B 438 TRP cc_start: 0.7998 (t-100) cc_final: 0.7665 (t-100) REVERT: B 441 CYS cc_start: 0.8076 (m) cc_final: 0.7679 (m) REVERT: B 460 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5736 (tt) REVERT: B 563 LYS cc_start: 0.8188 (mttt) cc_final: 0.7456 (mptt) REVERT: C 29 GLU cc_start: 0.7947 (tp30) cc_final: 0.7590 (tp30) REVERT: C 48 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: C 362 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6358 (ttm170) REVERT: C 365 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7421 (mtpp) REVERT: C 430 MET cc_start: 0.8887 (mtm) cc_final: 0.8679 (mtp) REVERT: C 436 MET cc_start: 0.8346 (mtp) cc_final: 0.8139 (mtp) REVERT: C 438 TRP cc_start: 0.7989 (t-100) cc_final: 0.7688 (t-100) REVERT: C 441 CYS cc_start: 0.8062 (m) cc_final: 0.7667 (m) REVERT: C 460 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5727 (tt) REVERT: C 563 LYS cc_start: 0.8192 (mttt) cc_final: 0.7459 (mptt) REVERT: D 29 GLU cc_start: 0.7952 (tp30) cc_final: 0.7594 (tp30) REVERT: D 48 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: D 119 LYS cc_start: 0.7711 (mmmt) cc_final: 0.7419 (mmmm) REVERT: D 365 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7471 (mtpp) REVERT: D 430 MET cc_start: 0.8897 (mtm) cc_final: 0.8693 (mtp) REVERT: D 436 MET cc_start: 0.8341 (mtp) cc_final: 0.8135 (mtp) REVERT: D 438 TRP cc_start: 0.7991 (t-100) cc_final: 0.7688 (t-100) REVERT: D 441 CYS cc_start: 0.8071 (m) cc_final: 0.7679 (m) REVERT: D 460 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5752 (tt) REVERT: D 521 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7177 (p0) REVERT: D 524 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 563 LYS cc_start: 0.8188 (mttt) cc_final: 0.7458 (mptt) outliers start: 39 outliers final: 24 residues processed: 307 average time/residue: 0.6074 time to fit residues: 215.7459 Evaluate side-chains 315 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 239 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 156 optimal weight: 0.0170 chunk 194 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 86 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN D 86 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108225 restraints weight = 27380.579| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.85 r_work: 0.3142 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24784 Z= 0.139 Angle : 0.543 8.337 33524 Z= 0.272 Chirality : 0.040 0.256 3796 Planarity : 0.004 0.044 4140 Dihedral : 9.297 89.681 3564 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.88 % Allowed : 17.11 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.15), residues: 2920 helix: 2.29 (0.11), residues: 2184 sheet: None (None), residues: 0 loop : -0.68 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 248 TYR 0.022 0.001 TYR D 410 PHE 0.015 0.001 PHE A 572 TRP 0.009 0.001 TRP A 322 HIS 0.003 0.000 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (24768) covalent geometry : angle 0.54273 / 0.27 (33512) hydrogen bonds : bond 0.04297 / 2.89 ( 1572) hydrogen bonds : angle 3.38953 / 2.42 ( 4656) metal coordination : bond 0.00947 / 0.73 ( 16) metal coordination : angle 1.49037 / 1.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8527.14 seconds wall clock time: 145 minutes 55.38 seconds (8755.38 seconds total)