Starting phenix.real_space_refine on Sun Jan 26 02:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.map" model { file = "/net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etj_24396/01_2025/8etj_24396.cif" } resolution = 3.2 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1961 5.49 5 S 99 5.16 5 C 42587 2.51 5 N 14882 2.21 5 O 20327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 79857 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 38913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1817, 38913 Classifications: {'RNA': 1817} Modifications used: {'rna2p_pur': 191, 'rna2p_pyr': 124, 'rna3p_pur': 839, 'rna3p_pyr': 663} Link IDs: {'rna2p': 314, 'rna3p': 1502} Chain breaks: 23 Chain: "2" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3069 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 8, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 23, 'rna3p': 120} Chain breaks: 3 Chain: "3" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1042 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2662 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2553 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 307} Chain breaks: 1 Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1283 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "F" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1307 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1290 Chain: "H" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "L" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1427 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Chain: "Q" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1032 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 278 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "V" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1026 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "W" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1057 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "a" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2837 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 246 Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "e" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "r" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1086 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Chain: "s" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 257 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "w" Number of atoms: 521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 509 Chain: "y" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "T" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 126 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 74416 SG CYS j 19 102.156 110.610 169.175 1.00 64.08 S ATOM 74444 SG CYS j 22 104.321 111.786 166.256 1.00 65.72 S ATOM 74540 SG CYS j 34 103.712 108.119 166.669 1.00 70.97 S ATOM 74557 SG CYS j 37 105.785 109.789 169.278 1.00 62.80 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASN G 182 " occ=0.62 ... (14 atoms not shown) pdb=" ND2BASN G 182 " occ=0.38 residue: pdb=" N AASP G 227 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.50 residue: pdb=" N AGLU w 243 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU w 243 " occ=0.50 Time building chain proxies: 32.62, per 1000 atoms: 0.41 Number of scatterers: 79857 At special positions: 0 Unit cell: (217.3, 178.08, 256.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 1961 15.00 O 20327 8.00 N 14882 7.00 C 42587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.92 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " Number of angles added : 6 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9394 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 57 sheets defined 43.2% alpha, 14.2% beta 586 base pairs and 1132 stacking pairs defined. Time for finding SS restraints: 31.35 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 72 through 77 removed outlier: 4.558A pdb=" N TRP 3 77 " --> pdb=" O PRO 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 96 Processing helix chain '3' and resid 104 through 124 removed outlier: 3.752A pdb=" N GLN 3 110 " --> pdb=" O HIS 3 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 3 113 " --> pdb=" O LYS 3 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG 3 114 " --> pdb=" O GLN 3 110 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU 3 119 " --> pdb=" O LEU 3 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 4.035A pdb=" N PHE B 16 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.738A pdb=" N ARG C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.095A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.872A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.576A pdb=" N LEU C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 4.186A pdb=" N TYR C 337 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.996A pdb=" N PHE E 65 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.902A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.709A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 36 through 80 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.708A pdb=" N GLN F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.512A pdb=" N VAL F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.112A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.565A pdb=" N ALA F 206 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.523A pdb=" N GLY F 232 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 241 No H-bonds generated for 'chain 'F' and resid 239 through 241' Processing helix chain 'F' and resid 242 through 250 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.678A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 5.113A pdb=" N PHE G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.713A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.054A pdb=" N LEU G 186 " --> pdb=" O AASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.116A pdb=" N ASN G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 66 through 84 removed outlier: 3.815A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 148 through 163 removed outlier: 3.528A pdb=" N CYS H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.882A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.575A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 3.996A pdb=" N GLY L 131 " --> pdb=" O PRO L 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.645A pdb=" N VAL L 152 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 175 through 200 removed outlier: 4.456A pdb=" N ASN L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.841A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 8 " --> pdb=" O TYR N 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.509A pdb=" N ARG N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 removed outlier: 3.717A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.579A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.624A pdb=" N VAL O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 41 removed outlier: 3.649A pdb=" N GLU O 41 " --> pdb=" O ARG O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 38 through 41' Processing helix chain 'O' and resid 47 through 59 removed outlier: 3.681A pdb=" N TYR O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 Processing helix chain 'O' and resid 187 through 196 removed outlier: 3.921A pdb=" N SER O 193 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN O 194 " --> pdb=" O LYS O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 36 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.541A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.707A pdb=" N LEU P 112 " --> pdb=" O MET P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 183 removed outlier: 3.793A pdb=" N ALA P 183 " --> pdb=" O ALA P 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.511A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 58 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 removed outlier: 3.757A pdb=" N ALA Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 130 through 134 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 134 Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.661A pdb=" N LEU W 53 " --> pdb=" O ARG W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.632A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.532A pdb=" N VAL W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 204 removed outlier: 3.697A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.574A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'a' and resid 7 through 11 Processing helix chain 'a' and resid 77 through 81 Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 104 through 107 Processing helix chain 'a' and resid 132 through 140 removed outlier: 3.716A pdb=" N ILE a 137 " --> pdb=" O ALA a 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 9 removed outlier: 4.114A pdb=" N ASN b 8 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE b 9 " --> pdb=" O PHE b 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5 through 9' Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 39 through 69 Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.585A pdb=" N ILE b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 118 removed outlier: 3.568A pdb=" N LYS b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 143 removed outlier: 3.720A pdb=" N ARG b 143 " --> pdb=" O THR b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 159 Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.546A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 276 Processing helix chain 'b' and resid 306 through 312 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 379 through 384 removed outlier: 3.588A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR b 384 " --> pdb=" O ASP b 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 379 through 384' Processing helix chain 'b' and resid 398 through 406 Processing helix chain 'b' and resid 415 through 420 removed outlier: 4.025A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR b 420 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 430 removed outlier: 3.574A pdb=" N TYR b 429 " --> pdb=" O SER b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 442 through 445 Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.747A pdb=" N GLU b 458 " --> pdb=" O LEU b 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.892A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 removed outlier: 3.855A pdb=" N ASN e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 43 Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.800A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 removed outlier: 3.529A pdb=" N LEU h 8 " --> pdb=" O LYS h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.540A pdb=" N GLU h 26 " --> pdb=" O GLU h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.418A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 removed outlier: 3.870A pdb=" N GLU i 57 " --> pdb=" O ARG i 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU i 58 " --> pdb=" O ARG i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 95 removed outlier: 3.534A pdb=" N GLU i 87 " --> pdb=" O GLY i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 64 through 75 removed outlier: 3.643A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 3.636A pdb=" N GLU r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR r 42 " --> pdb=" O TYR r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 removed outlier: 3.651A pdb=" N GLU r 69 " --> pdb=" O ILE r 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU r 70 " --> pdb=" O LYS r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 32 removed outlier: 4.617A pdb=" N GLU s 20 " --> pdb=" O ARG s 16 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS s 21 " --> pdb=" O SER s 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.591A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 67 through 71 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.629A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN u 99 " --> pdb=" O LYS u 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU u 107 " --> pdb=" O LYS u 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 227 through 234 removed outlier: 4.026A pdb=" N LYS w 231 " --> pdb=" O ASN w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 264 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 292 Processing helix chain 'w' and resid 296 through 305 removed outlier: 4.023A pdb=" N ASP w 305 " --> pdb=" O LEU w 301 " (cutoff:3.500A) Processing helix chain 'w' and resid 310 through 329 Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.757A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU y 41 " --> pdb=" O VAL y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 removed outlier: 3.568A pdb=" N ILE y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 103 through 107' Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 88 through 99 Processing helix chain 'z' and resid 101 through 116 removed outlier: 4.371A pdb=" N ASN z 107 " --> pdb=" O LYS z 103 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS z 112 " --> pdb=" O SER z 108 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 52 through 56 removed outlier: 3.635A pdb=" N MET 3 64 " --> pdb=" O GLN 3 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN 3 78 " --> pdb=" O MET 3 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.680A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.110A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.115A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AB2, first strand: chain 'F' and resid 122 through 125 removed outlier: 3.566A pdb=" N ILE F 91 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AB5, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.008A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.667A pdb=" N ARG H 87 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG H 182 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB9, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AC1, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.677A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.474A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.059A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AC7, first strand: chain 'P' and resid 15 through 22 removed outlier: 3.890A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AC9, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD1, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.433A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 139 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD3, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.095A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 87 through 95 removed outlier: 4.311A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AD6, first strand: chain 'V' and resid 24 through 27 removed outlier: 6.839A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP V 58 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 87 through 88 Processing sheet with id=AD8, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.828A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'W' and resid 135 through 137 removed outlier: 6.360A pdb=" N ILE W 137 " --> pdb=" O PRO W 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE2, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AE3, first strand: chain 'Y' and resid 93 through 98 removed outlier: 7.007A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 72 through 74 removed outlier: 5.905A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.315A pdb=" N ILE a 101 " --> pdb=" O GLN a 125 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL a 124 " --> pdb=" O GLU a 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'b' and resid 206 through 212 Processing sheet with id=AE7, first strand: chain 'b' and resid 254 through 256 Processing sheet with id=AE8, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AE9, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AF1, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AF2, first strand: chain 'f' and resid 9 through 19 removed outlier: 6.892A pdb=" N ILE f 30 " --> pdb=" O LEU f 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE f 17 " --> pdb=" O THR f 28 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR f 28 " --> pdb=" O PHE f 17 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ARG f 19 " --> pdb=" O PRO f 26 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL f 60 " --> pdb=" O SER f 63 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE f 65 " --> pdb=" O LYS f 58 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N LYS f 58 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N VAL f 67 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N SER f 56 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N TRP f 69 " --> pdb=" O TYR f 54 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N TYR f 54 " --> pdb=" O TRP f 69 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N THR f 71 " --> pdb=" O TYR f 52 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N TYR f 52 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N ALA f 73 " --> pdb=" O VAL f 50 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N VAL f 50 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF4, first strand: chain 'r' and resid 180 through 184 removed outlier: 6.545A pdb=" N VAL r 219 " --> pdb=" O LYS r 200 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.523A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AF7, first strand: chain 'w' and resid 255 through 257 removed outlier: 6.084A pdb=" N VAL w 256 " --> pdb=" O VAL w 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'y' and resid 3 through 4 removed outlier: 5.883A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.408A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AG2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AG3, first strand: chain 'y' and resid 153 through 154 removed outlier: 6.230A pdb=" N ALA y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1435 hydrogen bonds 2330 hydrogen bond angles 0 basepair planarities 586 basepair parallelities 1132 stacking parallelities Total time for adding SS restraints: 76.62 Time building geometry restraints manager: 17.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13229 1.33 - 1.45: 32556 1.45 - 1.58: 35611 1.58 - 1.70: 3894 1.70 - 1.83: 156 Bond restraints: 85446 Sorted by residual: bond pdb=" CA PRO F 103 " pdb=" C PRO F 103 " ideal model delta sigma weight residual 1.514 1.528 -0.014 5.50e-03 3.31e+04 6.32e+00 bond pdb=" CA TRP N 120 " pdb=" C TRP N 120 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.25e-02 6.40e+03 3.90e+00 bond pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta sigma weight residual 1.455 1.431 0.024 1.25e-02 6.40e+03 3.76e+00 bond pdb=" O3' A 13267 " pdb=" P U 13268 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.26e+00 bond pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 1.526 1.504 0.022 1.20e-02 6.94e+03 3.25e+00 ... (remaining 85441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 123855 2.53 - 5.05: 1014 5.05 - 7.58: 102 7.58 - 10.11: 19 10.11 - 12.64: 2 Bond angle restraints: 124992 Sorted by residual: angle pdb=" N ILE b 12 " pdb=" CA ILE b 12 " pdb=" C ILE b 12 " ideal model delta sigma weight residual 108.63 115.30 -6.67 8.60e-01 1.35e+00 6.01e+01 angle pdb=" N TYR H 6 " pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 107.70 120.34 -12.64 2.09e+00 2.29e-01 3.65e+01 angle pdb=" C4' U 1 270 " pdb=" C3' U 1 270 " pdb=" O3' U 1 270 " ideal model delta sigma weight residual 109.40 116.92 -7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" O3' U 13268 " pdb=" C3' U 13268 " pdb=" C2' U 13268 " ideal model delta sigma weight residual 109.50 116.93 -7.43 1.50e+00 4.44e-01 2.45e+01 angle pdb=" CA GLU E 33 " pdb=" CB GLU E 33 " pdb=" CG GLU E 33 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 ... (remaining 124987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 48261 35.96 - 71.93: 4999 71.93 - 107.89: 579 107.89 - 143.86: 31 143.86 - 179.82: 43 Dihedral angle restraints: 53913 sinusoidal: 39448 harmonic: 14465 Sorted by residual: dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual -160.00 19.82 -179.82 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 164 " pdb=" C1' U 2 164 " pdb=" N1 U 2 164 " pdb=" C2 U 2 164 " ideal model delta sinusoidal sigma weight residual 200.00 21.56 178.44 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual -160.00 16.32 -176.32 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 53910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 15573 0.130 - 0.260: 79 0.260 - 0.390: 5 0.390 - 0.521: 0 0.521 - 0.651: 1 Chirality restraints: 15658 Sorted by residual: chirality pdb=" CG LEU b 456 " pdb=" CB LEU b 456 " pdb=" CD1 LEU b 456 " pdb=" CD2 LEU b 456 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU u 69 " pdb=" CB LEU u 69 " pdb=" CD1 LEU u 69 " pdb=" CD2 LEU u 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' C 1 626 " pdb=" C4' C 1 626 " pdb=" O3' C 1 626 " pdb=" C2' C 1 626 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 15655 not shown) Planarity restraints: 8644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 10 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO b 11 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO b 11 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO b 11 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY i 4 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C GLY i 4 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY i 4 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU i 5 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 118 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ASN G 118 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN G 118 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY G 119 " 0.015 2.00e-02 2.50e+03 ... (remaining 8641 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1793 2.63 - 3.20: 70218 3.20 - 3.76: 154614 3.76 - 4.33: 206583 4.33 - 4.90: 285803 Nonbonded interactions: 719011 Sorted by model distance: nonbonded pdb=" O ASP M 82 " pdb=" OD1 ASP M 82 " model vdw 2.061 3.040 nonbonded pdb=" O2' C 11308 " pdb=" O5' A 11309 " model vdw 2.106 3.040 nonbonded pdb=" O2' G 13387 " pdb=" O5' C 13388 " model vdw 2.155 3.040 nonbonded pdb=" N GLU T 144 " pdb=" OE1 GLU T 144 " model vdw 2.172 3.120 nonbonded pdb=" N GLN O 190 " pdb=" OE1 GLN O 190 " model vdw 2.177 3.120 ... (remaining 719006 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.310 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: 0.060 Extract box with map and model: 2.560 Check model and map are aligned: 0.470 Set scattering table: 0.580 Process input model: 211.110 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.300 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: 0.030 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 85446 Z= 0.230 Angle : 0.606 12.635 124992 Z= 0.322 Chirality : 0.036 0.651 15658 Planarity : 0.005 0.079 8644 Dihedral : 23.137 179.822 44519 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.91 % Rotamer: Outliers : 0.81 % Allowed : 11.11 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.83 (0.12), residues: 4886 helix: 0.17 (0.12), residues: 1856 sheet: -0.73 (0.21), residues: 597 loop : -1.03 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP b 427 HIS 0.017 0.001 HIS T 139 PHE 0.027 0.002 PHE b 444 TYR 0.040 0.002 TYR 3 32 ARG 0.018 0.001 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 682 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.5822 (t80) cc_final: 0.5553 (p90) REVERT: B 214 MET cc_start: 0.8362 (tpp) cc_final: 0.8075 (ttm) REVERT: C 155 ASP cc_start: 0.6904 (p0) cc_final: 0.6506 (p0) REVERT: E 176 GLU cc_start: 0.7685 (tp30) cc_final: 0.7400 (tp30) REVERT: P 99 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7928 (tm-30) REVERT: b 412 TYR cc_start: 0.8922 (t80) cc_final: 0.8644 (t80) REVERT: b 432 MET cc_start: 0.7197 (ttt) cc_final: 0.6989 (ttt) REVERT: d 107 GLU cc_start: 0.7760 (mp0) cc_final: 0.7551 (mp0) REVERT: e 36 ASP cc_start: 0.7502 (m-30) cc_final: 0.7240 (t0) REVERT: h 22 GLU cc_start: 0.8222 (pp20) cc_final: 0.7866 (tm-30) REVERT: i 85 ILE cc_start: 0.8754 (pt) cc_final: 0.8516 (mt) REVERT: r 67 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8061 (tm-30) REVERT: r 70 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7383 (tm-30) REVERT: u 105 GLU cc_start: 0.8002 (pp20) cc_final: 0.7473 (pp20) REVERT: y 95 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 29 outliers final: 13 residues processed: 693 average time/residue: 0.7731 time to fit residues: 908.7448 Evaluate side-chains 612 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 599 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 120 TRP Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain h residue 13 GLN Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain y residue 118 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 1.9990 chunk 513 optimal weight: 0.0970 chunk 284 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 614 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN E 75 GLN E 127 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 ASN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 149 ASN P 145 HIS Q 78 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 HIS h 11 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 GLN j 76 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN y 140 GLN z 98 HIS ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092585 restraints weight = 324660.579| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.70 r_work: 0.3067 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 85446 Z= 0.234 Angle : 0.656 11.326 124992 Z= 0.333 Chirality : 0.039 0.273 15658 Planarity : 0.005 0.062 8644 Dihedral : 23.951 179.893 35681 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 2.19 % Allowed : 11.46 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.52 (0.12), residues: 4886 helix: 0.54 (0.12), residues: 1888 sheet: -0.66 (0.20), residues: 624 loop : -0.93 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP z 94 HIS 0.011 0.001 HIS d 48 PHE 0.015 0.001 PHE z 110 TYR 0.023 0.002 TYR u 55 ARG 0.013 0.001 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 661 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.5952 (t80) cc_final: 0.5713 (p90) REVERT: C 155 ASP cc_start: 0.6850 (p0) cc_final: 0.6491 (p0) REVERT: G 98 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8075 (mtp180) REVERT: H 175 ASP cc_start: 0.7641 (m-30) cc_final: 0.7330 (m-30) REVERT: L 174 ASN cc_start: 0.8586 (p0) cc_final: 0.8330 (p0) REVERT: M 122 GLU cc_start: 0.8456 (pp20) cc_final: 0.8219 (pp20) REVERT: P 29 SER cc_start: 0.9225 (p) cc_final: 0.9013 (m) REVERT: P 141 SER cc_start: 0.7511 (p) cc_final: 0.7068 (m) REVERT: b 128 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8534 (mp10) REVERT: b 153 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8743 (mm-40) REVERT: b 396 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.3579 (ppt90) REVERT: d 57 ASP cc_start: 0.8652 (t0) cc_final: 0.8393 (t0) REVERT: d 107 GLU cc_start: 0.8054 (mp0) cc_final: 0.7648 (mp0) REVERT: e 36 ASP cc_start: 0.7779 (m-30) cc_final: 0.7425 (t0) REVERT: h 18 GLU cc_start: 0.8887 (pp20) cc_final: 0.8664 (pp20) REVERT: h 21 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8566 (tm-30) REVERT: h 25 GLN cc_start: 0.8608 (mp10) cc_final: 0.8353 (mp10) REVERT: i 93 GLN cc_start: 0.8658 (mp10) cc_final: 0.7981 (pp30) REVERT: r 70 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7170 (tm-30) REVERT: u 42 MET cc_start: 0.8473 (mpp) cc_final: 0.7859 (mpp) REVERT: u 105 GLU cc_start: 0.8473 (pp20) cc_final: 0.8001 (pp20) REVERT: y 95 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8068 (tm-30) REVERT: z 96 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7682 (tttm) outliers start: 80 outliers final: 49 residues processed: 699 average time/residue: 0.8396 time to fit residues: 1011.7582 Evaluate side-chains 644 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 594 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 391 ASN Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain e residue 78 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 10 SER Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain z residue 98 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 348 optimal weight: 4.9990 chunk 628 optimal weight: 0.0070 chunk 658 optimal weight: 0.9980 chunk 352 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 579 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 254 optimal weight: 2.9990 chunk 582 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN E 75 GLN F 69 GLN H 77 ASN H 151 ASN L 181 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 123 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 55 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN r 3 GLN y 140 GLN z 98 HIS T 152 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.115987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093315 restraints weight = 309751.594| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.40 r_work: 0.3089 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 85446 Z= 0.194 Angle : 0.600 11.357 124992 Z= 0.307 Chirality : 0.037 0.280 15658 Planarity : 0.004 0.065 8644 Dihedral : 23.774 179.907 35669 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.60 % Allowed : 13.76 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.31 (0.12), residues: 4886 helix: 0.75 (0.12), residues: 1889 sheet: -0.63 (0.20), residues: 619 loop : -0.82 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP z 94 HIS 0.023 0.001 HIS z 98 PHE 0.021 0.001 PHE N 129 TYR 0.025 0.002 TYR Q 32 ARG 0.017 0.000 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 654 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6040 (t80) cc_final: 0.5715 (p90) REVERT: C 155 ASP cc_start: 0.6657 (p0) cc_final: 0.6380 (p0) REVERT: F 69 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8491 (tp40) REVERT: G 98 ARG cc_start: 0.8297 (mtp180) cc_final: 0.8023 (mtp180) REVERT: L 174 ASN cc_start: 0.8735 (p0) cc_final: 0.8499 (p0) REVERT: N 4 TYR cc_start: 0.8772 (m-80) cc_final: 0.8569 (m-10) REVERT: O 59 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8206 (mm) REVERT: P 29 SER cc_start: 0.9223 (p) cc_final: 0.9020 (m) REVERT: P 141 SER cc_start: 0.7514 (p) cc_final: 0.7077 (m) REVERT: P 181 ARG cc_start: 0.5697 (tpp80) cc_final: 0.5493 (tpp80) REVERT: S 108 ASP cc_start: 0.8531 (t70) cc_final: 0.8278 (t0) REVERT: b 84 ASN cc_start: 0.8317 (m-40) cc_final: 0.7696 (m110) REVERT: b 144 GLN cc_start: 0.8572 (mp10) cc_final: 0.8234 (mp10) REVERT: b 153 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8796 (mm-40) REVERT: b 396 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.4067 (ppt90) REVERT: d 31 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8642 (mmmt) REVERT: d 57 ASP cc_start: 0.8658 (t0) cc_final: 0.8359 (t0) REVERT: d 107 GLU cc_start: 0.8122 (mp0) cc_final: 0.7739 (mp0) REVERT: e 36 ASP cc_start: 0.7748 (m-30) cc_final: 0.7402 (t0) REVERT: i 93 GLN cc_start: 0.8541 (mp10) cc_final: 0.8213 (pp30) REVERT: j 29 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8244 (mm) REVERT: j 64 MET cc_start: 0.8548 (mtt) cc_final: 0.8330 (mtt) REVERT: r 69 GLU cc_start: 0.7981 (pm20) cc_final: 0.7765 (pm20) REVERT: r 70 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7230 (tm-30) REVERT: y 95 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8169 (tm-30) REVERT: y 188 ARG cc_start: 0.8442 (mtm110) cc_final: 0.8168 (mtm180) REVERT: z 96 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7607 (tttm) outliers start: 95 outliers final: 50 residues processed: 702 average time/residue: 0.7752 time to fit residues: 930.1024 Evaluate side-chains 650 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 596 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 181 ASN Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain z residue 96 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 311 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 630 optimal weight: 0.8980 chunk 428 optimal weight: 0.9990 chunk 287 optimal weight: 7.9990 chunk 568 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN E 75 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN V 83 GLN b 394 ASN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN h 15 ASN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN y 140 GLN y 162 HIS z 98 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090433 restraints weight = 289118.175| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.50 r_work: 0.3020 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 85446 Z= 0.383 Angle : 0.704 10.592 124992 Z= 0.356 Chirality : 0.042 0.291 15658 Planarity : 0.005 0.070 8644 Dihedral : 23.752 179.973 35663 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 3.58 % Allowed : 15.17 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.49 (0.12), residues: 4886 helix: 0.66 (0.12), residues: 1893 sheet: -0.72 (0.20), residues: 625 loop : -0.98 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP z 94 HIS 0.008 0.001 HIS d 48 PHE 0.017 0.002 PHE C 221 TYR 0.025 0.002 TYR u 55 ARG 0.011 0.001 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 608 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 123 ARG cc_start: 0.3538 (ttp-170) cc_final: 0.2420 (ttt180) REVERT: B 184 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: C 363 ASN cc_start: 0.7524 (t0) cc_final: 0.7244 (t0) REVERT: F 101 ASN cc_start: 0.8145 (t0) cc_final: 0.7897 (t0) REVERT: F 110 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8638 (mmt) REVERT: G 98 ARG cc_start: 0.8344 (mtp180) cc_final: 0.8128 (mtp180) REVERT: H 174 LEU cc_start: 0.8224 (pp) cc_final: 0.7988 (pp) REVERT: L 46 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8509 (pp) REVERT: L 92 THR cc_start: 0.8630 (p) cc_final: 0.8425 (p) REVERT: M 114 MET cc_start: 0.8540 (tpp) cc_final: 0.8162 (tpt) REVERT: N 4 TYR cc_start: 0.8869 (m-80) cc_final: 0.8654 (m-80) REVERT: O 59 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8317 (mm) REVERT: P 141 SER cc_start: 0.7694 (p) cc_final: 0.7247 (m) REVERT: V 5 ARG cc_start: 0.5821 (pmt170) cc_final: 0.4302 (tpt90) REVERT: b 69 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8542 (t80) REVERT: b 84 ASN cc_start: 0.8337 (m-40) cc_final: 0.7673 (m110) REVERT: b 124 TYR cc_start: 0.7873 (t80) cc_final: 0.7535 (t80) REVERT: b 128 GLN cc_start: 0.9355 (mm-40) cc_final: 0.8547 (mp10) REVERT: b 153 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8778 (mm-40) REVERT: b 396 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.4280 (ppt90) REVERT: d 21 MET cc_start: 0.8951 (mmm) cc_final: 0.8018 (mmm) REVERT: d 31 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8714 (mmmt) REVERT: d 57 ASP cc_start: 0.8771 (t0) cc_final: 0.8464 (t0) REVERT: d 107 GLU cc_start: 0.8133 (mp0) cc_final: 0.7900 (mp0) REVERT: h 21 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8859 (tp-100) REVERT: h 22 GLU cc_start: 0.9305 (tm-30) cc_final: 0.9062 (tm-30) REVERT: h 25 GLN cc_start: 0.8629 (mt0) cc_final: 0.8340 (mp10) REVERT: h 63 SER cc_start: 0.8712 (m) cc_final: 0.8413 (p) REVERT: i 70 LEU cc_start: 0.9065 (tp) cc_final: 0.8632 (pp) REVERT: i 93 GLN cc_start: 0.8561 (mp10) cc_final: 0.8219 (pp30) REVERT: r 3 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7996 (mm-40) REVERT: r 70 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7253 (tm-30) REVERT: u 42 MET cc_start: 0.8322 (mpp) cc_final: 0.7687 (mpp) outliers start: 131 outliers final: 87 residues processed: 689 average time/residue: 0.7646 time to fit residues: 899.2620 Evaluate side-chains 659 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 566 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 26 MET Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 15 ASN Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 10 SER Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 91 LEU Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 374 optimal weight: 3.9990 chunk 432 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 510 optimal weight: 0.7980 chunk 575 optimal weight: 1.9990 chunk 652 optimal weight: 6.9990 chunk 472 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN b 55 GLN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN y 140 GLN y 162 HIS z 98 HIS ** z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088302 restraints weight = 283068.756| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.63 r_work: 0.3017 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 85446 Z= 0.343 Angle : 0.671 10.506 124992 Z= 0.340 Chirality : 0.040 0.296 15658 Planarity : 0.005 0.075 8644 Dihedral : 23.736 179.673 35663 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 3.71 % Allowed : 16.85 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.45 (0.12), residues: 4886 helix: 0.70 (0.12), residues: 1889 sheet: -0.69 (0.20), residues: 615 loop : -0.96 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP z 94 HIS 0.010 0.001 HIS d 48 PHE 0.017 0.002 PHE i 37 TYR 0.026 0.002 TYR Q 32 ARG 0.013 0.001 ARG y 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 612 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6262 (t80) cc_final: 0.5830 (p90) REVERT: 3 114 ARG cc_start: 0.7113 (mtt-85) cc_final: 0.6832 (mtt-85) REVERT: 3 123 ARG cc_start: 0.3517 (ttp-170) cc_final: 0.2447 (ttt180) REVERT: B 184 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: B 308 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8079 (ttm) REVERT: B 345 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5392 (p-80) REVERT: C 363 ASN cc_start: 0.7614 (t0) cc_final: 0.7284 (t0) REVERT: F 101 ASN cc_start: 0.8283 (t0) cc_final: 0.7977 (t0) REVERT: G 131 ASN cc_start: 0.8595 (p0) cc_final: 0.8078 (m-40) REVERT: H 174 LEU cc_start: 0.8051 (pp) cc_final: 0.7849 (pp) REVERT: L 174 ASN cc_start: 0.8668 (p0) cc_final: 0.8275 (p0) REVERT: M 114 MET cc_start: 0.8636 (tpp) cc_final: 0.8366 (tpt) REVERT: N 4 TYR cc_start: 0.8931 (m-80) cc_final: 0.8722 (m-80) REVERT: O 59 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (mm) REVERT: P 103 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7996 (mm-30) REVERT: P 141 SER cc_start: 0.7699 (p) cc_final: 0.7224 (m) REVERT: S 89 MET cc_start: 0.7998 (mtt) cc_final: 0.7216 (mtt) REVERT: b 6 PHE cc_start: 0.6456 (m-10) cc_final: 0.6171 (m-10) REVERT: b 69 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8546 (t80) REVERT: b 84 ASN cc_start: 0.8462 (m-40) cc_final: 0.7909 (m110) REVERT: b 153 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8542 (mm-40) REVERT: b 396 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.4287 (ppt90) REVERT: d 23 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8642 (pttt) REVERT: d 31 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8698 (mmmt) REVERT: d 57 ASP cc_start: 0.8737 (t0) cc_final: 0.8424 (t0) REVERT: f 99 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8856 (mt) REVERT: h 21 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8717 (tp-100) REVERT: h 22 GLU cc_start: 0.9338 (tm-30) cc_final: 0.8970 (tm-30) REVERT: h 25 GLN cc_start: 0.8608 (mt0) cc_final: 0.8149 (mp10) REVERT: h 63 SER cc_start: 0.8728 (m) cc_final: 0.8423 (p) REVERT: i 70 LEU cc_start: 0.9071 (tp) cc_final: 0.8648 (pp) REVERT: j 29 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8180 (mm) REVERT: u 19 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8642 (mp) outliers start: 136 outliers final: 97 residues processed: 698 average time/residue: 0.7721 time to fit residues: 922.2648 Evaluate side-chains 682 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 576 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 26 MET Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain h residue 15 ASN Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 98 HIS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 473 optimal weight: 0.0970 chunk 130 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 612 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 669 optimal weight: 8.9990 chunk 405 optimal weight: 0.9980 chunk 314 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 110 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN h 15 ASN h 19 GLN ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN y 21 ASN y 140 GLN y 162 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.113049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.088395 restraints weight = 272423.171| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.51 r_work: 0.3030 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 85446 Z= 0.311 Angle : 0.658 10.861 124992 Z= 0.334 Chirality : 0.039 0.295 15658 Planarity : 0.005 0.070 8644 Dihedral : 23.686 179.931 35663 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.28 % Rotamer: Outliers : 3.96 % Allowed : 17.69 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.41 (0.12), residues: 4886 helix: 0.73 (0.12), residues: 1894 sheet: -0.69 (0.20), residues: 605 loop : -0.93 (0.13), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP z 94 HIS 0.052 0.001 HIS z 98 PHE 0.040 0.002 PHE N 129 TYR 0.027 0.002 TYR Q 32 ARG 0.011 0.001 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 611 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6234 (t80) cc_final: 0.5823 (p90) REVERT: 3 74 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7566 (t) REVERT: 3 114 ARG cc_start: 0.7121 (mtt-85) cc_final: 0.6807 (mtt-85) REVERT: 3 123 ARG cc_start: 0.3657 (ttp-170) cc_final: 0.2335 (ttt180) REVERT: B 184 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: B 345 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5354 (p-80) REVERT: C 363 ASN cc_start: 0.7677 (t0) cc_final: 0.7329 (t0) REVERT: F 101 ASN cc_start: 0.8333 (t0) cc_final: 0.8027 (t0) REVERT: G 131 ASN cc_start: 0.8568 (p0) cc_final: 0.8044 (m-40) REVERT: L 174 ASN cc_start: 0.8636 (p0) cc_final: 0.8419 (p0) REVERT: M 114 MET cc_start: 0.8740 (tpp) cc_final: 0.8507 (tpt) REVERT: O 59 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8323 (mm) REVERT: P 103 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8115 (mm-30) REVERT: P 141 SER cc_start: 0.7695 (p) cc_final: 0.7225 (m) REVERT: S 89 MET cc_start: 0.7931 (mtt) cc_final: 0.7320 (mtt) REVERT: V 5 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.4116 (tpt90) REVERT: b 6 PHE cc_start: 0.6632 (m-10) cc_final: 0.6321 (m-10) REVERT: b 69 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8524 (t80) REVERT: b 84 ASN cc_start: 0.8562 (m-40) cc_final: 0.8003 (m-40) REVERT: b 153 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8572 (mm-40) REVERT: b 396 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.4549 (ppt90) REVERT: d 19 ILE cc_start: 0.8727 (tp) cc_final: 0.8494 (tp) REVERT: d 23 LYS cc_start: 0.8845 (ptmm) cc_final: 0.8574 (pttt) REVERT: d 31 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8713 (mmmt) REVERT: d 57 ASP cc_start: 0.8804 (t0) cc_final: 0.8474 (t0) REVERT: h 21 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8670 (tp-100) REVERT: h 22 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8895 (tm-30) REVERT: h 25 GLN cc_start: 0.8610 (mt0) cc_final: 0.8169 (mp10) REVERT: h 63 SER cc_start: 0.8787 (m) cc_final: 0.8417 (p) REVERT: i 63 GLN cc_start: 0.8453 (mt0) cc_final: 0.8095 (mt0) REVERT: i 70 LEU cc_start: 0.9096 (tp) cc_final: 0.8707 (pp) REVERT: i 93 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8292 (pp30) REVERT: u 19 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8596 (mp) outliers start: 145 outliers final: 105 residues processed: 702 average time/residue: 0.7724 time to fit residues: 925.9814 Evaluate side-chains 691 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 578 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 91 LEU Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 348 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 526 optimal weight: 1.9990 chunk 352 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 658 optimal weight: 7.9990 chunk 463 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 122 ASN Q 78 GLN S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN b 128 GLN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087511 restraints weight = 248526.255| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.36 r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 85446 Z= 0.326 Angle : 0.668 13.202 124992 Z= 0.339 Chirality : 0.040 0.297 15658 Planarity : 0.005 0.071 8644 Dihedral : 23.655 179.564 35663 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 4.12 % Allowed : 18.34 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.40 (0.12), residues: 4886 helix: 0.75 (0.12), residues: 1888 sheet: -0.75 (0.21), residues: 605 loop : -0.92 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP z 94 HIS 0.013 0.001 HIS C 314 PHE 0.022 0.002 PHE j 78 TYR 0.035 0.002 TYR i 51 ARG 0.010 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 611 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6146 (t80) cc_final: 0.5786 (p90) REVERT: 3 49 ARG cc_start: 0.6403 (pmt-80) cc_final: 0.6166 (pmt-80) REVERT: 3 74 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7652 (t) REVERT: 3 114 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6855 (mtt-85) REVERT: 3 123 ARG cc_start: 0.3725 (ttp-170) cc_final: 0.2422 (ttt180) REVERT: B 184 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: B 345 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5216 (p-80) REVERT: C 363 ASN cc_start: 0.7753 (t0) cc_final: 0.7399 (t0) REVERT: F 101 ASN cc_start: 0.8345 (t0) cc_final: 0.8030 (t0) REVERT: G 131 ASN cc_start: 0.8551 (p0) cc_final: 0.8086 (m-40) REVERT: L 92 THR cc_start: 0.8602 (p) cc_final: 0.8367 (p) REVERT: L 114 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: L 174 ASN cc_start: 0.8682 (p0) cc_final: 0.8411 (p0) REVERT: O 59 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (mm) REVERT: P 103 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8058 (mm-30) REVERT: P 107 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8114 (mp) REVERT: P 141 SER cc_start: 0.7693 (p) cc_final: 0.7227 (m) REVERT: S 88 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7480 (t0) REVERT: S 89 MET cc_start: 0.7827 (mtt) cc_final: 0.7543 (mtm) REVERT: V 76 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6279 (ppp) REVERT: V 126 ASP cc_start: 0.8914 (t0) cc_final: 0.8665 (t0) REVERT: b 6 PHE cc_start: 0.6789 (m-10) cc_final: 0.6510 (m-10) REVERT: b 69 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8513 (t80) REVERT: b 84 ASN cc_start: 0.8548 (m-40) cc_final: 0.7982 (m-40) REVERT: b 153 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8577 (mm-40) REVERT: b 396 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.4688 (ppt90) REVERT: d 23 LYS cc_start: 0.8872 (ptmm) cc_final: 0.8575 (pttt) REVERT: d 31 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8690 (mmmt) REVERT: d 57 ASP cc_start: 0.8772 (t0) cc_final: 0.8451 (t0) REVERT: h 22 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8967 (tm-30) REVERT: h 25 GLN cc_start: 0.8652 (mt0) cc_final: 0.8309 (mt0) REVERT: i 63 GLN cc_start: 0.8436 (mt0) cc_final: 0.8190 (mt0) REVERT: i 70 LEU cc_start: 0.9106 (tp) cc_final: 0.8758 (pp) REVERT: u 19 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8589 (mp) outliers start: 151 outliers final: 114 residues processed: 700 average time/residue: 0.7650 time to fit residues: 915.2415 Evaluate side-chains 704 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 579 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 38 CYS Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 88 ASN Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 15 ASN Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 10 SER Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 91 LEU Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 157 optimal weight: 6.9990 chunk 634 optimal weight: 2.9990 chunk 395 optimal weight: 5.9990 chunk 560 optimal weight: 9.9990 chunk 460 optimal weight: 0.9990 chunk 668 optimal weight: 8.9990 chunk 645 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.111070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087807 restraints weight = 292829.783| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.78 r_work: 0.2971 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 85446 Z= 0.470 Angle : 0.765 10.645 124992 Z= 0.385 Chirality : 0.044 0.314 15658 Planarity : 0.006 0.080 8644 Dihedral : 23.726 179.922 35663 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Rotamer: Outliers : 4.01 % Allowed : 19.34 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.58 (0.12), residues: 4886 helix: 0.63 (0.12), residues: 1875 sheet: -0.76 (0.21), residues: 606 loop : -1.07 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP z 94 HIS 0.011 0.002 HIS z 98 PHE 0.029 0.002 PHE N 129 TYR 0.044 0.002 TYR i 51 ARG 0.012 0.001 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 589 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 49 ARG cc_start: 0.6550 (pmt-80) cc_final: 0.6290 (pmt-80) REVERT: 3 74 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7646 (t) REVERT: 3 114 ARG cc_start: 0.7368 (mtt-85) cc_final: 0.7094 (mtt-85) REVERT: B 184 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: C 97 ARG cc_start: 0.7206 (ttt-90) cc_final: 0.6974 (ttt-90) REVERT: C 101 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.5480 (ppp) REVERT: C 363 ASN cc_start: 0.7769 (t0) cc_final: 0.7458 (t0) REVERT: G 131 ASN cc_start: 0.8621 (p0) cc_final: 0.8016 (m-40) REVERT: L 92 THR cc_start: 0.8567 (p) cc_final: 0.8329 (p) REVERT: L 114 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: L 174 ASN cc_start: 0.8610 (p0) cc_final: 0.8335 (p0) REVERT: L 178 THR cc_start: 0.8404 (p) cc_final: 0.8191 (p) REVERT: O 59 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8355 (mm) REVERT: P 53 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: P 141 SER cc_start: 0.7647 (p) cc_final: 0.7205 (m) REVERT: P 166 ARG cc_start: 0.6395 (mpt180) cc_final: 0.6119 (mpt180) REVERT: V 76 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6534 (ppp) REVERT: b 6 PHE cc_start: 0.7198 (m-10) cc_final: 0.6852 (m-10) REVERT: b 69 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8612 (t80) REVERT: b 84 ASN cc_start: 0.8673 (m-40) cc_final: 0.8050 (m-40) REVERT: b 128 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8551 (mp10) REVERT: b 153 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8688 (mm-40) REVERT: b 396 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.4675 (ppt90) REVERT: d 23 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8620 (pttm) REVERT: d 31 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8707 (mmmt) REVERT: d 57 ASP cc_start: 0.8761 (t0) cc_final: 0.8443 (t0) REVERT: h 22 GLU cc_start: 0.9371 (tm-30) cc_final: 0.8929 (tm-30) REVERT: i 63 GLN cc_start: 0.8582 (mt0) cc_final: 0.8361 (mt0) REVERT: i 70 LEU cc_start: 0.9202 (tp) cc_final: 0.8815 (pp) REVERT: i 93 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8361 (pp30) REVERT: y 95 GLN cc_start: 0.8754 (tm-30) cc_final: 0.7908 (tm-30) REVERT: T 146 ASN cc_start: 0.7589 (p0) cc_final: 0.7315 (p0) outliers start: 147 outliers final: 120 residues processed: 683 average time/residue: 0.8006 time to fit residues: 932.9265 Evaluate side-chains 696 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 567 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 38 CYS Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 26 MET Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 142 optimal weight: 8.9990 chunk 517 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 488 optimal weight: 20.0000 chunk 554 optimal weight: 5.9990 chunk 599 optimal weight: 0.9980 chunk 420 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 351 optimal weight: 0.9990 chunk 401 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN O 32 GLN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.114079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089416 restraints weight = 259342.692| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.22 r_work: 0.3092 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 85446 Z= 0.179 Angle : 0.622 11.382 124992 Z= 0.317 Chirality : 0.037 0.286 15658 Planarity : 0.004 0.064 8644 Dihedral : 23.636 179.931 35663 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 2.87 % Allowed : 20.83 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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: -0.31 (0.12), residues: 4886 helix: 0.82 (0.12), residues: 1875 sheet: -0.67 (0.21), residues: 615 loop : -0.87 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP z 94 HIS 0.005 0.001 HIS d 48 PHE 0.026 0.001 PHE i 37 TYR 0.040 0.002 TYR i 51 ARG 0.009 0.001 ARG h 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 639 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6194 (t80) cc_final: 0.5861 (p90) REVERT: 3 49 ARG cc_start: 0.6597 (pmt-80) cc_final: 0.6335 (pmt-80) REVERT: 3 74 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7496 (t) REVERT: 3 114 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6846 (mtt-85) REVERT: B 184 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: C 363 ASN cc_start: 0.7702 (t0) cc_final: 0.7427 (t0) REVERT: F 101 ASN cc_start: 0.8235 (t0) cc_final: 0.7948 (t0) REVERT: G 98 ARG cc_start: 0.8370 (mtp180) cc_final: 0.8139 (mtp180) REVERT: G 131 ASN cc_start: 0.8526 (p0) cc_final: 0.8170 (m-40) REVERT: L 92 THR cc_start: 0.8508 (p) cc_final: 0.8305 (p) REVERT: L 114 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: L 174 ASN cc_start: 0.8722 (p0) cc_final: 0.8421 (p0) REVERT: O 59 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (mm) REVERT: P 103 GLU cc_start: 0.8405 (tp30) cc_final: 0.8159 (mm-30) REVERT: Q 92 GLU cc_start: 0.7957 (pm20) cc_final: 0.7535 (pm20) REVERT: V 76 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6405 (ppp) REVERT: V 91 ASP cc_start: 0.8470 (t0) cc_final: 0.8175 (t0) REVERT: b 6 PHE cc_start: 0.7014 (m-10) cc_final: 0.6684 (m-10) REVERT: b 69 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8519 (t80) REVERT: b 84 ASN cc_start: 0.8514 (m-40) cc_final: 0.7924 (m-40) REVERT: b 128 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9092 (mm110) REVERT: b 153 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8605 (mm-40) REVERT: b 396 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.4692 (ppt90) REVERT: d 23 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8449 (pttt) REVERT: d 31 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8644 (mmmt) REVERT: d 107 GLU cc_start: 0.8171 (mp0) cc_final: 0.7945 (mp0) REVERT: h 22 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8727 (tm-30) REVERT: i 51 TYR cc_start: 0.7363 (p90) cc_final: 0.6938 (p90) REVERT: i 70 LEU cc_start: 0.9107 (tp) cc_final: 0.8776 (pp) REVERT: i 93 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8353 (pp30) outliers start: 105 outliers final: 78 residues processed: 696 average time/residue: 0.7551 time to fit residues: 904.4938 Evaluate side-chains 664 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 579 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain z residue 98 HIS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 38 optimal weight: 5.9990 chunk 543 optimal weight: 5.9990 chunk 560 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 492 optimal weight: 0.7980 chunk 533 optimal weight: 50.0000 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 675 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 655 optimal weight: 0.0670 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN O 51 ASN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN V 22 GLN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089432 restraints weight = 297466.318| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.50 r_work: 0.3002 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 85446 Z= 0.392 Angle : 0.715 11.711 124992 Z= 0.362 Chirality : 0.042 0.303 15658 Planarity : 0.005 0.078 8644 Dihedral : 23.597 179.510 35663 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 2.79 % Allowed : 21.57 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % 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 (0.12), residues: 4886 helix: 0.74 (0.12), residues: 1874 sheet: -0.68 (0.21), residues: 606 loop : -0.98 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP z 94 HIS 0.046 0.002 HIS z 98 PHE 0.023 0.002 PHE i 37 TYR 0.055 0.002 TYR i 51 ARG 0.012 0.001 ARG a 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 590 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 49 ARG cc_start: 0.6695 (pmt-80) cc_final: 0.6435 (pmt-80) REVERT: 3 74 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7576 (t) REVERT: 3 114 ARG cc_start: 0.7217 (mtt-85) cc_final: 0.6899 (mtt-85) REVERT: B 184 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: C 101 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.5157 (ppp) REVERT: C 363 ASN cc_start: 0.7766 (t0) cc_final: 0.7493 (t0) REVERT: F 82 TYR cc_start: 0.8443 (m-80) cc_final: 0.8098 (m-80) REVERT: F 101 ASN cc_start: 0.8338 (t0) cc_final: 0.8057 (t0) REVERT: G 131 ASN cc_start: 0.8598 (p0) cc_final: 0.8126 (m-40) REVERT: L 92 THR cc_start: 0.8533 (p) cc_final: 0.8313 (p) REVERT: L 114 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: L 174 ASN cc_start: 0.8710 (p0) cc_final: 0.8419 (p0) REVERT: L 178 THR cc_start: 0.8400 (p) cc_final: 0.8164 (p) REVERT: O 59 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8333 (mm) REVERT: P 141 SER cc_start: 0.7749 (p) cc_final: 0.7284 (m) REVERT: S 23 LEU cc_start: 0.8743 (mt) cc_final: 0.8515 (mp) REVERT: b 6 PHE cc_start: 0.7185 (m-10) cc_final: 0.6880 (m-10) REVERT: b 69 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8596 (t80) REVERT: b 84 ASN cc_start: 0.8693 (m-40) cc_final: 0.8102 (m-40) REVERT: b 128 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9119 (mm110) REVERT: b 153 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8653 (mm-40) REVERT: b 396 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.4629 (ppt90) REVERT: d 23 LYS cc_start: 0.8844 (ptmm) cc_final: 0.8595 (pttt) REVERT: d 31 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8722 (mmmt) REVERT: d 107 GLU cc_start: 0.8186 (mp0) cc_final: 0.7920 (mp0) REVERT: h 63 SER cc_start: 0.8794 (m) cc_final: 0.8427 (p) REVERT: i 70 LEU cc_start: 0.9187 (tp) cc_final: 0.8830 (pp) REVERT: i 93 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8418 (pp30) REVERT: y 95 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7961 (tm-30) REVERT: T 146 ASN cc_start: 0.7596 (p0) cc_final: 0.7353 (p0) outliers start: 102 outliers final: 91 residues processed: 647 average time/residue: 0.7698 time to fit residues: 850.9481 Evaluate side-chains 679 residues out of total 4253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 581 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 86 HIS Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 26 MET Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain z residue 98 HIS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 chunk 439 optimal weight: 40.0000 chunk 672 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 514 optimal weight: 5.9990 chunk 492 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 537 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.111892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087031 restraints weight = 254995.245| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.37 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3245 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: