Starting phenix.real_space_refine on Sat Jun 28 20:44:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugf_42223/06_2025/8ugf_42223.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 26 5.49 5 S 169 5.16 5 C 21570 2.51 5 N 5626 2.21 5 O 6150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33551 Number of models: 1 Model: "" Number of chains: 34 Chain: "3A" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3411 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 421} Chain breaks: 1 Chain: "3B" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3138 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "3C" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3025 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 356} Chain: "3D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1888 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 21, 'TRANS': 215} Chain: "3E" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1518 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "3F" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 868 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "3G" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 628 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain breaks: 1 Chain: "3H" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 533 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "3I" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 337 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "3J" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 464 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "3N" Number of atoms: 3424 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 445, 3415 Classifications: {'peptide': 445} Incomplete info: {'n_c_alpha_c_only': 3} Link IDs: {'PTRANS': 18, 'TRANS': 426} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Conformer: "B" Number of residues, atoms: 445, 3415 Classifications: {'peptide': 445} Incomplete info: {'n_c_alpha_c_only': 3} Link IDs: {'PTRANS': 18, 'TRANS': 426} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 bond proxies already assigned to first conformer: 3477 Chain: "3O" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3124 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 11, 'TRANS': 405} Unresolved chain links: 1 Unresolved chain link angles: 10 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "3P" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3024 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "3Q" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1904 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 21, 'TRANS': 217} Chain: "3R" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1518 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "3S" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 868 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "3T" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 628 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "3U" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 533 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "3V" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 223 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "3W" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 464 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "3X" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "3Y" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "3A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Chain: "3C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 258 Unusual residues: {'3PE': 2, 'CDL': 1, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 141 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "3D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'HEC:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'3PE': 1, 'FES': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "3G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "3N" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "3P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 183 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 50 Chain: "3Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "3R" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'3PE': 1, 'FES': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "3T" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 87 Chain: "3X" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "3Y" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12554 SG CYS3E 217 71.823 44.626 22.636 1.00170.40 S ATOM 12690 SG CYS3E 236 72.447 40.372 22.007 1.00182.91 S ATOM 12690 SG CYS3E 236 72.447 40.372 22.007 1.00182.91 S ATOM 28378 SG CYS3R 217 85.523 101.602 43.153 1.00186.14 S ATOM 28514 SG CYS3R 236 83.884 104.201 40.782 1.00191.57 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN3N 207 " occ=0.40 ... (16 atoms not shown) pdb=" NE2BGLN3N 207 " occ=0.60 Time building chain proxies: 20.93, per 1000 atoms: 0.62 Number of scatterers: 33551 At special positions: 0 Unit cell: (150.29, 136.99, 171.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 169 16.00 P 26 15.00 O 6150 8.00 N 5626 7.00 C 21570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS3E 222 " - pdb=" SG CYS3E 238 " distance=2.03 Simple disulfide: pdb=" SG CYS3H 49 " - pdb=" SG CYS3H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS3H 65 " - pdb=" SG CYS3H 79 " distance=2.03 Simple disulfide: pdb=" SG CYS3U 24 " - pdb=" SG CYS3U 68 " distance=2.03 Simple disulfide: pdb=" SG CYS3U 40 " - pdb=" SG CYS3U 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.67 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES3E 301 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 236 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 219 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 217 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 239 " pdb=" FES3R 301 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 236 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 217 " pdb="FE2 FES3R 301 " - pdb=" ND1 HIS3R 239 " pdb="FE2 FES3R 301 " - pdb=" ND1 HIS3R 219 " Number of angles added : 6 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7688 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 13 sheets defined 58.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain '3A' and resid 4 through 10 Processing helix chain '3A' and resid 44 through 48 Processing helix chain '3A' and resid 54 through 64 removed outlier: 4.322A pdb=" N PHE3A 64 " --> pdb=" O GLU3A 60 " (cutoff:3.500A) Processing helix chain '3A' and resid 72 through 82 removed outlier: 4.090A pdb=" N GLU3A 76 " --> pdb=" O GLY3A 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET3A 82 " --> pdb=" O GLU3A 78 " (cutoff:3.500A) Processing helix chain '3A' and resid 105 through 119 removed outlier: 3.609A pdb=" N GLN3A 118 " --> pdb=" O ALA3A 114 " (cutoff:3.500A) Processing helix chain '3A' and resid 123 through 143 removed outlier: 3.905A pdb=" N SER3A 143 " --> pdb=" O GLN3A 139 " (cutoff:3.500A) Processing helix chain '3A' and resid 144 through 158 Processing helix chain '3A' and resid 161 through 165 Processing helix chain '3A' and resid 170 through 177 Processing helix chain '3A' and resid 178 through 189 Processing helix chain '3A' and resid 191 through 194 Processing helix chain '3A' and resid 204 through 216 Processing helix chain '3A' and resid 266 through 278 Processing helix chain '3A' and resid 292 through 302 Processing helix chain '3A' and resid 330 through 348 Processing helix chain '3A' and resid 350 through 369 removed outlier: 3.802A pdb=" N VAL3A 354 " --> pdb=" O THR3A 350 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU3A 369 " --> pdb=" O LEU3A 365 " (cutoff:3.500A) Processing helix chain '3A' and resid 371 through 385 Processing helix chain '3A' and resid 391 through 401 removed outlier: 3.824A pdb=" N GLU3A 401 " --> pdb=" O SER3A 397 " (cutoff:3.500A) Processing helix chain '3A' and resid 403 through 415 Processing helix chain '3A' and resid 433 through 441 removed outlier: 3.552A pdb=" N MET3A 441 " --> pdb=" O ILE3A 437 " (cutoff:3.500A) Processing helix chain '3B' and resid 54 through 58 removed outlier: 3.706A pdb=" N TYR3B 57 " --> pdb=" O GLY3B 54 " (cutoff:3.500A) Processing helix chain '3B' and resid 64 through 71 Processing helix chain '3B' and resid 81 through 93 removed outlier: 3.716A pdb=" N VAL3B 92 " --> pdb=" O GLY3B 88 " (cutoff:3.500A) Processing helix chain '3B' and resid 115 through 129 removed outlier: 3.802A pdb=" N LEU3B 119 " --> pdb=" O ASP3B 115 " (cutoff:3.500A) Processing helix chain '3B' and resid 133 through 154 removed outlier: 4.329A pdb=" N SER3B 142 " --> pdb=" O ALA3B 138 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN3B 143 " --> pdb=" O ALA3B 139 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU3B 144 " --> pdb=" O LEU3B 140 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG3B 145 " --> pdb=" O GLN3B 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE3B 146 " --> pdb=" O SER3B 142 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN3B 154 " --> pdb=" O VAL3B 150 " (cutoff:3.500A) Processing helix chain '3B' and resid 154 through 168 removed outlier: 4.332A pdb=" N GLN3B 158 " --> pdb=" O ASN3B 154 " (cutoff:3.500A) Processing helix chain '3B' and resid 179 through 183 Processing helix chain '3B' and resid 187 through 199 Processing helix chain '3B' and resid 200 through 202 No H-bonds generated for 'chain '3B' and resid 200 through 202' Processing helix chain '3B' and resid 212 through 223 removed outlier: 3.601A pdb=" N VAL3B 219 " --> pdb=" O VAL3B 215 " (cutoff:3.500A) Processing helix chain '3B' and resid 266 through 280 Processing helix chain '3B' and resid 293 through 301 removed outlier: 3.517A pdb=" N LYS3B 301 " --> pdb=" O GLN3B 297 " (cutoff:3.500A) Processing helix chain '3B' and resid 332 through 350 Processing helix chain '3B' and resid 353 through 372 Processing helix chain '3B' and resid 374 through 388 Processing helix chain '3B' and resid 394 through 405 removed outlier: 3.948A pdb=" N GLN3B 400 " --> pdb=" O SER3B 396 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN3B 401 " --> pdb=" O THR3B 397 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL3B 405 " --> pdb=" O GLN3B 401 " (cutoff:3.500A) Processing helix chain '3B' and resid 406 through 411 removed outlier: 3.625A pdb=" N VAL3B 410 " --> pdb=" O ALA3B 406 " (cutoff:3.500A) Processing helix chain '3B' and resid 413 through 419 Processing helix chain '3C' and resid 3 through 7 Processing helix chain '3C' and resid 8 through 19 Processing helix chain '3C' and resid 28 through 30 No H-bonds generated for 'chain '3C' and resid 28 through 30' Processing helix chain '3C' and resid 31 through 53 removed outlier: 4.290A pdb=" N SER3C 35 " --> pdb=" O TRP3C 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY3C 38 " --> pdb=" O GLY3C 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY3C 48 " --> pdb=" O GLN3C 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU3C 49 " --> pdb=" O ILE3C 45 " (cutoff:3.500A) Processing helix chain '3C' and resid 61 through 72 Processing helix chain '3C' and resid 75 through 104 removed outlier: 3.860A pdb=" N ILE3C 79 " --> pdb=" O TYR3C 75 " (cutoff:3.500A) Processing helix chain '3C' and resid 105 through 108 removed outlier: 3.515A pdb=" N MET3C 108 " --> pdb=" O GLY3C 105 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 105 through 108' Processing helix chain '3C' and resid 109 through 133 Processing helix chain '3C' and resid 136 through 149 Processing helix chain '3C' and resid 150 through 153 Processing helix chain '3C' and resid 156 through 166 removed outlier: 3.739A pdb=" N VAL3C 161 " --> pdb=" O GLY3C 157 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU3C 162 " --> pdb=" O THR3C 158 " (cutoff:3.500A) Processing helix chain '3C' and resid 171 through 202 Proline residue: 3C 186 - end of helix removed outlier: 3.785A pdb=" N GLU3C 202 " --> pdb=" O LEU3C 198 " (cutoff:3.500A) Processing helix chain '3C' and resid 219 through 245 removed outlier: 4.340A pdb=" N TYR3C 223 " --> pdb=" O PRO3C 219 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR3C 225 " --> pdb=" O HIS3C 221 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE3C 226 " --> pdb=" O PRO3C 222 " (cutoff:3.500A) Processing helix chain '3C' and resid 246 through 250 removed outlier: 4.244A pdb=" N LEU3C 250 " --> pdb=" O PRO3C 247 " (cutoff:3.500A) Processing helix chain '3C' and resid 252 through 256 Processing helix chain '3C' and resid 274 through 284 removed outlier: 3.665A pdb=" N ILE3C 280 " --> pdb=" O PHE3C 276 " (cutoff:3.500A) Processing helix chain '3C' and resid 286 through 308 removed outlier: 3.946A pdb=" N ILE3C 298 " --> pdb=" O LEU3C 294 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU3C 301 " --> pdb=" O SER3C 297 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE3C 302 " --> pdb=" O ILE3C 298 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU3C 303 " --> pdb=" O LEU3C 299 " (cutoff:3.500A) Proline residue: 3C 305 - end of helix Processing helix chain '3C' and resid 314 through 317 removed outlier: 4.097A pdb=" N PHE3C 317 " --> pdb=" O SER3C 314 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 314 through 317' Processing helix chain '3C' and resid 318 through 341 Processing helix chain '3C' and resid 346 through 364 Processing helix chain '3C' and resid 364 through 376 Processing helix chain '3D' and resid 110 through 124 removed outlier: 3.602A pdb=" N GLN3D 119 " --> pdb=" O ARG3D 115 " (cutoff:3.500A) Processing helix chain '3D' and resid 135 through 140 removed outlier: 3.704A pdb=" N LEU3D 139 " --> pdb=" O ALA3D 135 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL3D 140 " --> pdb=" O TYR3D 136 " (cutoff:3.500A) No H-bonds generated for 'chain '3D' and resid 135 through 140' Processing helix chain '3D' and resid 145 through 156 removed outlier: 3.613A pdb=" N VAL3D 156 " --> pdb=" O LEU3D 152 " (cutoff:3.500A) Processing helix chain '3D' and resid 185 through 193 removed outlier: 3.611A pdb=" N ALA3D 189 " --> pdb=" O ASN3D 185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG3D 190 " --> pdb=" O PRO3D 186 " (cutoff:3.500A) Processing helix chain '3D' and resid 203 through 208 Processing helix chain '3D' and resid 211 through 221 Processing helix chain '3D' and resid 267 through 284 Processing helix chain '3D' and resid 286 through 317 removed outlier: 3.669A pdb=" N MET3D 299 " --> pdb=" O LEU3D 295 " (cutoff:3.500A) Proline residue: 3D 306 - end of helix Processing helix chain '3D' and resid 318 through 322 removed outlier: 3.654A pdb=" N SER3D 321 " --> pdb=" O VAL3D 318 " (cutoff:3.500A) Processing helix chain '3E' and resid 103 through 141 removed outlier: 4.069A pdb=" N ASP3E 108 " --> pdb=" O LYS3E 104 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA3E 109 " --> pdb=" O GLU3E 105 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE3E 136 " --> pdb=" O ALA3E 132 " (cutoff:3.500A) Processing helix chain '3E' and resid 145 through 150 Processing helix chain '3E' and resid 180 through 190 Processing helix chain '3E' and resid 200 through 205 Processing helix chain '3E' and resid 218 through 222 removed outlier: 3.752A pdb=" N CYS3E 222 " --> pdb=" O HIS3E 219 " (cutoff:3.500A) Processing helix chain '3F' and resid 25 through 37 removed outlier: 4.217A pdb=" N GLY3F 37 " --> pdb=" O TYR3F 33 " (cutoff:3.500A) Processing helix chain '3F' and resid 44 through 48 Processing helix chain '3F' and resid 52 through 61 removed outlier: 3.862A pdb=" N GLU3F 57 " --> pdb=" O ASP3F 53 " (cutoff:3.500A) Processing helix chain '3F' and resid 63 through 84 removed outlier: 3.530A pdb=" N PHE3F 72 " --> pdb=" O ASN3F 68 " (cutoff:3.500A) Processing helix chain '3F' and resid 88 through 92 removed outlier: 3.520A pdb=" N TRP3F 92 " --> pdb=" O LYS3F 89 " (cutoff:3.500A) Processing helix chain '3F' and resid 102 through 121 Processing helix chain '3G' and resid 34 through 72 removed outlier: 4.556A pdb=" N LEU3G 48 " --> pdb=" O ARG3G 44 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG3G 49 " --> pdb=" O ALA3G 45 " (cutoff:3.500A) Proline residue: 3G 52 - end of helix Processing helix chain '3H' and resid 40 through 51 removed outlier: 4.032A pdb=" N GLN3H 51 " --> pdb=" O GLU3H 47 " (cutoff:3.500A) Processing helix chain '3H' and resid 52 through 72 removed outlier: 3.679A pdb=" N ARG3H 72 " --> pdb=" O ARG3H 68 " (cutoff:3.500A) Processing helix chain '3H' and resid 79 through 96 removed outlier: 3.690A pdb=" N CYS3H 93 " --> pdb=" O ALA3H 89 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS3H 96 " --> pdb=" O HIS3H 92 " (cutoff:3.500A) Processing helix chain '3H' and resid 97 through 102 Processing helix chain '3I' and resid 51 through 56 Processing helix chain '3J' and resid 6 through 15 Processing helix chain '3J' and resid 17 through 48 removed outlier: 3.843A pdb=" N ARG3J 34 " --> pdb=" O LEU3J 30 " (cutoff:3.500A) Processing helix chain '3J' and resid 56 through 60 Processing helix chain '3N' and resid 44 through 48 removed outlier: 3.623A pdb=" N GLU3N 48 " --> pdb=" O SER3N 45 " (cutoff:3.500A) Processing helix chain '3N' and resid 54 through 64 removed outlier: 4.583A pdb=" N PHE3N 64 " --> pdb=" O GLU3N 60 " (cutoff:3.500A) Processing helix chain '3N' and resid 73 through 82 Processing helix chain '3N' and resid 107 through 115 removed outlier: 3.504A pdb=" N GLU3N 111 " --> pdb=" O PRO3N 107 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain '3N' and resid 124 through 132 WARNING: missing atoms! removed outlier: 3.759A pdb=" N ASP3N 132 " --> pdb=" O GLU3N 128 " (cutoff:3.500A) Processing helix chain '3N' and resid 135 through 144 Processing helix chain '3N' and resid 146 through 158 Processing helix chain '3N' and resid 161 through 165 Processing helix chain '3N' and resid 182 through 190 Processing helix chain '3N' and resid 204 through 217 removed outlier: 3.841A pdb=" N SER3N 217 " --> pdb=" O GLN3N 213 " (cutoff:3.500A) Processing helix chain '3N' and resid 266 through 278 Processing helix chain '3N' and resid 286 through 290 removed outlier: 3.551A pdb=" N HIS3N 289 " --> pdb=" O GLY3N 286 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET3N 290 " --> pdb=" O GLY3N 287 " (cutoff:3.500A) No H-bonds generated for 'chain '3N' and resid 286 through 290' Processing helix chain '3N' and resid 292 through 302 Processing helix chain '3N' and resid 327 through 329 No H-bonds generated for 'chain '3N' and resid 327 through 329' Processing helix chain '3N' and resid 330 through 349 removed outlier: 3.567A pdb=" N PHE3N 336 " --> pdb=" O ASP3N 332 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN3N 339 " --> pdb=" O MET3N 335 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA3N 349 " --> pdb=" O LEU3N 345 " (cutoff:3.500A) Processing helix chain '3N' and resid 350 through 369 removed outlier: 3.634A pdb=" N ARG3N 356 " --> pdb=" O SER3N 352 " (cutoff:3.500A) Processing helix chain '3N' and resid 371 through 386 removed outlier: 3.721A pdb=" N LEU3N 384 " --> pdb=" O GLY3N 380 " (cutoff:3.500A) Processing helix chain '3N' and resid 391 through 402 Processing helix chain '3N' and resid 403 through 415 Processing helix chain '3N' and resid 433 through 441 Processing helix chain '3O' and resid 64 through 72 Processing helix chain '3O' and resid 81 through 92 Processing helix chain '3O' and resid 115 through 125 removed outlier: 3.650A pdb=" N LEU3O 119 " --> pdb=" O ASP3O 115 " (cutoff:3.500A) Processing helix chain '3O' and resid 133 through 152 removed outlier: 4.387A pdb=" N SER3O 142 " --> pdb=" O ALA3O 138 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN3O 143 " --> pdb=" O ALA3O 139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU3O 144 " --> pdb=" O LEU3O 140 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG3O 145 " --> pdb=" O GLN3O 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE3O 146 " --> pdb=" O SER3O 142 " (cutoff:3.500A) Processing helix chain '3O' and resid 155 through 168 Processing helix chain '3O' and resid 179 through 183 removed outlier: 3.562A pdb=" N ILE3O 183 " --> pdb=" O ASP3O 180 " (cutoff:3.500A) Processing helix chain '3O' and resid 187 through 199 Processing helix chain '3O' and resid 200 through 202 No H-bonds generated for 'chain '3O' and resid 200 through 202' Processing helix chain '3O' and resid 212 through 224 Processing helix chain '3O' and resid 225 through 227 No H-bonds generated for 'chain '3O' and resid 225 through 227' Processing helix chain '3O' and resid 266 through 280 Processing helix chain '3O' and resid 293 through 301 Processing helix chain '3O' and resid 332 through 349 removed outlier: 3.513A pdb=" N LYS3O 338 " --> pdb=" O GLY3O 334 " (cutoff:3.500A) Processing helix chain '3O' and resid 353 through 372 Processing helix chain '3O' and resid 374 through 389 Processing helix chain '3O' and resid 394 through 404 Processing helix chain '3O' and resid 406 through 411 Processing helix chain '3O' and resid 413 through 419 Processing helix chain '3P' and resid 3 through 7 Processing helix chain '3P' and resid 8 through 19 removed outlier: 4.108A pdb=" N ILE3P 13 " --> pdb=" O PRO3P 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE3P 14 " --> pdb=" O LEU3P 10 " (cutoff:3.500A) Processing helix chain '3P' and resid 28 through 30 No H-bonds generated for 'chain '3P' and resid 28 through 30' Processing helix chain '3P' and resid 31 through 54 removed outlier: 4.236A pdb=" N SER3P 35 " --> pdb=" O TRP3P 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY3P 38 " --> pdb=" O GLY3P 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE3P 50 " --> pdb=" O LEU3P 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS3P 54 " --> pdb=" O PHE3P 50 " (cutoff:3.500A) Processing helix chain '3P' and resid 61 through 72 Processing helix chain '3P' and resid 75 through 104 Processing helix chain '3P' and resid 105 through 109 removed outlier: 3.748A pdb=" N MET3P 108 " --> pdb=" O GLY3P 105 " (cutoff:3.500A) Processing helix chain '3P' and resid 110 through 133 Processing helix chain '3P' and resid 136 through 149 Processing helix chain '3P' and resid 150 through 153 Processing helix chain '3P' and resid 156 through 166 Processing helix chain '3P' and resid 171 through 202 removed outlier: 3.556A pdb=" N ALA3P 180 " --> pdb=" O THR3P 176 " (cutoff:3.500A) Proline residue: 3P 186 - end of helix removed outlier: 3.762A pdb=" N GLU3P 202 " --> pdb=" O LEU3P 198 " (cutoff:3.500A) Processing helix chain '3P' and resid 224 through 246 Processing helix chain '3P' and resid 252 through 257 Processing helix chain '3P' and resid 274 through 284 removed outlier: 3.885A pdb=" N ILE3P 280 " --> pdb=" O PHE3P 276 " (cutoff:3.500A) Processing helix chain '3P' and resid 286 through 308 removed outlier: 3.857A pdb=" N ILE3P 298 " --> pdb=" O LEU3P 294 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU3P 301 " --> pdb=" O SER3P 297 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE3P 302 " --> pdb=" O ILE3P 298 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU3P 303 " --> pdb=" O LEU3P 299 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET3P 304 " --> pdb=" O ILE3P 300 " (cutoff:3.500A) Proline residue: 3P 305 - end of helix Processing helix chain '3P' and resid 318 through 341 Processing helix chain '3P' and resid 344 through 364 removed outlier: 4.082A pdb=" N ILE3P 349 " --> pdb=" O HIS3P 345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE3P 350 " --> pdb=" O PRO3P 346 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE3P 362 " --> pdb=" O TYR3P 358 " (cutoff:3.500A) Processing helix chain '3P' and resid 364 through 377 removed outlier: 3.598A pdb=" N ASN3P 374 " --> pdb=" O SER3P 370 " (cutoff:3.500A) Processing helix chain '3Q' and resid 12 through 16 removed outlier: 3.950A pdb=" N GLY3Q 16 " --> pdb=" O SER3Q 13 " (cutoff:3.500A) Processing helix chain '3Q' and resid 22 through 36 removed outlier: 3.630A pdb=" N GLN3Q 31 " --> pdb=" O ARG3Q 27 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL3Q 32 " --> pdb=" O ARG3Q 28 " (cutoff:3.500A) Processing helix chain '3Q' and resid 37 through 40 Processing helix chain '3Q' and resid 47 through 52 removed outlier: 3.912A pdb=" N LEU3Q 51 " --> pdb=" O ALA3Q 47 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL3Q 52 " --> pdb=" O TYR3Q 48 " (cutoff:3.500A) No H-bonds generated for 'chain '3Q' and resid 47 through 52' Processing helix chain '3Q' and resid 57 through 68 removed outlier: 3.951A pdb=" N VAL3Q 68 " --> pdb=" O LEU3Q 64 " (cutoff:3.500A) Processing helix chain '3Q' and resid 97 through 105 Processing helix chain '3Q' and resid 115 through 120 Processing helix chain '3Q' and resid 123 through 133 Processing helix chain '3Q' and resid 178 through 195 Processing helix chain '3Q' and resid 197 through 232 Proline residue: 3Q 217 - end of helix removed outlier: 4.962A pdb=" N VAL3Q 229 " --> pdb=" O HIS3Q 225 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU3Q 230 " --> pdb=" O LYS3Q 226 " (cutoff:3.500A) Processing helix chain '3R' and resid 102 through 141 removed outlier: 4.377A pdb=" N SER3R 106 " --> pdb=" O SER3R 102 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP3R 108 " --> pdb=" O LYS3R 104 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA3R 109 " --> pdb=" O GLU3R 105 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN3R 135 " --> pdb=" O ASN3R 131 " (cutoff:3.500A) Processing helix chain '3R' and resid 143 through 150 Processing helix chain '3R' and resid 168 through 172 Processing helix chain '3R' and resid 180 through 189 Processing helix chain '3R' and resid 200 through 205 Processing helix chain '3S' and resid 13 through 25 removed outlier: 4.020A pdb=" N GLY3S 25 " --> pdb=" O TYR3S 21 " (cutoff:3.500A) Processing helix chain '3S' and resid 32 through 37 Processing helix chain '3S' and resid 40 through 50 removed outlier: 3.665A pdb=" N ARG3S 48 " --> pdb=" O LYS3S 44 " (cutoff:3.500A) Processing helix chain '3S' and resid 51 through 72 Processing helix chain '3S' and resid 76 through 80 removed outlier: 3.548A pdb=" N TRP3S 80 " --> pdb=" O LYS3S 77 " (cutoff:3.500A) Processing helix chain '3S' and resid 90 through 109 Processing helix chain '3T' and resid 28 through 70 Proline residue: 3T 35 - end of helix removed outlier: 4.809A pdb=" N LEU3T 46 " --> pdb=" O ARG3T 42 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ARG3T 47 " --> pdb=" O ALA3T 43 " (cutoff:3.500A) Proline residue: 3T 50 - end of helix Processing helix chain '3U' and resid 15 through 26 removed outlier: 3.664A pdb=" N THR3U 19 " --> pdb=" O ASP3U 15 " (cutoff:3.500A) Processing helix chain '3U' and resid 27 through 47 removed outlier: 4.114A pdb=" N GLN3U 42 " --> pdb=" O GLU3U 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG3U 43 " --> pdb=" O LEU3U 39 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG3U 47 " --> pdb=" O ARG3U 43 " (cutoff:3.500A) Processing helix chain '3U' and resid 54 through 72 removed outlier: 3.700A pdb=" N CYS3U 68 " --> pdb=" O ALA3U 64 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS3U 71 " --> pdb=" O HIS3U 67 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS3U 72 " --> pdb=" O CYS3U 68 " (cutoff:3.500A) Processing helix chain '3V' and resid 51 through 56 removed outlier: 3.552A pdb=" N LEU3V 55 " --> pdb=" O CYS3V 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER3V 56 " --> pdb=" O ARG3V 52 " (cutoff:3.500A) No H-bonds generated for 'chain '3V' and resid 51 through 56' Processing helix chain '3W' and resid 5 through 14 Processing helix chain '3W' and resid 16 through 47 removed outlier: 3.564A pdb=" N PHE3W 30 " --> pdb=" O VAL3W 26 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG3W 33 " --> pdb=" O LEU3W 29 " (cutoff:3.500A) Processing helix chain '3W' and resid 51 through 56 Processing helix chain '3W' and resid 57 through 59 No H-bonds generated for 'chain '3W' and resid 57 through 59' Processing helix chain '3X' and resid 2 through 6 Processing helix chain '3X' and resid 7 through 37 Proline residue: 3X 19 - end of helix Processing helix chain '3X' and resid 38 through 43 Processing helix chain '3X' and resid 46 through 52 Processing helix chain '3Y' and resid 6 through 37 removed outlier: 4.294A pdb=" N TYR3Y 10 " --> pdb=" O LEU3Y 6 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG3Y 11 " --> pdb=" O GLY3Y 7 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU3Y 12 " --> pdb=" O PRO3Y 8 " (cutoff:3.500A) Proline residue: 3Y 19 - end of helix Processing helix chain '3Y' and resid 38 through 43 Processing helix chain '3Y' and resid 44 through 45 No H-bonds generated for 'chain '3Y' and resid 44 through 45' Processing helix chain '3Y' and resid 46 through 52 removed outlier: 3.871A pdb=" N ASN3Y 49 " --> pdb=" O PRO3Y 46 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS3Y 51 " --> pdb=" O ILE3Y 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3A' and resid 15 through 18 removed outlier: 3.578A pdb=" N THR3A 36 " --> pdb=" O ALA3A 200 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL3A 37 " --> pdb=" O ILE3A 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL3A 39 " --> pdb=" O TYR3A 97 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR3A 97 " --> pdb=" O VAL3A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3A' and resid 280 through 281 removed outlier: 3.645A pdb=" N CYS3A 326 " --> pdb=" O ALA3A 251 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL3G 15 " --> pdb=" O ARG3A 244 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR3G 18 " --> pdb=" O LYS3D 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3B' and resid 25 through 28 removed outlier: 7.122A pdb=" N VAL3B 34 " --> pdb=" O LEU3B 206 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY3B 208 " --> pdb=" O VAL3B 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA3B 36 " --> pdb=" O GLY3B 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU3B 96 " --> pdb=" O LEU3I 70 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY3I 69 " --> pdb=" O PRO3I 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3B' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain '3D' and resid 157 through 162 removed outlier: 3.622A pdb=" N ASP3D 160 " --> pdb=" O PHE3D 169 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE3D 169 " --> pdb=" O ASP3D 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3E' and resid 164 through 169 removed outlier: 3.896A pdb=" N VAL3E 176 " --> pdb=" O MET3E 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3N' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain '3N' and resid 308 through 310 removed outlier: 3.808A pdb=" N CYS3N 326 " --> pdb=" O ALA3N 251 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS3N 252 " --> pdb=" O LEU3N 425 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY3N 424 " --> pdb=" O SER3N 239 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE3N 241 " --> pdb=" O GLY3N 424 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLY3N 426 " --> pdb=" O ILE3N 241 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N HIS3N 243 " --> pdb=" O GLY3N 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL3T 13 " --> pdb=" O ARG3N 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3O' and resid 28 through 29 removed outlier: 7.623A pdb=" N MET3O 204 " --> pdb=" O GLY3O 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL3O 34 " --> pdb=" O MET3O 204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU3O 110 " --> pdb=" O LYS3O 95 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS3O 95 " --> pdb=" O GLU3O 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3O' and resid 245 through 246 Processing sheet with id=AB2, first strand: chain '3Q' and resid 69 through 74 removed outlier: 3.812A pdb=" N ASP3Q 72 " --> pdb=" O PHE3Q 81 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE3Q 81 " --> pdb=" O ASP3Q 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3R' and resid 163 through 166 Processing sheet with id=AB4, first strand: chain '3V' and resid 65 through 67 1738 hydrogen bonds defined for protein. 4981 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: 11.53 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.28: 5302 1.28 - 1.52: 23706 1.52 - 1.76: 5047 1.76 - 2.00: 273 2.00 - 2.24: 24 Bond restraints: 34352 Sorted by residual: bond pdb=" CG PRO3R 198 " pdb=" CD PRO3R 198 " ideal model delta sigma weight residual 1.503 1.107 0.396 3.40e-02 8.65e+02 1.36e+02 bond pdb=" CG PRO3I 41 " pdb=" CD PRO3I 41 " ideal model delta sigma weight residual 1.503 1.149 0.354 3.40e-02 8.65e+02 1.08e+02 bond pdb=" CG PRO3E 173 " pdb=" CD PRO3E 173 " ideal model delta sigma weight residual 1.503 1.155 0.348 3.40e-02 8.65e+02 1.05e+02 bond pdb=" CB PRO3I 41 " pdb=" CG PRO3I 41 " ideal model delta sigma weight residual 1.492 1.045 0.447 5.00e-02 4.00e+02 7.98e+01 bond pdb=" C8 U103C 504 " pdb=" C9 U103C 504 " ideal model delta sigma weight residual 1.470 1.322 0.148 2.00e-02 2.50e+03 5.47e+01 ... (remaining 34347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.75: 46503 14.75 - 29.51: 16 29.51 - 44.26: 3 44.26 - 59.02: 0 59.02 - 73.77: 2 Bond angle restraints: 46524 Sorted by residual: angle pdb=" CB PRO3I 41 " pdb=" CG PRO3I 41 " pdb=" CD PRO3I 41 " ideal model delta sigma weight residual 106.10 179.87 -73.77 3.20e+00 9.77e-02 5.31e+02 angle pdb=" CB PRO3R 198 " pdb=" CG PRO3R 198 " pdb=" CD PRO3R 198 " ideal model delta sigma weight residual 106.10 175.49 -69.39 3.20e+00 9.77e-02 4.70e+02 angle pdb=" N PRO3R 198 " pdb=" CD PRO3R 198 " pdb=" CG PRO3R 198 " ideal model delta sigma weight residual 103.20 72.96 30.24 1.50e+00 4.44e-01 4.06e+02 angle pdb=" N PRO3I 41 " pdb=" CD PRO3I 41 " pdb=" CG PRO3I 41 " ideal model delta sigma weight residual 103.20 75.66 27.54 1.50e+00 4.44e-01 3.37e+02 angle pdb=" CA PRO3I 41 " pdb=" CB PRO3I 41 " pdb=" CG PRO3I 41 " ideal model delta sigma weight residual 104.50 74.21 30.29 1.90e+00 2.77e-01 2.54e+02 ... (remaining 46519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 19532 35.95 - 71.90: 982 71.90 - 107.84: 80 107.84 - 143.79: 5 143.79 - 179.74: 6 Dihedral angle restraints: 20605 sinusoidal: 8660 harmonic: 11945 Sorted by residual: dihedral pdb=" CB CYS3U 24 " pdb=" SG CYS3U 24 " pdb=" SG CYS3U 68 " pdb=" CB CYS3U 68 " ideal model delta sinusoidal sigma weight residual 93.00 162.42 -69.42 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS3E 222 " pdb=" SG CYS3E 222 " pdb=" SG CYS3E 238 " pdb=" CB CYS3E 238 " ideal model delta sinusoidal sigma weight residual 93.00 25.26 67.74 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" C17 U103P 503 " pdb=" C18 U103P 503 " pdb=" C19 U103P 503 " pdb=" C21 U103P 503 " ideal model delta sinusoidal sigma weight residual 179.22 -1.04 -179.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3909 0.051 - 0.103: 947 0.103 - 0.154: 127 0.154 - 0.205: 17 0.205 - 0.257: 4 Chirality restraints: 5004 Sorted by residual: chirality pdb=" CB4 CDL3N 502 " pdb=" CB3 CDL3N 502 " pdb=" CB6 CDL3N 502 " pdb=" OB6 CDL3N 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU3F 80 " pdb=" CB LEU3F 80 " pdb=" CD1 LEU3F 80 " pdb=" CD2 LEU3F 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA4 CDL3T 101 " pdb=" CA3 CDL3T 101 " pdb=" CA6 CDL3T 101 " pdb=" OA6 CDL3T 101 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 5001 not shown) Planarity restraints: 5835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U103C 503 " -0.001 2.00e-02 2.50e+03 1.12e-01 2.18e+02 pdb=" C1M U103C 503 " 0.099 2.00e-02 2.50e+03 pdb=" C2 U103C 503 " -0.011 2.00e-02 2.50e+03 pdb=" C3 U103C 503 " -0.136 2.00e-02 2.50e+03 pdb=" C4 U103C 503 " 0.193 2.00e-02 2.50e+03 pdb=" C5 U103C 503 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U103C 503 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U103P 504 " -0.004 2.00e-02 2.50e+03 7.24e-02 9.17e+01 pdb=" C1M U103P 504 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U103P 504 " 0.079 2.00e-02 2.50e+03 pdb=" C3 U103P 504 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U103P 504 " -0.112 2.00e-02 2.50e+03 pdb=" C5 U103P 504 " 0.120 2.00e-02 2.50e+03 pdb=" C6 U103P 504 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U103C 504 " 0.003 2.00e-02 2.50e+03 6.05e-02 6.41e+01 pdb=" C1M U103C 504 " -0.059 2.00e-02 2.50e+03 pdb=" C2 U103C 504 " 0.012 2.00e-02 2.50e+03 pdb=" C3 U103C 504 " 0.065 2.00e-02 2.50e+03 pdb=" C4 U103C 504 " -0.100 2.00e-02 2.50e+03 pdb=" C5 U103C 504 " -0.008 2.00e-02 2.50e+03 pdb=" C6 U103C 504 " 0.088 2.00e-02 2.50e+03 ... (remaining 5832 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 7 2.16 - 2.84: 12020 2.84 - 3.53: 52439 3.53 - 4.21: 83123 4.21 - 4.90: 144764 Nonbonded interactions: 292353 Sorted by model distance: nonbonded pdb=" CD1 TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 1.469 3.660 nonbonded pdb=" O HIS3P 221 " pdb=" OG1 THR3P 225 " model vdw 2.039 3.040 nonbonded pdb=" O HIS3C 221 " pdb=" OG1 THR3C 225 " model vdw 2.061 3.040 nonbonded pdb=" OG SER3C 25 " pdb=" OD2 ASP3C 216 " model vdw 2.100 3.040 nonbonded pdb=" OD2 ASP3N 433 " pdb=" OH TYR3P 223 " model vdw 2.140 3.040 ... (remaining 292348 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 '3A' and (resid 2 or (resid 3 and (name N or name CA or name C or name CB \ or name OG1 or name CG2)) or (resid 4 and (name N or name CA or name C or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or resid 5 through 7 or (resid 8 and (name N or name CA or name C or name \ CB or name CG or name CD1 or name CD2)) or (resid 9 and (name N or name CA or n \ ame C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 or \ (resid 11 and (name N or name CA or name C or name CB or name CG1 or name CG2)) \ or (resid 12 and (name N or name CA or name C or name CB or name CG or name CD ) \ ) or resid 13 or (resid 14 and (name N or name CA or name C or name CB or name O \ G1 or name CG2)) or resid 15 or (resid 16 and (name N or name CA or name C or na \ me CB or name CG1 or name CG2)) or (resid 17 and (name N or name CA or name C or \ name CB or name OG )) or resid 18 through 22 or (resid 23 and (name N or name C \ A or name C or name CB or name CG or name CD1 or name CD2)) or resid 24 through \ 27 or (resid 28 and (name N or name CA or name C or name CB or name CG or name C \ D or name OE1 or name OE2)) or resid 29 through 35 or (resid 36 and (name N or n \ ame CA or name C or name CB or name OG1 or name CG2)) or (resid 37 and (name N o \ r name CA or name C or name CB or name CG1 or name CG2)) or resid 38 through 42 \ or (resid 43 and (name N or name CA or name C or name CB )) or resid 44 through \ 65 or (resid 66 and (name N or name CA or name C )) or resid 67 through 88 or (r \ esid 89 and (name N or name CA or name C or name CB or name CG or name CD1 or na \ me CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 90 through 96 o \ r (resid 97 and (name N or name CA or name C or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 98 through \ 108 or (resid 109 and (name N or name CA or name C or name CB )) or resid 110 th \ rough 111 or (resid 112 and (name N or name CA or name C or name CB or name CG o \ r name CD1 or name CD2)) or resid 113 through 115 or (resid 116 and (name N or n \ ame CA or name C or name CB or name CG1 or name CG2 or name CD1)) or (resid 117 \ and (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 1 \ 18 through 120 or (resid 121 and (name N or name CA or name C or name CB or name \ OG )) or resid 122 through 125 or (resid 126 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 127 through 1 \ 31 or (resid 132 and (name N or name CA or name C or name CB or name CG or name \ OD1 or name OD2)) or (resid 133 and (name N or name CA or name C or name CB or n \ ame CG1 or name CG2)) or (resid 134 and (name N or name CA or name C or name CB \ or name CG1 or name CG2 or name CD1)) or resid 135 through 168 or (resid 169 and \ (name N or name CA or name C )) or resid 170 through 176 or (resid 177 and (nam \ e N or name CA or name C or name CB or name CG or name CD1 or name CD2)) or resi \ d 178 through 179 or (resid 180 and (name N or name CA or name C or name CB )) o \ r (resid 181 and (name N or name CA or name C or name CB or name CG or name OD1 \ or name OD2)) or resid 182 through 191 or (resid 192 and (name N or name CA or n \ ame C or name CB )) or (resid 193 and (name N or name CA or name C or name CB or \ name CG or name CD )) or resid 194 or (resid 195 and (name N or name CA or name \ C or name CB or name CG or name SD or name CE )) or resid 196 through 197 or (r \ esid 198 and (name N or name CA or name C or name CB )) or resid 199 through 201 \ or (resid 202 and (name N or name CA or name C )) or resid 203 through 206 or r \ esid 208 through 221 or (resid 222 and (name N or name CA or name C or name CB o \ r name OG1 or name CG2)) or resid 228 through 445 or (resid 446 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 503 and (name N or name C1 or name C11 \ or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P )))) selection = (chain '3N' and (resid 2 through 206 or resid 208 through 222 or resid 228 throu \ gh 446 or resid 503)) } ncs_group { reference = (chain '3B' and (resid 22 through 23 or (resid 24 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2)) or resid 25 through 54 or (re \ sid 55 and (name N or name CA or name C or name CB or name OG )) or resid 56 thr \ ough 124 or (resid 125 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2)) or resid 126 through 127 or (resid 128 and (name N or na \ me CA or name C or name CB )) or resid 129 through 153 or (resid 154 and (name N \ or name CA or name C or name CB or name CG or name OD1 or name ND2)) or resid 1 \ 55 through 171 or (resid 172 and (name N or name CA or name C or name CB or name \ CG or name CD1 or name CD2)) or resid 173 through 182 or (resid 183 and (name N \ or name CA or name C or name CB or name CG1 or name CG2 or name CD1)) or resid \ 184 through 438)) selection = chain '3O' } ncs_group { reference = (chain '3C' and (resid 1 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 501 through 504)) \ selection = (chain '3P' and (resid 1 through 379 or resid 501 through 502 or (resid 503 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C1M or name C2 or name \ C20 or name C21 or name C3 or name C3M or name C4 or name C4M or name C5 or name \ C6 or name C7 or name C8 or name C9 or name O2 or name O3 or name O4 or name O5 \ )) or (resid 504 and (name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C1M or name C2 or name C3 or name C3M \ or name C4 or name C4M or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 or name O5 )))) } ncs_group { reference = chain '3D' selection = (chain '3Q' and (resid 4 through 240 or (resid 501 and (name NB or name ND or na \ me C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C o \ r name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C \ 4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or na \ me CBA or name CBB or name CBC or name CBD or name CGA or name CGD or name CHA o \ r name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name C \ MD or name NA or name NC or name O1A or name O1D or name O2A or name FE )))) } ncs_group { reference = (chain '3E' and (resid 79 through 274 or resid 301 through 302 or (resid 303 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C3 or nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C3A or name C3B or name C3C or name C3D or name C3 \ E or name C3F or name C3G or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain '3R' and (resid 79 through 274 or resid 301 or (resid 302 and (name N or \ name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C \ 3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or resid 303)) } ncs_group { reference = chain '3F' selection = chain '3S' } ncs_group { reference = (chain '3G' and (resid 4 through 83 or resid 102)) selection = (chain '3T' and (resid 2 through 75 or resid 102)) } ncs_group { reference = chain '3H' selection = chain '3U' } ncs_group { reference = chain '3J' selection = chain '3W' } ncs_group { reference = (chain '3X' and resid 2 through 52) selection = (chain '3Y' and resid 2 through 52) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.050 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 81.300 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.010 0.447 34373 Z= 0.401 Angle : 1.084 73.772 46540 Z= 0.511 Chirality : 0.044 0.257 5004 Planarity : 0.006 0.146 5835 Dihedral : 19.950 179.741 12902 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.62 % Favored : 93.11 % Rotamer: Outliers : 1.18 % Allowed : 31.88 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4064 helix: 0.74 (0.11), residues: 2056 sheet: -1.71 (0.30), residues: 305 loop : -0.96 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP3E 210 HIS 0.012 0.001 HIS3P 308 PHE 0.040 0.002 PHE3G 57 TYR 0.029 0.002 TYR3F 32 ARG 0.009 0.001 ARG3G 11 Details of bonding type rmsd hydrogen bonds : bond 0.15566 ( 1738) hydrogen bonds : angle 6.76056 ( 4981) metal coordination : bond 0.22113 ( 8) metal coordination : angle 16.57353 ( 6) SS BOND : bond 0.00189 ( 5) SS BOND : angle 2.77061 ( 10) covalent geometry : bond 0.00935 (34352) covalent geometry : angle 1.06649 (46524) Misc. bond : bond 0.20498 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 570 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 116 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3N 121 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP3N 132 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 177 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP3N 181 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3O 183 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 136 GLN cc_start: 0.8417 (mp10) cc_final: 0.8058 (mp10) REVERT: 3B 108 THR cc_start: 0.8886 (m) cc_final: 0.8539 (p) REVERT: 3B 304 HIS cc_start: 0.7939 (m90) cc_final: 0.7695 (m90) REVERT: 3C 67 THR cc_start: 0.8972 (p) cc_final: 0.8771 (p) REVERT: 3D 293 MET cc_start: 0.7822 (mtp) cc_final: 0.7562 (mmm) REVERT: 3E 121 THR cc_start: 0.9236 (m) cc_final: 0.8758 (p) REVERT: 3E 140 MET cc_start: 0.8828 (mmp) cc_final: 0.8575 (mmp) REVERT: 3G 5 GLU cc_start: 0.7438 (pm20) cc_final: 0.7148 (pm20) REVERT: 3G 70 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9051 (mtmm) REVERT: 3N 343 MET cc_start: 0.8379 (mmp) cc_final: 0.8177 (mmp) REVERT: 3P 316 MET cc_start: 0.8487 (tpp) cc_final: 0.7995 (tpp) REVERT: 3R 149 MET cc_start: 0.8392 (mmt) cc_final: 0.8166 (mmt) REVERT: 3T 59 TYR cc_start: 0.9127 (t80) cc_final: 0.8894 (t80) REVERT: 3W 15 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8247 (ttm-80) REVERT: 3W 23 THR cc_start: 0.9296 (m) cc_final: 0.8926 (p) REVERT: 3X 16 ASN cc_start: 0.8182 (m-40) cc_final: 0.7938 (m110) REVERT: 3Y 12 GLU cc_start: 0.8061 (pm20) cc_final: 0.7810 (pm20) REVERT: 3Y 16 ASN cc_start: 0.9142 (m-40) cc_final: 0.8838 (m-40) outliers start: 39 outliers final: 22 residues processed: 597 average time/residue: 0.4579 time to fit residues: 442.7383 Evaluate side-chains 467 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 445 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3C residue 271 GLU Chi-restraints excluded: chain 3E residue 120 THR Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 116 ILE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 121 SER Chi-restraints excluded: chain 3N residue 132 ASP Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 177 LEU Chi-restraints excluded: chain 3N residue 181 ASP Chi-restraints excluded: chain 3N residue 184 GLU Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 183 ILE Chi-restraints excluded: chain 3P residue 43 LEU Chi-restraints excluded: chain 3P residue 373 GLU Chi-restraints excluded: chain 3R residue 176 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 312 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 362 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 289 HIS ** 3A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN 3B 162 ASN 3C 68 HIS ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 267 HIS 3D 270 GLN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 339 GLN ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 166 ASN 3Q 225 HIS ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3S 56 ASN 3W 57 HIS 3X 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066805 restraints weight = 139001.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069321 restraints weight = 56740.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070956 restraints weight = 31746.452| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 34373 Z= 0.146 Angle : 0.679 17.597 46540 Z= 0.329 Chirality : 0.042 0.226 5004 Planarity : 0.005 0.051 5835 Dihedral : 14.481 163.192 5374 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.10 % Favored : 94.63 % Rotamer: Outliers : 4.93 % Allowed : 27.53 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 4064 helix: 1.17 (0.11), residues: 2071 sheet: -1.49 (0.29), residues: 322 loop : -0.76 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP3E 210 HIS 0.006 0.001 HIS3O 254 PHE 0.035 0.002 PHE3R 175 TYR 0.018 0.001 TYR3P 223 ARG 0.006 0.001 ARG3Q 118 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1738) hydrogen bonds : angle 5.17837 ( 4981) metal coordination : bond 0.06020 ( 8) metal coordination : angle 11.51430 ( 6) SS BOND : bond 0.00459 ( 5) SS BOND : angle 1.23174 ( 10) covalent geometry : bond 0.00336 (34352) covalent geometry : angle 0.66617 (46524) Misc. bond : bond 0.14426 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 538 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 77 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9051 (tppp) REVERT: 3A 105 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7074 (p0) REVERT: 3A 136 GLN cc_start: 0.8588 (mp10) cc_final: 0.8242 (mp10) REVERT: 3A 175 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8235 (mtm180) REVERT: 3A 329 MET cc_start: 0.9082 (mmm) cc_final: 0.8785 (mmt) REVERT: 3A 381 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (mtm110) REVERT: 3B 98 VAL cc_start: 0.9057 (t) cc_final: 0.8760 (t) REVERT: 3B 113 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8119 (ptm160) REVERT: 3C 108 MET cc_start: 0.9185 (mmt) cc_final: 0.8835 (mmp) REVERT: 3D 268 MET cc_start: 0.8280 (tpp) cc_final: 0.8040 (tpp) REVERT: 3D 284 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8267 (pp20) REVERT: 3E 121 THR cc_start: 0.9193 (m) cc_final: 0.8658 (p) REVERT: 3E 206 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7142 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7275 (t80) cc_final: 0.6786 (t80) REVERT: 3F 97 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7983 (tm-30) REVERT: 3G 38 ASN cc_start: 0.8592 (t0) cc_final: 0.7465 (t0) REVERT: 3G 66 GLN cc_start: 0.7832 (pt0) cc_final: 0.7518 (pt0) REVERT: 3G 70 LYS cc_start: 0.9382 (ttpp) cc_final: 0.9073 (mtmm) REVERT: 3H 53 GLU cc_start: 0.8085 (pp20) cc_final: 0.7665 (pp20) REVERT: 3H 54 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7643 (mmmt) REVERT: 3I 77 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7831 (ttp80) REVERT: 3J 49 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: 3N 383 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9077 (mp) REVERT: 3N 428 ILE cc_start: 0.9282 (pp) cc_final: 0.8953 (pt) REVERT: 3O 95 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8411 (mttm) REVERT: 3O 260 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: 3O 349 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: 3P 12 LYS cc_start: 0.8993 (tppt) cc_final: 0.8564 (mmtm) REVERT: 3P 80 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8134 (tmt90) REVERT: 3P 111 GLU cc_start: 0.8445 (mp0) cc_final: 0.8198 (mp0) REVERT: 3P 282 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8090 (mpp80) REVERT: 3P 316 MET cc_start: 0.8778 (tpp) cc_final: 0.8043 (tpp) REVERT: 3Q 211 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7557 (ttt) REVERT: 3R 149 MET cc_start: 0.8432 (mmt) cc_final: 0.8129 (mmt) REVERT: 3R 151 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7203 (pttp) REVERT: 3R 196 ARG cc_start: 0.3945 (ttt180) cc_final: 0.3713 (ttt180) REVERT: 3S 55 TYR cc_start: 0.8504 (t80) cc_final: 0.8295 (t80) REVERT: 3T 68 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8334 (mmmt) REVERT: 3U 39 LEU cc_start: 0.9446 (mt) cc_final: 0.9100 (mm) REVERT: 3W 15 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: 3W 23 THR cc_start: 0.9205 (m) cc_final: 0.8794 (p) REVERT: 3W 32 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8466 (tm-30) REVERT: 3X 12 GLU cc_start: 0.8660 (tt0) cc_final: 0.8385 (pt0) REVERT: 3X 23 MET cc_start: 0.9163 (ppp) cc_final: 0.8755 (ppp) REVERT: 3Y 12 GLU cc_start: 0.7878 (pm20) cc_final: 0.7453 (mp0) REVERT: 3Y 16 ASN cc_start: 0.9040 (m-40) cc_final: 0.8781 (m-40) outliers start: 169 outliers final: 62 residues processed: 660 average time/residue: 0.4514 time to fit residues: 481.9876 Evaluate side-chains 548 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 470 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 77 LYS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 105 ASP Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 182 LEU Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 381 ARG Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 253 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 320 LEU Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 301 MET Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 202 LEU Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3F residue 87 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 49 GLN Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 148 VAL Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 383 LEU Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 95 LYS Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 260 GLU Chi-restraints excluded: chain 3O residue 349 GLN Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 306 MET Chi-restraints excluded: chain 3P residue 372 ILE Chi-restraints excluded: chain 3P residue 373 GLU Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3Q residue 211 MET Chi-restraints excluded: chain 3R residue 151 LYS Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 248 ARG Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 227 optimal weight: 7.9990 chunk 370 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 189 HIS ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 264 ASN ** 3A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 339 GLN 3A 435 ASN 3B 174 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 80 HIS 3E 194 GLN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 51 GLN 3H 88 HIS 3N 118 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 279 HIS 3N 339 GLN 3O 394 GLN ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062628 restraints weight = 162756.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065654 restraints weight = 60756.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066582 restraints weight = 27534.659| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.443 34373 Z= 0.259 Angle : 0.748 18.098 46540 Z= 0.357 Chirality : 0.044 0.214 5004 Planarity : 0.005 0.053 5835 Dihedral : 13.864 142.918 5350 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.76 % Favored : 93.97 % Rotamer: Outliers : 5.88 % Allowed : 27.13 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4064 helix: 1.12 (0.11), residues: 2095 sheet: -1.33 (0.29), residues: 306 loop : -0.87 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP3E 210 HIS 0.007 0.001 HIS3W 57 PHE 0.031 0.002 PHE3T 55 TYR 0.034 0.002 TYR3E 243 ARG 0.008 0.001 ARG3N 179 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 1738) hydrogen bonds : angle 5.12224 ( 4981) metal coordination : bond 0.05362 ( 8) metal coordination : angle 10.64640 ( 6) SS BOND : bond 0.00211 ( 5) SS BOND : angle 1.54047 ( 10) covalent geometry : bond 0.00603 (34352) covalent geometry : angle 0.73808 (46524) Misc. bond : bond 0.24350 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 461 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 136 GLN cc_start: 0.8786 (mp10) cc_final: 0.8439 (mp10) REVERT: 3A 175 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8473 (mtm110) REVERT: 3B 108 THR cc_start: 0.9306 (m) cc_final: 0.8905 (p) REVERT: 3B 113 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7625 (ptm160) REVERT: 3B 370 MET cc_start: 0.9029 (mtt) cc_final: 0.8750 (mtt) REVERT: 3C 89 MET cc_start: 0.8465 (tpp) cc_final: 0.8101 (tpp) REVERT: 3C 108 MET cc_start: 0.9440 (mmt) cc_final: 0.9057 (mmp) REVERT: 3C 121 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: 3C 160 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8782 (mp) REVERT: 3C 171 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8174 (t70) REVERT: 3C 172 LYS cc_start: 0.8707 (mppt) cc_final: 0.8094 (mppt) REVERT: 3D 249 MET cc_start: 0.8968 (ttp) cc_final: 0.8533 (ttp) REVERT: 3D 274 ASP cc_start: 0.7904 (m-30) cc_final: 0.7482 (m-30) REVERT: 3D 284 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: 3E 140 MET cc_start: 0.8712 (mmt) cc_final: 0.8161 (mmp) REVERT: 3E 206 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7268 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6864 (t80) REVERT: 3F 50 TYR cc_start: 0.8384 (t80) cc_final: 0.7943 (t80) REVERT: 3F 97 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8003 (tm-30) REVERT: 3G 70 LYS cc_start: 0.9419 (ttpp) cc_final: 0.9019 (mtmm) REVERT: 3H 52 ILE cc_start: 0.8939 (tp) cc_final: 0.8554 (tp) REVERT: 3H 60 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8310 (tm-30) REVERT: 3N 428 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9313 (pt) REVERT: 3O 95 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8293 (mttm) REVERT: 3O 260 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: 3O 349 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8500 (pm20) REVERT: 3O 370 MET cc_start: 0.8770 (mtm) cc_final: 0.8569 (mtm) REVERT: 3O 394 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: 3O 400 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: 3P 80 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8031 (tmt90) REVERT: 3P 111 GLU cc_start: 0.8412 (mp0) cc_final: 0.8150 (mp0) REVERT: 3P 177 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7791 (ptm160) REVERT: 3P 215 MET cc_start: 0.8835 (pp-130) cc_final: 0.7323 (pp-130) REVERT: 3P 282 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8188 (mpp80) REVERT: 3Q 43 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: 3Q 80 MET cc_start: 0.8028 (mmp) cc_final: 0.7779 (mmp) REVERT: 3R 239 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4837 (t-90) REVERT: 3S 94 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9043 (tm) REVERT: 3T 59 TYR cc_start: 0.9200 (t80) cc_final: 0.8886 (t80) REVERT: 3U 72 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8817 (mtmm) REVERT: 3W 15 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.7901 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9200 (ppp) cc_final: 0.8938 (ppp) REVERT: 3Y 12 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: 3Y 43 ASP cc_start: 0.8362 (m-30) cc_final: 0.8070 (m-30) outliers start: 202 outliers final: 96 residues processed: 609 average time/residue: 0.4672 time to fit residues: 463.5814 Evaluate side-chains 547 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 429 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3A residue 435 ASN Chi-restraints excluded: chain 3B residue 24 LEU Chi-restraints excluded: chain 3B residue 63 LEU Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 111 CYS Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 253 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 29 SER Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 160 LEU Chi-restraints excluded: chain 3C residue 171 ASP Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 338 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 120 THR Chi-restraints excluded: chain 3E residue 170 ARG Chi-restraints excluded: chain 3E residue 202 LEU Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 235 TYR Chi-restraints excluded: chain 3E residue 260 VAL Chi-restraints excluded: chain 3F residue 87 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 78 ASP Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 279 HIS Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3N residue 428 ILE Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 95 LYS Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 209 LEU Chi-restraints excluded: chain 3O residue 244 ILE Chi-restraints excluded: chain 3O residue 260 GLU Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 349 GLN Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 394 GLN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 56 THR Chi-restraints excluded: chain 3P residue 78 VAL Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 303 LEU Chi-restraints excluded: chain 3P residue 306 MET Chi-restraints excluded: chain 3P residue 327 MET Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 43 MET Chi-restraints excluded: chain 3Q residue 71 GLN Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3U residue 72 LYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 398 optimal weight: 0.6980 chunk 377 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 320 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 264 ASN ** 3A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 194 GLN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 67 GLN 3N 252 HIS 3N 279 HIS ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066071 restraints weight = 127481.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068496 restraints weight = 53882.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070048 restraints weight = 30482.321| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.293 34373 Z= 0.131 Angle : 0.645 15.685 46540 Z= 0.310 Chirality : 0.041 0.217 5004 Planarity : 0.004 0.050 5835 Dihedral : 13.411 147.295 5344 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.80 % Favored : 94.93 % Rotamer: Outliers : 4.50 % Allowed : 28.31 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 4064 helix: 1.35 (0.11), residues: 2080 sheet: -1.31 (0.29), residues: 316 loop : -0.69 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP3E 210 HIS 0.007 0.001 HIS3N 279 PHE 0.021 0.001 PHE3R 175 TYR 0.020 0.001 TYR3Q 95 ARG 0.005 0.000 ARG3G 11 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1738) hydrogen bonds : angle 4.84767 ( 4981) metal coordination : bond 0.04562 ( 8) metal coordination : angle 9.16321 ( 6) SS BOND : bond 0.00225 ( 5) SS BOND : angle 1.14796 ( 10) covalent geometry : bond 0.00308 (34352) covalent geometry : angle 0.63608 (46524) Misc. bond : bond 0.17140 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 475 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 77 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9062 (tppp) REVERT: 3A 105 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7159 (p0) REVERT: 3A 136 GLN cc_start: 0.8613 (mp10) cc_final: 0.8267 (mp10) REVERT: 3A 175 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8529 (mtm110) REVERT: 3A 323 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8394 (t-90) REVERT: 3A 343 MET cc_start: 0.8977 (mmm) cc_final: 0.8338 (mmm) REVERT: 3A 434 TYR cc_start: 0.8942 (t80) cc_final: 0.8521 (t80) REVERT: 3B 108 THR cc_start: 0.9272 (m) cc_final: 0.8947 (p) REVERT: 3B 113 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7663 (ptm160) REVERT: 3B 370 MET cc_start: 0.8962 (mtt) cc_final: 0.8705 (mtt) REVERT: 3C 89 MET cc_start: 0.8384 (tpp) cc_final: 0.8031 (tpp) REVERT: 3C 108 MET cc_start: 0.9277 (mmt) cc_final: 0.9046 (mmp) REVERT: 3C 121 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: 3C 171 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.7960 (t70) REVERT: 3C 172 LYS cc_start: 0.8591 (mppt) cc_final: 0.7965 (mppt) REVERT: 3C 249 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8537 (tm) REVERT: 3D 133 TYR cc_start: 0.8167 (m-80) cc_final: 0.7871 (m-80) REVERT: 3D 268 MET cc_start: 0.8260 (tpp) cc_final: 0.7990 (tpp) REVERT: 3D 284 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8360 (pp20) REVERT: 3D 301 MET cc_start: 0.8767 (mmt) cc_final: 0.8120 (mmt) REVERT: 3E 121 THR cc_start: 0.9287 (m) cc_final: 0.8759 (p) REVERT: 3E 131 ASN cc_start: 0.8311 (t0) cc_final: 0.7870 (t0) REVERT: 3E 147 LEU cc_start: 0.9073 (pp) cc_final: 0.8865 (tt) REVERT: 3E 206 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7278 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7295 (t80) cc_final: 0.6873 (t80) REVERT: 3F 50 TYR cc_start: 0.8339 (t80) cc_final: 0.8051 (t80) REVERT: 3F 82 MET cc_start: 0.9184 (ttp) cc_final: 0.8815 (ttp) REVERT: 3F 97 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8031 (tm-30) REVERT: 3G 57 PHE cc_start: 0.9497 (t80) cc_final: 0.9248 (t80) REVERT: 3G 66 GLN cc_start: 0.7826 (pt0) cc_final: 0.7507 (pt0) REVERT: 3G 70 LYS cc_start: 0.9409 (ttpp) cc_final: 0.9016 (mtmm) REVERT: 3H 54 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7398 (mmmt) REVERT: 3H 60 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8230 (tm-30) REVERT: 3N 343 MET cc_start: 0.8970 (mmp) cc_final: 0.8763 (mmp) REVERT: 3O 260 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: 3O 349 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: 3O 400 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: 3P 80 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7866 (tmt90) REVERT: 3P 111 GLU cc_start: 0.8378 (mp0) cc_final: 0.8097 (mp0) REVERT: 3P 215 MET cc_start: 0.8749 (pp-130) cc_final: 0.7318 (pp-130) REVERT: 3P 282 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8245 (mpp80) REVERT: 3P 316 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8436 (ttm) REVERT: 3R 131 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8480 (t0) REVERT: 3S 94 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9056 (tm) REVERT: 3T 59 TYR cc_start: 0.9161 (t80) cc_final: 0.8835 (t80) REVERT: 3U 39 LEU cc_start: 0.9435 (mt) cc_final: 0.9229 (mt) REVERT: 3W 15 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.7705 (ttm-80) REVERT: 3Y 12 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7932 (pm20) outliers start: 154 outliers final: 87 residues processed: 585 average time/residue: 0.4477 time to fit residues: 424.6744 Evaluate side-chains 540 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 434 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 77 LYS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 105 ASP Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 171 ASP Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 249 LEU Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 282 ARG Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3D residue 319 LEU Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 87 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 67 GLN Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 78 TYR Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 260 GLU Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 349 GLN Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 303 LEU Chi-restraints excluded: chain 3P residue 306 MET Chi-restraints excluded: chain 3P residue 316 MET Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 212 MET Chi-restraints excluded: chain 3R residue 131 ASN Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 180 THR Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 248 ARG Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 23 MET Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 126 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 365 optimal weight: 0.8980 chunk 335 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 53 ASN ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 264 ASN ** 3A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 289 HIS ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3X 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064942 restraints weight = 135882.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067471 restraints weight = 55173.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069100 restraints weight = 30516.054| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.342 34373 Z= 0.182 Angle : 0.664 15.845 46540 Z= 0.318 Chirality : 0.042 0.255 5004 Planarity : 0.004 0.051 5835 Dihedral : 13.269 150.521 5342 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.20 % Favored : 94.51 % Rotamer: Outliers : 5.10 % Allowed : 28.28 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 4064 helix: 1.36 (0.11), residues: 2086 sheet: -1.25 (0.29), residues: 319 loop : -0.69 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP3N 443 HIS 0.007 0.001 HIS3T 6 PHE 0.028 0.001 PHE3O 223 TYR 0.016 0.001 TYR3Q 95 ARG 0.007 0.001 ARG3G 11 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 1738) hydrogen bonds : angle 4.81861 ( 4981) metal coordination : bond 0.04289 ( 8) metal coordination : angle 8.94357 ( 6) SS BOND : bond 0.00193 ( 5) SS BOND : angle 1.26541 ( 10) covalent geometry : bond 0.00434 (34352) covalent geometry : angle 0.65569 (46524) Misc. bond : bond 0.20137 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 432 time to evaluate : 3.546 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 23 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8816 (mm) REVERT: 3A 77 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9016 (tppp) REVERT: 3A 105 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7420 (p0) REVERT: 3A 136 GLN cc_start: 0.8629 (mp10) cc_final: 0.8385 (mp10) REVERT: 3A 175 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8452 (mtm110) REVERT: 3A 323 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8553 (t-90) REVERT: 3A 343 MET cc_start: 0.9003 (mmm) cc_final: 0.8385 (mmm) REVERT: 3B 108 THR cc_start: 0.9268 (m) cc_final: 0.8885 (p) REVERT: 3B 113 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7770 (ptm160) REVERT: 3B 120 MET cc_start: 0.8396 (ttp) cc_final: 0.8195 (ttp) REVERT: 3B 370 MET cc_start: 0.8988 (mtt) cc_final: 0.8724 (mtt) REVERT: 3C 89 MET cc_start: 0.8423 (tpp) cc_final: 0.8052 (tpp) REVERT: 3C 121 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: 3C 171 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8434 (t70) REVERT: 3C 172 LYS cc_start: 0.8558 (mppt) cc_final: 0.7924 (mmtm) REVERT: 3C 249 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8575 (tm) REVERT: 3C 378 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8036 (mmtt) REVERT: 3D 133 TYR cc_start: 0.8184 (m-80) cc_final: 0.7866 (m-80) REVERT: 3D 168 MET cc_start: 0.7616 (mmp) cc_final: 0.7391 (mmp) REVERT: 3D 284 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8329 (pp20) REVERT: 3D 301 MET cc_start: 0.8777 (mmt) cc_final: 0.8219 (mmt) REVERT: 3E 121 THR cc_start: 0.9337 (m) cc_final: 0.8796 (p) REVERT: 3E 131 ASN cc_start: 0.8430 (t0) cc_final: 0.7977 (t0) REVERT: 3E 140 MET cc_start: 0.8669 (tpp) cc_final: 0.8248 (mpp) REVERT: 3E 147 LEU cc_start: 0.9025 (pp) cc_final: 0.8788 (tt) REVERT: 3E 165 MET cc_start: 0.7032 (tpt) cc_final: 0.6781 (tpp) REVERT: 3E 206 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7333 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7267 (t80) cc_final: 0.6834 (t80) REVERT: 3F 80 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9157 (mm) REVERT: 3F 82 MET cc_start: 0.9269 (ttp) cc_final: 0.8881 (ttp) REVERT: 3F 84 GLN cc_start: 0.8209 (tt0) cc_final: 0.7999 (tt0) REVERT: 3F 97 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8040 (tm-30) REVERT: 3G 57 PHE cc_start: 0.9518 (t80) cc_final: 0.9239 (t80) REVERT: 3G 66 GLN cc_start: 0.7862 (pt0) cc_final: 0.7542 (pt0) REVERT: 3G 70 LYS cc_start: 0.9390 (ttpp) cc_final: 0.8981 (mtmm) REVERT: 3H 46 ARG cc_start: 0.8963 (mtp180) cc_final: 0.8232 (mtp180) REVERT: 3H 53 GLU cc_start: 0.8787 (pm20) cc_final: 0.8538 (pm20) REVERT: 3H 60 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8194 (tm-30) REVERT: 3N 343 MET cc_start: 0.9049 (mmp) cc_final: 0.8826 (mmp) REVERT: 3O 260 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: 3O 349 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: 3O 400 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: 3P 80 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7787 (tmt90) REVERT: 3P 111 GLU cc_start: 0.8404 (mp0) cc_final: 0.8114 (mp0) REVERT: 3P 177 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7733 (ptm160) REVERT: 3P 215 MET cc_start: 0.8859 (pp-130) cc_final: 0.7392 (pp-130) REVERT: 3P 235 MET cc_start: 0.9127 (tmm) cc_final: 0.8723 (tmm) REVERT: 3P 282 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (mpp80) REVERT: 3P 316 MET cc_start: 0.8700 (ttm) cc_final: 0.8458 (ttm) REVERT: 3Q 82 MET cc_start: 0.8017 (mmm) cc_final: 0.7110 (mmm) REVERT: 3R 131 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8439 (t0) REVERT: 3R 196 ARG cc_start: 0.4385 (ttt180) cc_final: 0.4139 (ttt180) REVERT: 3R 199 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6382 (tp-100) REVERT: 3S 94 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9019 (tm) REVERT: 3W 15 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: 3Y 12 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7927 (pm20) outliers start: 175 outliers final: 109 residues processed: 564 average time/residue: 0.4696 time to fit residues: 435.6197 Evaluate side-chains 545 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 414 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 77 LYS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 105 ASP Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 262 TRP Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3A residue 381 ARG Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 171 ASP Chi-restraints excluded: chain 3C residue 177 ARG Chi-restraints excluded: chain 3C residue 249 LEU Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3D residue 319 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3F residue 80 LEU Chi-restraints excluded: chain 3F residue 87 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 76 GLU Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 443 TRP Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 244 ILE Chi-restraints excluded: chain 3O residue 260 GLU Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 349 GLN Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 303 LEU Chi-restraints excluded: chain 3P residue 327 MET Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 72 ASP Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3Q residue 212 MET Chi-restraints excluded: chain 3R residue 131 ASN Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 180 THR Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 137 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 322 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 335 optimal weight: 3.9990 chunk 375 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 264 ASN 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 67 GLN ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3P 374 ASN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.080304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066682 restraints weight = 124492.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069172 restraints weight = 51960.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070746 restraints weight = 29175.738| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.303 34373 Z= 0.132 Angle : 0.638 13.735 46540 Z= 0.306 Chirality : 0.041 0.274 5004 Planarity : 0.004 0.058 5835 Dihedral : 13.018 152.671 5342 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.83 % Favored : 94.88 % Rotamer: Outliers : 4.81 % Allowed : 28.13 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 4064 helix: 1.46 (0.11), residues: 2088 sheet: -1.20 (0.29), residues: 325 loop : -0.60 (0.17), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP3N 443 HIS 0.005 0.001 HIS3N 279 PHE 0.022 0.001 PHE3R 175 TYR 0.017 0.001 TYR3S 21 ARG 0.010 0.000 ARG3F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1738) hydrogen bonds : angle 4.69885 ( 4981) metal coordination : bond 0.04471 ( 8) metal coordination : angle 7.86656 ( 6) SS BOND : bond 0.00148 ( 5) SS BOND : angle 1.09739 ( 10) covalent geometry : bond 0.00313 (34352) covalent geometry : angle 0.63211 (46524) Misc. bond : bond 0.17429 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 459 time to evaluate : 3.465 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 23 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8780 (mm) REVERT: 3A 58 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: 3A 77 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9025 (tppp) REVERT: 3A 105 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7261 (p0) REVERT: 3A 136 GLN cc_start: 0.8685 (mp10) cc_final: 0.8359 (mp10) REVERT: 3A 175 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8383 (mtm110) REVERT: 3A 323 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8588 (t-90) REVERT: 3A 343 MET cc_start: 0.9006 (mmm) cc_final: 0.8333 (mmm) REVERT: 3B 108 THR cc_start: 0.9298 (m) cc_final: 0.9009 (p) REVERT: 3B 113 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8393 (ptm160) REVERT: 3B 370 MET cc_start: 0.8990 (mtt) cc_final: 0.8713 (mtt) REVERT: 3C 121 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: 3C 171 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8380 (t70) REVERT: 3C 172 LYS cc_start: 0.8498 (mppt) cc_final: 0.8019 (mmtm) REVERT: 3C 249 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8534 (tm) REVERT: 3C 373 GLU cc_start: 0.8780 (tp30) cc_final: 0.8570 (tp30) REVERT: 3D 133 TYR cc_start: 0.8073 (m-80) cc_final: 0.7752 (m-80) REVERT: 3D 168 MET cc_start: 0.7678 (mmp) cc_final: 0.7462 (mmp) REVERT: 3D 268 MET cc_start: 0.8155 (tpp) cc_final: 0.7949 (tpp) REVERT: 3D 284 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: 3D 301 MET cc_start: 0.8742 (mmt) cc_final: 0.8146 (mmt) REVERT: 3E 121 THR cc_start: 0.9306 (m) cc_final: 0.8770 (p) REVERT: 3E 131 ASN cc_start: 0.8322 (t0) cc_final: 0.7900 (t0) REVERT: 3E 147 LEU cc_start: 0.9022 (pp) cc_final: 0.8775 (tt) REVERT: 3E 206 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7313 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7210 (t80) cc_final: 0.6797 (t80) REVERT: 3F 82 MET cc_start: 0.9264 (ttp) cc_final: 0.8866 (ttp) REVERT: 3F 84 GLN cc_start: 0.8149 (tt0) cc_final: 0.7933 (tt0) REVERT: 3F 97 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8054 (tm-30) REVERT: 3G 66 GLN cc_start: 0.7836 (pt0) cc_final: 0.7513 (pt0) REVERT: 3G 70 LYS cc_start: 0.9376 (ttpp) cc_final: 0.8978 (mtmm) REVERT: 3H 46 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8243 (mtp180) REVERT: 3H 53 GLU cc_start: 0.8814 (pm20) cc_final: 0.8603 (pm20) REVERT: 3H 54 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8073 (mmmt) REVERT: 3H 60 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8265 (tm-30) REVERT: 3N 343 MET cc_start: 0.8982 (mmp) cc_final: 0.8779 (mmp) REVERT: 3P 80 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7926 (tmt90) REVERT: 3P 177 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7575 (ptm160) REVERT: 3P 215 MET cc_start: 0.9004 (pp-130) cc_final: 0.7655 (pp-130) REVERT: 3P 235 MET cc_start: 0.9109 (tmm) cc_final: 0.8680 (tmm) REVERT: 3P 282 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8104 (mpp80) REVERT: 3P 316 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8394 (ttm) REVERT: 3Q 82 MET cc_start: 0.7937 (mmm) cc_final: 0.7655 (mmm) REVERT: 3Q 211 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (tpp) REVERT: 3R 131 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8501 (t0) REVERT: 3R 199 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6446 (tp-100) REVERT: 3S 94 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9006 (tm) REVERT: 3W 15 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9115 (tmm) cc_final: 0.8881 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7915 (pm20) outliers start: 165 outliers final: 111 residues processed: 582 average time/residue: 0.4376 time to fit residues: 414.8031 Evaluate side-chains 559 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 427 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 36 THR Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 77 LYS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 105 ASP Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 262 TRP Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3A residue 383 LEU Chi-restraints excluded: chain 3A residue 435 ASN Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 171 ASP Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 249 LEU Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 227 THR Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3F residue 87 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 67 GLN Chi-restraints excluded: chain 3H residue 76 GLU Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3N residue 443 TRP Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 349 GLN Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 303 LEU Chi-restraints excluded: chain 3P residue 316 MET Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 72 ASP Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3Q residue 211 MET Chi-restraints excluded: chain 3Q residue 212 MET Chi-restraints excluded: chain 3R residue 131 ASN Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 248 ARG Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 315 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 313 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 386 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 264 ASN 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 375 ASN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 257 ASN 3F 91 GLN ** 3G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 359 ASN ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 31 GLN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.076910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063612 restraints weight = 127264.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065990 restraints weight = 53139.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067484 restraints weight = 30004.633| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.456 34373 Z= 0.290 Angle : 0.749 16.982 46540 Z= 0.361 Chirality : 0.045 0.351 5004 Planarity : 0.005 0.068 5835 Dihedral : 13.266 162.950 5342 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.84 % Favored : 93.87 % Rotamer: Outliers : 4.96 % Allowed : 28.42 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 4064 helix: 1.25 (0.11), residues: 2089 sheet: -1.16 (0.30), residues: 318 loop : -0.77 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP3N 443 HIS 0.008 0.001 HIS3T 6 PHE 0.041 0.002 PHE3O 223 TYR 0.018 0.002 TYR3P 223 ARG 0.009 0.001 ARG3G 11 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1738) hydrogen bonds : angle 4.93412 ( 4981) metal coordination : bond 0.04277 ( 8) metal coordination : angle 8.73596 ( 6) SS BOND : bond 0.00241 ( 5) SS BOND : angle 1.17280 ( 10) covalent geometry : bond 0.00673 (34352) covalent geometry : angle 0.74230 (46524) Misc. bond : bond 0.29433 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 413 time to evaluate : 4.108 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 136 GLN cc_start: 0.8689 (mp10) cc_final: 0.8432 (mp10) REVERT: 3A 175 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8463 (mtm110) REVERT: 3A 323 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8487 (t-90) REVERT: 3A 343 MET cc_start: 0.9055 (mmm) cc_final: 0.8493 (mmm) REVERT: 3B 108 THR cc_start: 0.9325 (m) cc_final: 0.8910 (p) REVERT: 3B 113 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8196 (ppp80) REVERT: 3B 114 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: 3B 268 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7642 (mm-30) REVERT: 3B 370 MET cc_start: 0.9083 (mtt) cc_final: 0.8839 (mtt) REVERT: 3C 121 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: 3C 172 LYS cc_start: 0.8500 (mppt) cc_final: 0.8092 (mmtm) REVERT: 3C 249 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8569 (tm) REVERT: 3C 373 GLU cc_start: 0.8945 (tp30) cc_final: 0.8671 (tp30) REVERT: 3C 375 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8358 (t0) REVERT: 3D 133 TYR cc_start: 0.8374 (m-80) cc_final: 0.8003 (m-80) REVERT: 3D 168 MET cc_start: 0.7646 (mmp) cc_final: 0.7407 (mmp) REVERT: 3D 190 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7966 (mtt90) REVERT: 3D 249 MET cc_start: 0.8817 (ttm) cc_final: 0.8593 (ttm) REVERT: 3D 253 ILE cc_start: 0.9337 (tp) cc_final: 0.9092 (tp) REVERT: 3D 284 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8413 (pp20) REVERT: 3D 301 MET cc_start: 0.8702 (mmt) cc_final: 0.8274 (mmt) REVERT: 3E 131 ASN cc_start: 0.8303 (t0) cc_final: 0.7834 (t0) REVERT: 3E 140 MET cc_start: 0.8617 (tpp) cc_final: 0.8208 (mpp) REVERT: 3E 206 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7381 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6854 (t80) REVERT: 3F 54 ASP cc_start: 0.8988 (p0) cc_final: 0.8692 (p0) REVERT: 3F 82 MET cc_start: 0.9396 (ttp) cc_final: 0.9091 (ttp) REVERT: 3F 84 GLN cc_start: 0.8283 (tt0) cc_final: 0.7953 (tt0) REVERT: 3F 97 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8210 (tm-30) REVERT: 3G 47 ILE cc_start: 0.9256 (tp) cc_final: 0.9053 (tp) REVERT: 3H 46 ARG cc_start: 0.8910 (mtp180) cc_final: 0.8147 (mtp180) REVERT: 3H 53 GLU cc_start: 0.8899 (pm20) cc_final: 0.8665 (pm20) REVERT: 3H 54 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8075 (mmmt) REVERT: 3H 60 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8267 (tm-30) REVERT: 3O 147 ASP cc_start: 0.8656 (t0) cc_final: 0.8363 (t0) REVERT: 3O 400 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: 3P 80 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7686 (tmt90) REVERT: 3P 177 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7957 (ptm160) REVERT: 3P 215 MET cc_start: 0.9195 (pp-130) cc_final: 0.7609 (pp-130) REVERT: 3P 235 MET cc_start: 0.9171 (tmm) cc_final: 0.8780 (tmm) REVERT: 3P 282 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8159 (mpp80) REVERT: 3P 315 MET cc_start: 0.8925 (ttm) cc_final: 0.8707 (mtm) REVERT: 3Q 82 MET cc_start: 0.7920 (mmm) cc_final: 0.7426 (mmm) REVERT: 3Q 211 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8022 (ttt) REVERT: 3R 199 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6332 (tp-100) REVERT: 3S 83 TYR cc_start: 0.8851 (t80) cc_final: 0.8594 (t80) REVERT: 3S 94 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9011 (tm) REVERT: 3W 15 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9033 (tmm) cc_final: 0.8761 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7952 (pm20) outliers start: 170 outliers final: 124 residues processed: 541 average time/residue: 0.4665 time to fit residues: 406.7383 Evaluate side-chains 529 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 386 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 36 THR Chi-restraints excluded: chain 3A residue 41 ILE Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 67 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3A residue 381 ARG Chi-restraints excluded: chain 3B residue 63 LEU Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 95 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 114 ASP Chi-restraints excluded: chain 3B residue 119 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 129 MET Chi-restraints excluded: chain 3C residue 177 ARG Chi-restraints excluded: chain 3C residue 249 LEU Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 271 GLU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3C residue 375 ASN Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 190 ARG Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 227 THR Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 104 LYS Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 235 TYR Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 78 ASP Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 244 ILE Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 338 LYS Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 303 LEU Chi-restraints excluded: chain 3P residue 327 MET Chi-restraints excluded: chain 3P residue 372 ILE Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 72 ASP Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3Q residue 211 MET Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 2 LEU Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 43 optimal weight: 0.9990 chunk 132 optimal weight: 0.0980 chunk 328 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 355 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 375 ASN ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 67 GLN 3N 94 HIS ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065502 restraints weight = 125105.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067941 restraints weight = 52283.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069486 restraints weight = 29435.013| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.393 34373 Z= 0.142 Angle : 0.661 13.795 46540 Z= 0.317 Chirality : 0.042 0.239 5004 Planarity : 0.004 0.053 5835 Dihedral : 12.991 163.609 5342 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.88 % Favored : 94.85 % Rotamer: Outliers : 4.55 % Allowed : 28.97 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 4064 helix: 1.46 (0.11), residues: 2075 sheet: -1.19 (0.29), residues: 324 loop : -0.58 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP3N 443 HIS 0.007 0.001 HIS3T 6 PHE 0.033 0.001 PHE3E 231 TYR 0.019 0.001 TYR3F 50 ARG 0.008 0.000 ARG3G 11 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1738) hydrogen bonds : angle 4.72209 ( 4981) metal coordination : bond 0.04767 ( 8) metal coordination : angle 7.78467 ( 6) SS BOND : bond 0.00139 ( 5) SS BOND : angle 1.07187 ( 10) covalent geometry : bond 0.00336 (34352) covalent geometry : angle 0.65466 (46524) Misc. bond : bond 0.21830 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 440 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 23 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8808 (mm) REVERT: 3A 175 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8470 (mtm110) REVERT: 3A 323 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (t-90) REVERT: 3A 343 MET cc_start: 0.9045 (mmm) cc_final: 0.8411 (mmm) REVERT: 3B 108 THR cc_start: 0.9300 (m) cc_final: 0.8925 (p) REVERT: 3B 113 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6470 (ptp90) REVERT: 3B 114 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: 3B 268 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7575 (mm-30) REVERT: 3B 370 MET cc_start: 0.9024 (mtt) cc_final: 0.8762 (mtt) REVERT: 3C 121 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: 3C 172 LYS cc_start: 0.8383 (mppt) cc_final: 0.8020 (mmtm) REVERT: 3C 304 MET cc_start: 0.8201 (tpp) cc_final: 0.7984 (tpp) REVERT: 3C 373 GLU cc_start: 0.8956 (tp30) cc_final: 0.8679 (tp30) REVERT: 3C 375 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8352 (t0) REVERT: 3D 133 TYR cc_start: 0.8226 (m-80) cc_final: 0.7973 (m-80) REVERT: 3D 168 MET cc_start: 0.7612 (mmp) cc_final: 0.7369 (mmp) REVERT: 3D 253 ILE cc_start: 0.9307 (tp) cc_final: 0.9104 (tp) REVERT: 3D 268 MET cc_start: 0.8304 (tpp) cc_final: 0.8039 (tpp) REVERT: 3D 284 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8441 (pp20) REVERT: 3D 301 MET cc_start: 0.8781 (mmt) cc_final: 0.8175 (mmt) REVERT: 3E 140 MET cc_start: 0.8610 (tpp) cc_final: 0.8222 (mpp) REVERT: 3E 206 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7392 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7276 (t80) cc_final: 0.6838 (t80) REVERT: 3F 54 ASP cc_start: 0.8897 (p0) cc_final: 0.8637 (p0) REVERT: 3F 82 MET cc_start: 0.9353 (ttp) cc_final: 0.9047 (ttp) REVERT: 3F 97 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8222 (tm-30) REVERT: 3G 46 CYS cc_start: 0.7855 (p) cc_final: 0.7643 (p) REVERT: 3H 46 ARG cc_start: 0.8917 (mtp180) cc_final: 0.8437 (mtp180) REVERT: 3H 53 GLU cc_start: 0.8797 (pm20) cc_final: 0.8576 (pm20) REVERT: 3H 54 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8124 (mmmt) REVERT: 3H 60 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8338 (tm-30) REVERT: 3O 147 ASP cc_start: 0.8580 (t0) cc_final: 0.8334 (t0) REVERT: 3O 370 MET cc_start: 0.8673 (mtm) cc_final: 0.8307 (mtm) REVERT: 3O 400 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: 3P 80 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7894 (tmt90) REVERT: 3P 177 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7747 (ptm160) REVERT: 3P 215 MET cc_start: 0.8888 (pp-130) cc_final: 0.7620 (pp-130) REVERT: 3P 235 MET cc_start: 0.9152 (tmm) cc_final: 0.8734 (tmm) REVERT: 3P 282 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8189 (mpp80) REVERT: 3P 316 MET cc_start: 0.8738 (ttm) cc_final: 0.8226 (ttm) REVERT: 3Q 72 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5920 (m-30) REVERT: 3R 191 GLU cc_start: 0.8752 (pt0) cc_final: 0.8517 (pp20) REVERT: 3R 199 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6423 (tp-100) REVERT: 3S 83 TYR cc_start: 0.8826 (t80) cc_final: 0.8500 (t80) REVERT: 3S 94 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9024 (tm) REVERT: 3U 65 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8623 (ttp80) REVERT: 3W 15 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7743 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9037 (tmm) cc_final: 0.8752 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7934 (pm20) outliers start: 156 outliers final: 108 residues processed: 564 average time/residue: 0.4847 time to fit residues: 438.7255 Evaluate side-chains 532 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 406 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 36 THR Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 67 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 262 TRP Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 335 MET Chi-restraints excluded: chain 3A residue 435 ASN Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 114 ASP Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 212 SER Chi-restraints excluded: chain 3B residue 244 ILE Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 371 ILE Chi-restraints excluded: chain 3C residue 375 ASN Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 227 THR Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 80 THR Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 338 LYS Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 72 ASP Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3Q residue 212 MET Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 248 ARG Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 65 ARG Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 59 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 382 optimal weight: 0.6980 chunk 342 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 324 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN 3C 114 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 375 ASN ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 91 GLN 3H 67 GLN ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064832 restraints weight = 163148.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067556 restraints weight = 61706.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069265 restraints weight = 32893.534| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.373 34373 Z= 0.153 Angle : 0.680 13.917 46540 Z= 0.325 Chirality : 0.042 0.263 5004 Planarity : 0.004 0.053 5835 Dihedral : 12.811 165.515 5339 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.22 % Favored : 94.51 % Rotamer: Outliers : 4.18 % Allowed : 28.97 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 4064 helix: 1.47 (0.11), residues: 2083 sheet: -1.15 (0.30), residues: 324 loop : -0.56 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP3N 443 HIS 0.008 0.001 HIS3T 6 PHE 0.033 0.001 PHE3E 231 TYR 0.018 0.001 TYR3F 50 ARG 0.010 0.001 ARG3H 59 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 1738) hydrogen bonds : angle 4.70991 ( 4981) metal coordination : bond 0.04638 ( 8) metal coordination : angle 7.24452 ( 6) SS BOND : bond 0.00139 ( 5) SS BOND : angle 1.08278 ( 10) covalent geometry : bond 0.00365 (34352) covalent geometry : angle 0.67453 (46524) Misc. bond : bond 0.21828 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 424 time to evaluate : 7.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 23 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8804 (mm) REVERT: 3A 105 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7245 (p0) REVERT: 3A 175 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8432 (mtm110) REVERT: 3A 323 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8571 (t-90) REVERT: 3A 334 MET cc_start: 0.9292 (tpp) cc_final: 0.9081 (tpt) REVERT: 3A 343 MET cc_start: 0.9006 (mmm) cc_final: 0.8407 (mmm) REVERT: 3B 108 THR cc_start: 0.9314 (m) cc_final: 0.8912 (p) REVERT: 3B 113 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6639 (ptp90) REVERT: 3B 114 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: 3B 268 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7555 (mm-30) REVERT: 3B 370 MET cc_start: 0.9033 (mtt) cc_final: 0.8780 (mtt) REVERT: 3C 121 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8111 (m-10) REVERT: 3C 172 LYS cc_start: 0.8392 (mppt) cc_final: 0.8058 (mmtm) REVERT: 3C 177 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (ptp-170) REVERT: 3C 304 MET cc_start: 0.8146 (tpp) cc_final: 0.7923 (tpp) REVERT: 3C 373 GLU cc_start: 0.8888 (tp30) cc_final: 0.8642 (tp30) REVERT: 3C 375 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8208 (t0) REVERT: 3D 133 TYR cc_start: 0.8271 (m-80) cc_final: 0.8053 (m-80) REVERT: 3D 168 MET cc_start: 0.7651 (mmp) cc_final: 0.7391 (mmp) REVERT: 3D 268 MET cc_start: 0.8316 (tpp) cc_final: 0.8043 (tpp) REVERT: 3D 284 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: 3D 301 MET cc_start: 0.8825 (mmt) cc_final: 0.8227 (mmt) REVERT: 3E 140 MET cc_start: 0.8608 (tpp) cc_final: 0.8156 (mpp) REVERT: 3E 206 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7415 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7218 (t80) cc_final: 0.6790 (t80) REVERT: 3F 54 ASP cc_start: 0.9007 (p0) cc_final: 0.8670 (p0) REVERT: 3F 82 MET cc_start: 0.9337 (ttp) cc_final: 0.8901 (ttp) REVERT: 3F 97 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8241 (tm-30) REVERT: 3H 46 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8431 (mtp180) REVERT: 3H 54 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8108 (mmmt) REVERT: 3H 60 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8336 (tm-30) REVERT: 3O 145 ARG cc_start: 0.7592 (tmt170) cc_final: 0.7228 (tmt170) REVERT: 3O 147 ASP cc_start: 0.8613 (t0) cc_final: 0.8353 (t0) REVERT: 3O 400 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: 3P 80 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7975 (tmt90) REVERT: 3P 177 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7769 (ptm160) REVERT: 3P 215 MET cc_start: 0.8889 (pp-130) cc_final: 0.7627 (pp-130) REVERT: 3P 235 MET cc_start: 0.9166 (tmm) cc_final: 0.8790 (tmm) REVERT: 3P 282 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8189 (mpp80) REVERT: 3P 316 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8302 (ttm) REVERT: 3Q 208 MET cc_start: 0.9038 (tmm) cc_final: 0.8681 (tmm) REVERT: 3R 153 GLU cc_start: 0.7874 (mp0) cc_final: 0.7515 (mp0) REVERT: 3R 191 GLU cc_start: 0.8752 (pt0) cc_final: 0.8512 (pp20) REVERT: 3R 199 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6426 (tp-100) REVERT: 3S 94 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9016 (tm) REVERT: 3U 65 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8573 (ttp80) REVERT: 3V 52 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7494 (mtt90) REVERT: 3W 15 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.7747 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9018 (tmm) cc_final: 0.8723 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7922 (pm20) outliers start: 143 outliers final: 111 residues processed: 537 average time/residue: 0.5769 time to fit residues: 505.0146 Evaluate side-chains 538 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 407 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 36 THR Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 67 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 105 ASP Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 262 TRP Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 435 ASN Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 95 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 114 ASP Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 177 ARG Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 338 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 371 ILE Chi-restraints excluded: chain 3C residue 375 ASN Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 92 ILE Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 316 MET Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 248 ARG Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 65 ARG Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 42 LEU Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 2 LEU Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 393 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 375 ASN ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064647 restraints weight = 141848.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067187 restraints weight = 56523.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068797 restraints weight = 31282.407| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.393 34373 Z= 0.182 Angle : 0.698 15.261 46540 Z= 0.332 Chirality : 0.043 0.305 5004 Planarity : 0.004 0.061 5835 Dihedral : 12.759 170.261 5339 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.44 % Favored : 94.29 % Rotamer: Outliers : 4.18 % Allowed : 29.17 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 4064 helix: 1.45 (0.11), residues: 2083 sheet: -1.15 (0.30), residues: 326 loop : -0.58 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP3N 443 HIS 0.006 0.001 HIS3T 6 PHE 0.034 0.001 PHE3E 231 TYR 0.038 0.001 TYR3S 83 ARG 0.009 0.001 ARG3H 59 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 1738) hydrogen bonds : angle 4.73780 ( 4981) metal coordination : bond 0.04602 ( 8) metal coordination : angle 7.07778 ( 6) SS BOND : bond 0.00177 ( 5) SS BOND : angle 1.07237 ( 10) covalent geometry : bond 0.00432 (34352) covalent geometry : angle 0.69320 (46524) Misc. bond : bond 0.24009 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 412 time to evaluate : 3.764 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 154 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 23 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8814 (mm) REVERT: 3A 136 GLN cc_start: 0.8780 (mp10) cc_final: 0.8514 (mp10) REVERT: 3A 175 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8381 (mtm110) REVERT: 3A 323 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8615 (t-90) REVERT: 3A 334 MET cc_start: 0.9335 (tpp) cc_final: 0.9104 (tpt) REVERT: 3A 343 MET cc_start: 0.9017 (mmm) cc_final: 0.8426 (mmm) REVERT: 3B 108 THR cc_start: 0.9336 (m) cc_final: 0.8926 (p) REVERT: 3B 113 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6633 (ptp90) REVERT: 3B 114 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: 3B 370 MET cc_start: 0.9042 (mtt) cc_final: 0.8801 (mtt) REVERT: 3C 121 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: 3C 171 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8481 (t70) REVERT: 3C 172 LYS cc_start: 0.8389 (mppt) cc_final: 0.7897 (mmtm) REVERT: 3C 373 GLU cc_start: 0.8862 (tp30) cc_final: 0.8629 (tp30) REVERT: 3C 375 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8143 (t0) REVERT: 3D 133 TYR cc_start: 0.8296 (m-80) cc_final: 0.8081 (m-80) REVERT: 3D 168 MET cc_start: 0.7677 (mmp) cc_final: 0.7415 (mmp) REVERT: 3D 268 MET cc_start: 0.8310 (tpp) cc_final: 0.8078 (tpp) REVERT: 3D 284 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8399 (pp20) REVERT: 3D 301 MET cc_start: 0.8869 (mmt) cc_final: 0.8311 (mmt) REVERT: 3E 140 MET cc_start: 0.8629 (tpp) cc_final: 0.8210 (mpp) REVERT: 3E 206 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7421 (mmmt) REVERT: 3E 235 TYR cc_start: 0.7261 (t80) cc_final: 0.6820 (t80) REVERT: 3F 54 ASP cc_start: 0.8943 (p0) cc_final: 0.8714 (p0) REVERT: 3F 82 MET cc_start: 0.9293 (ttp) cc_final: 0.8865 (ttp) REVERT: 3F 97 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8271 (tm-30) REVERT: 3H 46 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8416 (mtp180) REVERT: 3H 60 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8360 (tm-30) REVERT: 3O 145 ARG cc_start: 0.7672 (tmt170) cc_final: 0.7313 (tmt170) REVERT: 3O 147 ASP cc_start: 0.8697 (t0) cc_final: 0.8411 (t0) REVERT: 3O 400 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: 3P 80 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7981 (tmt90) REVERT: 3P 177 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: 3P 215 MET cc_start: 0.8895 (pp-130) cc_final: 0.7633 (pp-130) REVERT: 3P 235 MET cc_start: 0.9164 (tmm) cc_final: 0.8802 (tmm) REVERT: 3P 282 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8196 (mpp80) REVERT: 3P 316 MET cc_start: 0.8751 (ttm) cc_final: 0.8334 (ttp) REVERT: 3Q 208 MET cc_start: 0.9080 (tmm) cc_final: 0.8766 (tmm) REVERT: 3R 153 GLU cc_start: 0.7842 (mp0) cc_final: 0.7532 (mp0) REVERT: 3R 191 GLU cc_start: 0.8733 (pt0) cc_final: 0.8424 (pp20) REVERT: 3R 199 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6535 (tp-100) REVERT: 3S 94 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9020 (tm) REVERT: 3U 65 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8652 (ttp80) REVERT: 3W 15 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.7786 (ttm-80) REVERT: 3X 23 MET cc_start: 0.9021 (tmm) cc_final: 0.8733 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: 3Y 38 TRP cc_start: 0.9247 (t60) cc_final: 0.8952 (t60) outliers start: 143 outliers final: 115 residues processed: 526 average time/residue: 0.4919 time to fit residues: 416.9547 Evaluate side-chains 539 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 406 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 36 THR Chi-restraints excluded: chain 3A residue 41 ILE Chi-restraints excluded: chain 3A residue 50 GLU Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 67 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 175 ARG Chi-restraints excluded: chain 3A residue 176 LYS Chi-restraints excluded: chain 3A residue 203 VAL Chi-restraints excluded: chain 3A residue 248 LEU Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 435 ASN Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 95 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 113 ARG Chi-restraints excluded: chain 3B residue 114 ASP Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 212 SER Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 121 PHE Chi-restraints excluded: chain 3C residue 122 THR Chi-restraints excluded: chain 3C residue 171 ASP Chi-restraints excluded: chain 3C residue 264 THR Chi-restraints excluded: chain 3C residue 267 HIS Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 294 LEU Chi-restraints excluded: chain 3C residue 299 LEU Chi-restraints excluded: chain 3C residue 338 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 371 ILE Chi-restraints excluded: chain 3C residue 375 ASN Chi-restraints excluded: chain 3D residue 112 THR Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 194 ASN Chi-restraints excluded: chain 3D residue 227 THR Chi-restraints excluded: chain 3D residue 284 GLU Chi-restraints excluded: chain 3D residue 304 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 206 LYS Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3F residue 49 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 36 ILE Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 69 GLU Chi-restraints excluded: chain 3H residue 67 GLN Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 51 CYS Chi-restraints excluded: chain 3I residue 65 VAL Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 18 THR Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 195 MET Chi-restraints excluded: chain 3N residue 203 VAL Chi-restraints excluded: chain 3N residue 220 SER Chi-restraints excluded: chain 3N residue 228 VAL Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 288 THR Chi-restraints excluded: chain 3N residue 307 PHE Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 26 PHE Chi-restraints excluded: chain 3O residue 34 VAL Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 154 ASN Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 196 GLN Chi-restraints excluded: chain 3O residue 285 VAL Chi-restraints excluded: chain 3O residue 326 THR Chi-restraints excluded: chain 3O residue 354 ASN Chi-restraints excluded: chain 3O residue 400 GLN Chi-restraints excluded: chain 3P residue 54 HIS Chi-restraints excluded: chain 3P residue 56 THR Chi-restraints excluded: chain 3P residue 80 ARG Chi-restraints excluded: chain 3P residue 92 ILE Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 177 ARG Chi-restraints excluded: chain 3P residue 271 GLU Chi-restraints excluded: chain 3P residue 281 LEU Chi-restraints excluded: chain 3P residue 282 ARG Chi-restraints excluded: chain 3P residue 287 LYS Chi-restraints excluded: chain 3Q residue 32 VAL Chi-restraints excluded: chain 3Q residue 199 ASP Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 199 GLN Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 239 HIS Chi-restraints excluded: chain 3R residue 258 LEU Chi-restraints excluded: chain 3R residue 260 VAL Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3S residue 94 LEU Chi-restraints excluded: chain 3T residue 19 SER Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 38 GLU Chi-restraints excluded: chain 3U residue 65 ARG Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 42 LEU Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 2 LEU Chi-restraints excluded: chain 3Y residue 12 GLU Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 32 LEU Chi-restraints excluded: chain 3Y residue 40 LEU Chi-restraints excluded: chain 3Y residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 227 optimal weight: 0.5980 chunk 281 optimal weight: 6.9990 chunk 187 optimal weight: 0.0570 chunk 352 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 325 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 147 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 435 ASN ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 375 ASN ** 3D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 135 GLN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 85 HIS ** 3P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3R 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068015 restraints weight = 128554.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070555 restraints weight = 53112.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072165 restraints weight = 29648.762| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.291 34373 Z= 0.125 Angle : 0.687 14.555 46540 Z= 0.327 Chirality : 0.042 0.333 5004 Planarity : 0.004 0.053 5835 Dihedral : 12.411 170.894 5339 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.56 % Favored : 95.17 % Rotamer: Outliers : 3.63 % Allowed : 29.78 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 4064 helix: 1.52 (0.11), residues: 2068 sheet: -1.10 (0.30), residues: 324 loop : -0.52 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP3R 169 HIS 0.006 0.001 HIS3T 6 PHE 0.037 0.001 PHE3E 231 TYR 0.029 0.001 TYR3S 83 ARG 0.011 0.001 ARG3A 436 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1738) hydrogen bonds : angle 4.62069 ( 4981) metal coordination : bond 0.04838 ( 8) metal coordination : angle 6.52930 ( 6) SS BOND : bond 0.00177 ( 5) SS BOND : angle 1.01588 ( 10) covalent geometry : bond 0.00284 (34352) covalent geometry : angle 0.68294 (46524) Misc. bond : bond 0.17153 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13331.93 seconds wall clock time: 236 minutes 46.66 seconds (14206.66 seconds total)