Starting phenix.real_space_refine on Wed Aug 27 01:41:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzh_34398/08_2025/8gzh_34398.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18123 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 2 5.21 5 S 84 5.16 5 C 18744 2.51 5 N 5390 2.21 5 O 6012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30339 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1675 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1673 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8171 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 990} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4862 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 585} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 450 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "Z" Number of atoms: 8860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 8860 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 44, 'TRANS': 1172} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 435 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 17, 'GLU:plan': 25, 'TRP:plan': 1, 'ARG:plan': 15, 'ASN:plan1': 5, 'TYR:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 369 Chain: "1" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1031 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "3" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12047 SG CYS D 71 117.205 56.559 69.453 1.00 19.83 S ATOM 12067 SG CYS D 73 118.776 56.116 65.335 1.00 22.80 S ATOM 12170 SG CYS D 86 121.000 55.682 69.194 1.00 25.00 S ATOM 20997 SG CYS Z 214 86.351 75.790 126.040 1.00 18.67 S ATOM 21530 SG CYS Z 286 85.589 76.041 122.144 1.00 18.67 S ATOM 21579 SG CYS Z 293 84.540 72.699 124.196 1.00 18.67 S ATOM 21602 SG CYS Z 296 82.454 75.901 125.023 1.00 18.67 S Time building chain proxies: 6.88, per 1000 atoms: 0.23 Number of scatterers: 30339 At special positions: 0 Unit cell: (157.3, 155.1, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 84 16.00 P 105 15.00 Mg 2 11.99 O 6012 8.00 N 5390 7.00 C 18744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb=" ZN Z2001 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 293 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 296 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 214 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 286 " Number of angles added : 6 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6810 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 55 sheets defined 35.7% alpha, 18.3% beta 39 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 209 through 231 Proline residue: A 227 - end of helix Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.628A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.638A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.828A pdb=" N GLN B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 112 " --> pdb=" O ALA B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 112' Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.627A pdb=" N SER B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.774A pdb=" N ASP B 226 " --> pdb=" O PRO B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.538A pdb=" N GLU C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.584A pdb=" N GLY C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.589A pdb=" N ILE C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 209 removed outlier: 4.035A pdb=" N TYR C 201 " --> pdb=" O HIS C 197 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.640A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.663A pdb=" N GLY C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 Processing helix chain 'C' and resid 275 through 289 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 309 through 336 removed outlier: 3.605A pdb=" N LEU C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.774A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 342 through 347' Processing helix chain 'C' and resid 349 through 362 Processing helix chain 'C' and resid 373 through 381 removed outlier: 3.708A pdb=" N LYS C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.506A pdb=" N HIS C 409 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.502A pdb=" N VAL C 506 " --> pdb=" O PRO C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 523 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 543 Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.100A pdb=" N GLY C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 793 through 795 No H-bonds generated for 'chain 'C' and resid 793 through 795' Processing helix chain 'C' and resid 857 through 863 removed outlier: 4.090A pdb=" N SER C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 removed outlier: 3.651A pdb=" N PHE C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 894 removed outlier: 3.955A pdb=" N MET C 892 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 893 " --> pdb=" O ASP C 890 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 894 " --> pdb=" O GLU C 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 889 through 894' Processing helix chain 'C' and resid 896 through 911 Processing helix chain 'C' and resid 955 through 959 Processing helix chain 'C' and resid 988 through 998 Processing helix chain 'C' and resid 1000 through 1009 Processing helix chain 'C' and resid 1014 through 1027 Processing helix chain 'C' and resid 1037 through 1050 removed outlier: 3.753A pdb=" N LYS C1041 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 27 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.682A pdb=" N VAL D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 132 through 141 removed outlier: 3.530A pdb=" N TYR D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 188 through 199 removed outlier: 3.884A pdb=" N ALA D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 214 removed outlier: 4.288A pdb=" N LEU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 237 removed outlier: 3.736A pdb=" N ALA D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 271 through 292 removed outlier: 3.721A pdb=" N LEU D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 377 through 384 removed outlier: 3.972A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 395 Processing helix chain 'D' and resid 400 through 411 removed outlier: 3.639A pdb=" N GLY D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 3.986A pdb=" N TRP D 416 " --> pdb=" O ASP D 412 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER D 417 " --> pdb=" O PRO D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.668A pdb=" N ASN D 496 " --> pdb=" O ALA D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 521 Processing helix chain 'D' and resid 537 through 547 removed outlier: 3.719A pdb=" N ALA D 541 " --> pdb=" O GLY D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 625 Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.556A pdb=" N ALA E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 44 removed outlier: 3.783A pdb=" N VAL E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 68 Processing helix chain 'F' and resid 71 through 82 Processing helix chain 'F' and resid 87 through 116 Processing helix chain 'F' and resid 174 through 196 Processing helix chain 'F' and resid 197 through 206 removed outlier: 3.883A pdb=" N VAL F 201 " --> pdb=" O ASN F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 231 Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.851A pdb=" N LYS F 237 " --> pdb=" O ASP F 234 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY F 238 " --> pdb=" O HIS F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 238' Processing helix chain 'F' and resid 240 through 260 removed outlier: 4.417A pdb=" N TYR F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 288 Processing helix chain 'F' and resid 293 through 302 Processing helix chain 'F' and resid 304 through 315 Processing helix chain 'F' and resid 332 through 337 removed outlier: 3.616A pdb=" N ILE F 337 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 362 Processing helix chain 'F' and resid 365 through 377 Processing helix chain 'F' and resid 385 through 393 removed outlier: 3.710A pdb=" N ILE F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.883A pdb=" N ILE F 400 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 424 removed outlier: 4.009A pdb=" N GLU F 422 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE F 424 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 24 removed outlier: 3.970A pdb=" N ARG Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR Z 24 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 48 removed outlier: 3.588A pdb=" N GLY Z 48 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 83 removed outlier: 3.569A pdb=" N GLY Z 83 " --> pdb=" O ARG Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 116 Processing helix chain 'Z' and resid 120 through 128 Processing helix chain 'Z' and resid 133 through 141 removed outlier: 3.932A pdb=" N VAL Z 137 " --> pdb=" O ASN Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 189 removed outlier: 3.738A pdb=" N GLY Z 178 " --> pdb=" O ILE Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 204 removed outlier: 3.609A pdb=" N SER Z 204 " --> pdb=" O LEU Z 200 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 239 Processing helix chain 'Z' and resid 264 through 273 Processing helix chain 'Z' and resid 294 through 298 removed outlier: 3.505A pdb=" N GLY Z 298 " --> pdb=" O GLN Z 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 294 through 298' Processing helix chain 'Z' and resid 312 through 331 Proline residue: Z 324 - end of helix Processing helix chain 'Z' and resid 332 through 336 removed outlier: 3.584A pdb=" N THR Z 335 " --> pdb=" O THR Z 332 " (cutoff:3.500A) Processing helix chain 'Z' and resid 630 through 632 No H-bonds generated for 'chain 'Z' and resid 630 through 632' Processing helix chain 'Z' and resid 978 through 991 Proline residue: Z 984 - end of helix Processing helix chain 'Z' and resid 1060 through 1073 Processing helix chain 'Z' and resid 1077 through 1103 Processing helix chain 'Z' and resid 1109 through 1121 removed outlier: 3.794A pdb=" N ILE Z1113 " --> pdb=" O SER Z1109 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE Z1116 " --> pdb=" O HIS Z1112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1142 through 1154 Processing helix chain 'Z' and resid 1170 through 1175 Processing helix chain 'Z' and resid 1178 through 1186 Processing helix chain 'Z' and resid 1187 through 1199 Processing helix chain 'Z' and resid 1206 through 1214 removed outlier: 3.757A pdb=" N ASN Z1210 " --> pdb=" O GLY Z1206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1219 through 1223 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 3.648A pdb=" N GLU A 26 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 22 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 196 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 195 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 179 " --> pdb=" O TRP A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 3.939A pdb=" N ALA A 55 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 53 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLY A 147 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 102 removed outlier: 3.999A pdb=" N GLY A 147 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 14 removed outlier: 6.679A pdb=" N LYS B 22 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 11 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR B 20 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 13 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 18 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 19 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 102 removed outlier: 7.705A pdb=" N GLU B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE B 58 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 56 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.675A pdb=" N GLY B 105 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 128 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 149 removed outlier: 4.232A pdb=" N GLY B 147 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.926A pdb=" N GLU C 46 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 84 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 48 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 82 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.926A pdb=" N GLU C 46 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 84 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 48 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 82 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 75 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP C 100 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET C 77 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AB5, first strand: chain 'C' and resid 305 through 308 removed outlier: 6.241A pdb=" N ASN C 121 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 134 removed outlier: 3.540A pdb=" N THR C 142 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR C 143 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'C' and resid 490 through 494 Processing sheet with id=AC1, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC2, first strand: chain 'C' and resid 572 through 573 removed outlier: 6.693A pdb=" N ILE C 572 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 605 through 608 removed outlier: 6.664A pdb=" N GLN C 591 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 580 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 613 through 614 Processing sheet with id=AC5, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AC6, first strand: chain 'C' and resid 926 through 927 removed outlier: 6.866A pdb=" N ILE C 672 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU C 836 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 674 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 673 " --> pdb=" O ALA C 853 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ILE C 852 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 657 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU C 854 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA C 659 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR C 943 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.331A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR C 809 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.331A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 705 through 706 removed outlier: 3.500A pdb=" N THR C 744 " --> pdb=" O ARG C 770 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 738 through 740 removed outlier: 6.660A pdb=" N LEU C 774 " --> pdb=" O LEU C 739 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 961 through 963 removed outlier: 7.830A pdb=" N ILE D 454 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 361 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU D 456 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL D 363 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 986 through 987 Processing sheet with id=AD4, first strand: chain 'C' and resid 1064 through 1066 Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 113 removed outlier: 7.153A pdb=" N ASP D 247 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N ALA D 110 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N THR D 245 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 161 through 162 removed outlier: 5.681A pdb=" N VAL D 147 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY D 187 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 185 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.241A pdb=" N PHE D 267 " --> pdb=" O ILE F 319 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 534 through 535 removed outlier: 7.547A pdb=" N PHE D 535 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 585 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 576 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 209 through 211 removed outlier: 3.692A pdb=" N ARG Z 210 " --> pdb=" O VAL Z 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'Z' and resid 220 through 222 removed outlier: 4.708A pdb=" N LEU Z 243 " --> pdb=" O ARG Z 281 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 225 through 226 removed outlier: 6.843A pdb=" N MET Z 225 " --> pdb=" O LYS Z 232 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 248 through 249 removed outlier: 6.848A pdb=" N VAL Z 248 " --> pdb=" O ILE Z 256 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 346 through 347 removed outlier: 3.822A pdb=" N THR Z 420 " --> pdb=" O GLU Z 347 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU Z 421 " --> pdb=" O LEU Z 404 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER Z 403 " --> pdb=" O VAL Z 377 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA Z 374 " --> pdb=" O VAL Z 366 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 394 through 398 removed outlier: 3.602A pdb=" N GLN Z 395 " --> pdb=" O TRP Z 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY Z 353 " --> pdb=" O VAL Z 413 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 431 through 438 removed outlier: 3.673A pdb=" N PHE Z 971 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL Z 438 " --> pdb=" O VAL Z 967 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL Z 967 " --> pdb=" O VAL Z 438 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG Z 465 " --> pdb=" O LEU Z 952 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR Z 464 " --> pdb=" O LYS Z 456 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 889 through 894 removed outlier: 3.853A pdb=" N VAL Z 937 " --> pdb=" O GLU Z 926 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU Z 926 " --> pdb=" O VAL Z 937 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG Z 939 " --> pdb=" O VAL Z 924 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL Z 924 " --> pdb=" O ARG Z 939 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA Z 941 " --> pdb=" O GLY Z 922 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY Z 922 " --> pdb=" O ALA Z 941 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 889 through 894 removed outlier: 5.560A pdb=" N ARG Z 940 " --> pdb=" O SER Z 477 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG Z 942 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 479 through 482 removed outlier: 3.968A pdb=" N LEU Z 882 " --> pdb=" O ARG Z 869 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG Z 869 " --> pdb=" O LEU Z 882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR Z 867 " --> pdb=" O GLU Z 884 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY Z 866 " --> pdb=" O VAL Z 497 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 559 through 560 removed outlier: 3.713A pdb=" N ALA Z 576 " --> pdb=" O LEU Z 782 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR Z 780 " --> pdb=" O LEU Z 578 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 618 through 619 removed outlier: 4.003A pdb=" N ILE Z 618 " --> pdb=" O MET Z 590 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET Z 590 " --> pdb=" O ILE Z 618 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 607 through 608 Processing sheet with id=AF4, first strand: chain 'Z' and resid 614 through 615 removed outlier: 3.870A pdb=" N TYR Z 731 " --> pdb=" O LEU Z 615 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 621 through 628 removed outlier: 3.600A pdb=" N ILE Z 625 " --> pdb=" O ARG Z 668 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG Z 668 " --> pdb=" O ILE Z 625 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS Z 627 " --> pdb=" O ILE Z 666 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE Z 666 " --> pdb=" O LYS Z 627 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU Z 669 " --> pdb=" O VAL Z 661 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL Z 661 " --> pdb=" O GLU Z 669 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 677 through 678 removed outlier: 3.929A pdb=" N LEU Z 724 " --> pdb=" O GLU Z 713 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU Z 713 " --> pdb=" O LEU Z 724 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 801 through 802 removed outlier: 3.549A pdb=" N ILE Z 801 " --> pdb=" O VAL Z 817 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 911 through 913 Processing sheet with id=AF9, first strand: chain 'Z' and resid 1006 through 1007 removed outlier: 4.167A pdb=" N VAL Z1023 " --> pdb=" O GLY Z1006 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 1139 through 1141 removed outlier: 3.510A pdb=" N ASP Z1127 " --> pdb=" O ARG Z1161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG Z1161 " --> pdb=" O ASP Z1127 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 8.85 Time building geometry restraints manager: 3.40 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: 8376 1.33 - 1.45: 5380 1.45 - 1.57: 16939 1.57 - 1.69: 208 1.69 - 1.81: 143 Bond restraints: 31046 Sorted by residual: bond pdb=" N ARG A 153 " pdb=" CA ARG A 153 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" C3' DA 2 17 " pdb=" O3' DA 2 17 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.84e+00 bond pdb=" CA THR Z 528 " pdb=" CB THR Z 528 " ideal model delta sigma weight residual 1.527 1.562 -0.035 1.61e-02 3.86e+03 4.83e+00 bond pdb=" C VAL Z 900 " pdb=" N LYS Z 901 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.59e-02 3.96e+03 4.37e+00 ... (remaining 31041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 41850 2.46 - 4.91: 609 4.91 - 7.37: 75 7.37 - 9.83: 16 9.83 - 12.28: 4 Bond angle restraints: 42554 Sorted by residual: angle pdb=" C ILE C 169 " pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 120.82 130.37 -9.55 1.50e+00 4.44e-01 4.06e+01 angle pdb=" N VAL Z1042 " pdb=" CA VAL Z1042 " pdb=" C VAL Z1042 " ideal model delta sigma weight residual 113.53 108.10 5.43 9.80e-01 1.04e+00 3.06e+01 angle pdb=" C ILE Z 527 " pdb=" N THR Z 528 " pdb=" CA THR Z 528 " ideal model delta sigma weight residual 122.82 129.93 -7.11 1.42e+00 4.96e-01 2.51e+01 angle pdb=" C GLY D 74 " pdb=" N LYS D 75 " pdb=" CA LYS D 75 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ALA Z 289 " pdb=" N ARG Z 290 " pdb=" CA ARG Z 290 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 42549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 17955 35.17 - 70.35: 628 70.35 - 105.52: 28 105.52 - 140.70: 1 140.70 - 175.87: 6 Dihedral angle restraints: 18618 sinusoidal: 8026 harmonic: 10592 Sorted by residual: dihedral pdb=" CA GLY Z 870 " pdb=" C GLY Z 870 " pdb=" N ILE Z 871 " pdb=" CA ILE Z 871 " ideal model delta harmonic sigma weight residual 180.00 -142.35 -37.65 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" O3B CTP 23001 " pdb=" O3A CTP 23001 " pdb=" PB CTP 23001 " pdb=" PA CTP 23001 " ideal model delta sinusoidal sigma weight residual 320.71 149.07 171.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA LYS A 15 " pdb=" C LYS A 15 " pdb=" N ASN A 16 " pdb=" CA ASN A 16 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 18615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3696 0.053 - 0.105: 924 0.105 - 0.158: 250 0.158 - 0.211: 30 0.211 - 0.263: 5 Chirality restraints: 4905 Sorted by residual: chirality pdb=" CB ILE B 68 " pdb=" CA ILE B 68 " pdb=" CG1 ILE B 68 " pdb=" CG2 ILE B 68 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE C 852 " pdb=" CA ILE C 852 " pdb=" CG1 ILE C 852 " pdb=" CG2 ILE C 852 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE Z 927 " pdb=" CA ILE Z 927 " pdb=" CG1 ILE Z 927 " pdb=" CG2 ILE Z 927 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4902 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 252 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO D 253 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 149 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO Z 150 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO Z 150 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO Z 150 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 373 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO C 374 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.035 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 71 2.46 - 3.07: 16726 3.07 - 3.68: 44821 3.68 - 4.29: 66574 4.29 - 4.90: 109642 Nonbonded interactions: 237834 Sorted by model distance: nonbonded pdb="MG MG D2003 " pdb=" O1B CTP 23001 " model vdw 1.845 2.170 nonbonded pdb="MG MG D2001 " pdb=" O2A CTP 23001 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 469 " pdb="MG MG D2001 " model vdw 2.154 2.170 nonbonded pdb=" OD1 ASP D 467 " pdb="MG MG D2001 " model vdw 2.160 2.170 nonbonded pdb="MG MG D2003 " pdb=" O2A CTP 23001 " model vdw 2.224 2.170 ... (remaining 237829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 154 or resid 166 through 187 or (resid 188 throu \ gh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 thr \ ough 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) \ or resid 193 through 230)) selection = (chain 'B' and (resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O )) or resid 52 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or (resid 133 through 135 and (name N \ or name CA or name C or name O or name CB )) or resid 136 through 151 or (resid \ 152 through 153 and (name N or name CA or name C or name O or name CB )) or resi \ d 154 through 225 or (resid 226 and (name N or name CA or name C or name O or na \ me CB )))) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.005 0.182 31053 Z= 0.217 Angle : 0.771 12.282 42560 Z= 0.433 Chirality : 0.051 0.263 4905 Planarity : 0.006 0.075 5204 Dihedral : 16.759 175.871 11808 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.11), residues: 3665 helix: -2.26 (0.11), residues: 1193 sheet: -0.99 (0.21), residues: 501 loop : -2.44 (0.11), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 242 TYR 0.026 0.002 TYR C 680 PHE 0.019 0.002 PHE Z1179 TRP 0.022 0.002 TRP C 875 HIS 0.006 0.001 HIS D 547 Details of bonding type rmsd covalent geometry : bond 0.00429 (31046) covalent geometry : angle 0.76912 (42554) hydrogen bonds : bond 0.19006 ( 1231) hydrogen bonds : angle 7.32973 ( 3403) metal coordination : bond 0.16141 ( 7) metal coordination : angle 4.21800 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 484 time to evaluate : 1.055 Fit side-chains REVERT: A 95 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7346 (mm110) REVERT: C 132 LYS cc_start: 0.7788 (ptmt) cc_final: 0.7579 (ttmt) REVERT: C 358 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7136 (tp30) REVERT: C 610 GLN cc_start: 0.8251 (pt0) cc_final: 0.8044 (pt0) REVERT: C 698 GLN cc_start: 0.7271 (mt0) cc_final: 0.7035 (mm-40) REVERT: C 800 PRO cc_start: 0.7476 (Cg_endo) cc_final: 0.7217 (Cg_exo) REVERT: C 804 MET cc_start: 0.8027 (ptp) cc_final: 0.7720 (ptp) REVERT: C 887 THR cc_start: 0.8949 (t) cc_final: 0.8745 (m) REVERT: C 1016 GLN cc_start: 0.7318 (mp10) cc_final: 0.6869 (mm-40) REVERT: D 311 ASP cc_start: 0.8050 (m-30) cc_final: 0.7759 (m-30) REVERT: D 406 LYS cc_start: 0.8088 (tttt) cc_final: 0.7804 (ttmp) REVERT: E 17 GLU cc_start: 0.7597 (tp30) cc_final: 0.7266 (tm-30) REVERT: F 104 LEU cc_start: 0.7678 (tp) cc_final: 0.7443 (tp) REVERT: F 347 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6762 (mm-30) REVERT: F 374 LEU cc_start: 0.7902 (mp) cc_final: 0.7567 (mm) REVERT: Z 365 LYS cc_start: 0.6670 (pttp) cc_final: 0.5185 (mtpm) REVERT: Z 437 ASP cc_start: 0.5653 (m-30) cc_final: 0.5355 (m-30) outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 0.8839 time to fit residues: 492.5379 Evaluate side-chains 301 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 916 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 169 GLN B 205 GLN C 76 GLN C 496 GLN C 778 ASN C 903 HIS C 923 HIS D 114 HIS D 149 ASN D 157 GLN D 240 GLN D 283 ASN D 472 GLN D 553 HIS F 97 GLN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 108 GLN Z 305 HIS Z 462 ASN Z 468 GLN Z1059 ASN Z1102 GLN Z1210 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.171583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132112 restraints weight = 34981.197| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.05 r_work: 0.3030 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31053 Z= 0.149 Angle : 0.570 9.359 42560 Z= 0.308 Chirality : 0.044 0.217 4905 Planarity : 0.005 0.072 5204 Dihedral : 16.418 177.446 5191 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.36 % Allowed : 12.08 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 3665 helix: -0.24 (0.14), residues: 1217 sheet: -0.51 (0.21), residues: 536 loop : -2.03 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 48 TYR 0.020 0.002 TYR C 680 PHE 0.019 0.001 PHE A 174 TRP 0.011 0.001 TRP C 875 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00342 (31046) covalent geometry : angle 0.57006 (42554) hydrogen bonds : bond 0.05447 ( 1231) hydrogen bonds : angle 4.94929 ( 3403) metal coordination : bond 0.00439 ( 7) metal coordination : angle 1.06682 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 326 time to evaluate : 1.229 Fit side-chains REVERT: A 95 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7916 (mm110) REVERT: B 14 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7221 (mtm180) REVERT: B 87 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8285 (pt) REVERT: B 136 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7092 (tp) REVERT: C 53 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7485 (p0) REVERT: C 82 ARG cc_start: 0.6068 (ttp80) cc_final: 0.5268 (ptm160) REVERT: C 132 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8008 (ttmt) REVERT: C 158 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6833 (tt0) REVERT: C 264 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6957 (mtm180) REVERT: C 358 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8054 (tp30) REVERT: C 497 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: C 698 GLN cc_start: 0.7510 (mt0) cc_final: 0.6653 (tm-30) REVERT: C 794 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6049 (mtmm) REVERT: C 804 MET cc_start: 0.8481 (ptp) cc_final: 0.8223 (ptp) REVERT: C 887 THR cc_start: 0.9077 (t) cc_final: 0.8829 (m) REVERT: C 949 MET cc_start: 0.9269 (mmt) cc_final: 0.8832 (mmm) REVERT: C 1016 GLN cc_start: 0.8088 (mp10) cc_final: 0.7654 (mm-40) REVERT: D 23 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: D 329 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8276 (ttp80) REVERT: D 406 LYS cc_start: 0.8365 (tttt) cc_final: 0.7868 (ttmp) REVERT: D 506 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8639 (pt) REVERT: D 569 LYS cc_start: 0.6810 (mtmt) cc_final: 0.6477 (mttp) REVERT: E 17 GLU cc_start: 0.8245 (tp30) cc_final: 0.7503 (tm-30) REVERT: F 301 MET cc_start: 0.7153 (mmm) cc_final: 0.6715 (mmm) REVERT: F 347 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7439 (mm-30) REVERT: F 395 VAL cc_start: 0.5888 (OUTLIER) cc_final: 0.5654 (t) REVERT: F 419 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6415 (tp) REVERT: Z 34 ASP cc_start: 0.8622 (t70) cc_final: 0.8291 (t0) REVERT: Z 365 LYS cc_start: 0.5779 (pttp) cc_final: 0.4017 (mtpm) REVERT: Z 1038 GLN cc_start: 0.5476 (mp10) cc_final: 0.4652 (pt0) outliers start: 69 outliers final: 17 residues processed: 362 average time/residue: 0.8066 time to fit residues: 338.2703 Evaluate side-chains 318 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 135 optimal weight: 1.9990 chunk 335 optimal weight: 0.0980 chunk 121 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 364 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 16 ASN C 610 GLN C 778 ASN D 143 ASN D 149 ASN D 307 GLN D 328 ASN ** D 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 ASN F 195 GLN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 664 ASN Z1059 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132810 restraints weight = 35169.936| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.98 r_work: 0.3012 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31053 Z= 0.119 Angle : 0.521 9.736 42560 Z= 0.280 Chirality : 0.042 0.168 4905 Planarity : 0.005 0.074 5204 Dihedral : 16.244 176.510 5189 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.74 % Allowed : 13.76 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3665 helix: 0.66 (0.15), residues: 1210 sheet: -0.35 (0.22), residues: 543 loop : -1.76 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 48 TYR 0.016 0.001 TYR C 680 PHE 0.014 0.001 PHE Z 43 TRP 0.010 0.001 TRP C 875 HIS 0.003 0.001 HIS C 577 Details of bonding type rmsd covalent geometry : bond 0.00269 (31046) covalent geometry : angle 0.52067 (42554) hydrogen bonds : bond 0.04683 ( 1231) hydrogen bonds : angle 4.52336 ( 3403) metal coordination : bond 0.00106 ( 7) metal coordination : angle 0.98424 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 307 time to evaluate : 0.883 Fit side-chains REVERT: A 48 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 95 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7888 (mm110) REVERT: A 138 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8983 (ttp) REVERT: B 14 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7322 (mtm180) REVERT: B 74 ASP cc_start: 0.7119 (p0) cc_final: 0.6871 (p0) REVERT: B 87 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8203 (pt) REVERT: B 136 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6999 (tp) REVERT: B 143 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: C 57 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7807 (mmtp) REVERT: C 78 TYR cc_start: 0.7973 (m-80) cc_final: 0.7739 (m-80) REVERT: C 82 ARG cc_start: 0.6072 (ttp80) cc_final: 0.5316 (ptm160) REVERT: C 132 LYS cc_start: 0.8323 (ptmt) cc_final: 0.7972 (ttmt) REVERT: C 158 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: C 358 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8020 (tp30) REVERT: C 497 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: C 698 GLN cc_start: 0.7535 (mt0) cc_final: 0.6563 (tm-30) REVERT: C 728 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: C 794 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6506 (mtmt) REVERT: C 804 MET cc_start: 0.8420 (ptp) cc_final: 0.8168 (ptp) REVERT: C 887 THR cc_start: 0.8936 (t) cc_final: 0.8717 (m) REVERT: C 949 MET cc_start: 0.9232 (mmt) cc_final: 0.8866 (mmm) REVERT: C 1016 GLN cc_start: 0.8074 (mp10) cc_final: 0.7615 (mm-40) REVERT: D 23 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: D 329 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.8228 (ttp80) REVERT: D 406 LYS cc_start: 0.8366 (tttt) cc_final: 0.7862 (ttmp) REVERT: D 506 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8676 (pt) REVERT: D 569 LYS cc_start: 0.6872 (mtmt) cc_final: 0.6476 (mttp) REVERT: D 622 GLU cc_start: 0.7683 (pt0) cc_final: 0.7364 (pp20) REVERT: E 17 GLU cc_start: 0.8223 (tp30) cc_final: 0.7496 (tm-30) REVERT: F 301 MET cc_start: 0.7017 (mmm) cc_final: 0.6566 (mmm) REVERT: F 347 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7380 (mm-30) REVERT: F 395 VAL cc_start: 0.5972 (OUTLIER) cc_final: 0.5747 (t) REVERT: Z 34 ASP cc_start: 0.8514 (t70) cc_final: 0.8160 (t0) REVERT: Z 225 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7985 (ttp) REVERT: Z 365 LYS cc_start: 0.6112 (pttp) cc_final: 0.4372 (mtpm) REVERT: Z 447 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4165 (mt) REVERT: Z 452 VAL cc_start: 0.5619 (OUTLIER) cc_final: 0.5219 (p) REVERT: Z 653 GLN cc_start: 0.4899 (tp40) cc_final: 0.4512 (tm130) outliers start: 80 outliers final: 22 residues processed: 355 average time/residue: 0.7128 time to fit residues: 294.2908 Evaluate side-chains 325 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 728 ARG Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain C residue 911 GLN Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 225 MET Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 1124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 330 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 111 GLN B 16 ASN C 610 GLN C 654 GLN C 778 ASN ** D 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 664 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129870 restraints weight = 34745.133| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.84 r_work: 0.2993 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31053 Z= 0.157 Angle : 0.554 9.959 42560 Z= 0.296 Chirality : 0.044 0.174 4905 Planarity : 0.005 0.062 5204 Dihedral : 16.295 176.464 5189 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.29 % Allowed : 14.75 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.13), residues: 3665 helix: 0.94 (0.15), residues: 1213 sheet: -0.23 (0.22), residues: 535 loop : -1.63 (0.12), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 447 TYR 0.021 0.002 TYR C 680 PHE 0.019 0.002 PHE Z 3 TRP 0.009 0.001 TRP C 875 HIS 0.004 0.001 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.00371 (31046) covalent geometry : angle 0.55420 (42554) hydrogen bonds : bond 0.05089 ( 1231) hydrogen bonds : angle 4.43753 ( 3403) metal coordination : bond 0.00090 ( 7) metal coordination : angle 0.71208 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 307 time to evaluate : 1.148 Fit side-chains REVERT: A 48 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 95 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7829 (mm110) REVERT: A 137 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 138 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.9040 (ttp) REVERT: A 141 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7675 (ttp-170) REVERT: B 14 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7209 (mtm180) REVERT: B 87 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 136 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7081 (tp) REVERT: C 57 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7887 (mmtp) REVERT: C 78 TYR cc_start: 0.8042 (m-80) cc_final: 0.7830 (m-80) REVERT: C 82 ARG cc_start: 0.6120 (ttp80) cc_final: 0.5401 (ptm160) REVERT: C 132 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8026 (ttmt) REVERT: C 158 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: C 170 ASP cc_start: 0.4264 (OUTLIER) cc_final: 0.3834 (p0) REVERT: C 330 ARG cc_start: 0.6695 (mtp-110) cc_final: 0.6487 (ttp-170) REVERT: C 358 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8019 (tp30) REVERT: C 497 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: C 646 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8360 (pp20) REVERT: C 697 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6644 (mmm160) REVERT: C 804 MET cc_start: 0.8449 (ptp) cc_final: 0.8208 (ptp) REVERT: C 887 THR cc_start: 0.8999 (t) cc_final: 0.8725 (m) REVERT: C 949 MET cc_start: 0.9248 (mmt) cc_final: 0.8836 (mmm) REVERT: D 23 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: D 329 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8253 (ttp80) REVERT: D 406 LYS cc_start: 0.8400 (tttt) cc_final: 0.7882 (ttmp) REVERT: D 506 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8643 (pt) REVERT: D 578 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6232 (mm-30) REVERT: D 622 GLU cc_start: 0.7688 (pt0) cc_final: 0.7472 (pp20) REVERT: E 17 GLU cc_start: 0.8211 (tp30) cc_final: 0.7502 (tm-30) REVERT: E 24 SER cc_start: 0.7677 (p) cc_final: 0.7285 (t) REVERT: F 301 MET cc_start: 0.7059 (mmm) cc_final: 0.6578 (mmm) REVERT: F 347 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7419 (mm-30) REVERT: F 395 VAL cc_start: 0.6062 (OUTLIER) cc_final: 0.5806 (t) REVERT: F 419 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6750 (tp) REVERT: Z 34 ASP cc_start: 0.8665 (t70) cc_final: 0.8294 (t0) REVERT: Z 365 LYS cc_start: 0.6147 (pttp) cc_final: 0.4337 (mtpm) REVERT: Z 447 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.4152 (mt) REVERT: Z 452 VAL cc_start: 0.5634 (OUTLIER) cc_final: 0.5221 (p) REVERT: Z 653 GLN cc_start: 0.4960 (OUTLIER) cc_final: 0.4395 (tm130) REVERT: Z 1132 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.4765 (p) outliers start: 96 outliers final: 43 residues processed: 365 average time/residue: 0.6664 time to fit residues: 283.6045 Evaluate side-chains 359 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 728 ARG Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 911 GLN Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 170 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 867 THR Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 959 LEU Chi-restraints excluded: chain Z residue 966 LEU Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1124 VAL Chi-restraints excluded: chain Z residue 1132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 350 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 111 GLN A 124 ASN B 16 ASN C 610 GLN C 698 GLN C 778 ASN D 526 ASN D 608 GLN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 482 ASN Z 664 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127847 restraints weight = 34959.834| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.76 r_work: 0.2941 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31053 Z= 0.242 Angle : 0.640 9.750 42560 Z= 0.340 Chirality : 0.047 0.205 4905 Planarity : 0.006 0.071 5204 Dihedral : 16.493 177.638 5189 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.04 % Allowed : 15.57 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 3665 helix: 0.78 (0.15), residues: 1213 sheet: -0.33 (0.21), residues: 561 loop : -1.64 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 48 TYR 0.025 0.002 TYR C 680 PHE 0.030 0.002 PHE A 174 TRP 0.012 0.002 TRP C 732 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00591 (31046) covalent geometry : angle 0.63995 (42554) hydrogen bonds : bond 0.06038 ( 1231) hydrogen bonds : angle 4.60049 ( 3403) metal coordination : bond 0.00202 ( 7) metal coordination : angle 0.77746 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 297 time to evaluate : 1.154 Fit side-chains REVERT: A 48 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 95 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7869 (mm110) REVERT: A 137 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: A 138 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.9042 (ttp) REVERT: B 14 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7302 (mtm180) REVERT: B 87 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8356 (pt) REVERT: B 113 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: B 136 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7031 (tp) REVERT: B 143 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 82 ARG cc_start: 0.6218 (ttp80) cc_final: 0.5840 (mtm180) REVERT: C 158 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: C 358 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8069 (tp30) REVERT: C 497 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: C 646 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: C 697 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6708 (mmm160) REVERT: C 698 GLN cc_start: 0.7693 (mt0) cc_final: 0.6919 (pt0) REVERT: C 949 MET cc_start: 0.9313 (mmt) cc_final: 0.8877 (mmm) REVERT: C 1016 GLN cc_start: 0.8151 (mp10) cc_final: 0.7704 (mm-40) REVERT: D 23 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7980 (mtp85) REVERT: D 406 LYS cc_start: 0.8478 (tttt) cc_final: 0.7972 (ttmp) REVERT: D 407 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8369 (mp) REVERT: D 506 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8563 (pt) REVERT: D 622 GLU cc_start: 0.7805 (pt0) cc_final: 0.7519 (pp20) REVERT: E 17 GLU cc_start: 0.8217 (tp30) cc_final: 0.7542 (tm-30) REVERT: E 24 SER cc_start: 0.7728 (p) cc_final: 0.7328 (t) REVERT: F 347 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 395 VAL cc_start: 0.5942 (OUTLIER) cc_final: 0.5670 (t) REVERT: F 402 GLN cc_start: 0.6918 (mt0) cc_final: 0.6405 (mt0) REVERT: Z 153 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.4760 (tt0) REVERT: Z 365 LYS cc_start: 0.6077 (pttp) cc_final: 0.4205 (mtpm) REVERT: Z 447 LEU cc_start: 0.4699 (OUTLIER) cc_final: 0.4207 (mt) REVERT: Z 452 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.5150 (p) REVERT: Z 653 GLN cc_start: 0.4884 (OUTLIER) cc_final: 0.4253 (tm130) REVERT: Z 966 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4502 (pp) outliers start: 118 outliers final: 57 residues processed: 376 average time/residue: 0.6357 time to fit residues: 281.2628 Evaluate side-chains 360 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 911 GLN Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 153 GLU Chi-restraints excluded: chain Z residue 154 ILE Chi-restraints excluded: chain Z residue 201 VAL Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 249 VAL Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 867 THR Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 966 LEU Chi-restraints excluded: chain Z residue 981 GLN Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 242 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 16 ASN C 610 GLN C 778 ASN D 526 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 482 ASN Z 664 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126543 restraints weight = 34827.429| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.95 r_work: 0.2948 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31053 Z= 0.223 Angle : 0.625 9.121 42560 Z= 0.333 Chirality : 0.047 0.208 4905 Planarity : 0.005 0.061 5204 Dihedral : 16.511 176.697 5189 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.45 % Allowed : 15.57 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 3665 helix: 0.81 (0.15), residues: 1213 sheet: -0.39 (0.21), residues: 571 loop : -1.57 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 210 TYR 0.023 0.002 TYR Z 6 PHE 0.022 0.002 PHE A 174 TRP 0.015 0.002 TRP C 875 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00543 (31046) covalent geometry : angle 0.62506 (42554) hydrogen bonds : bond 0.05848 ( 1231) hydrogen bonds : angle 4.58311 ( 3403) metal coordination : bond 0.00227 ( 7) metal coordination : angle 0.98086 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 286 time to evaluate : 0.908 Fit side-chains REVERT: A 48 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 92 ASP cc_start: 0.6867 (t0) cc_final: 0.6646 (t0) REVERT: A 95 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7864 (mm110) REVERT: A 137 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 138 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9033 (ttp) REVERT: B 14 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7374 (mtm180) REVERT: B 87 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8384 (pt) REVERT: B 136 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7098 (tp) REVERT: B 143 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: C 78 TYR cc_start: 0.8081 (m-80) cc_final: 0.7798 (m-80) REVERT: C 158 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: C 330 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6306 (ttp-170) REVERT: C 358 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8049 (tp30) REVERT: C 466 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7883 (pp20) REVERT: C 467 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: C 497 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: C 646 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8399 (pp20) REVERT: C 697 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6686 (mmm160) REVERT: C 698 GLN cc_start: 0.7715 (mt0) cc_final: 0.6954 (pt0) REVERT: C 949 MET cc_start: 0.9289 (mmt) cc_final: 0.8945 (mmm) REVERT: C 1016 GLN cc_start: 0.8129 (mp10) cc_final: 0.7687 (mm-40) REVERT: D 23 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7977 (mtp85) REVERT: D 41 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8678 (mtpp) REVERT: D 406 LYS cc_start: 0.8466 (tttt) cc_final: 0.7951 (ttmp) REVERT: D 407 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 506 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8543 (pt) REVERT: D 622 GLU cc_start: 0.7783 (pt0) cc_final: 0.7519 (pp20) REVERT: E 17 GLU cc_start: 0.8234 (tp30) cc_final: 0.7542 (tm-30) REVERT: E 24 SER cc_start: 0.7718 (p) cc_final: 0.7295 (t) REVERT: F 347 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7496 (mm-30) REVERT: F 395 VAL cc_start: 0.5955 (OUTLIER) cc_final: 0.5711 (t) REVERT: F 402 GLN cc_start: 0.7205 (mt0) cc_final: 0.6663 (mt0) REVERT: Z 365 LYS cc_start: 0.6063 (pttp) cc_final: 0.4122 (mtpm) REVERT: Z 447 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4136 (mt) REVERT: Z 452 VAL cc_start: 0.5599 (OUTLIER) cc_final: 0.5133 (p) REVERT: Z 454 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4560 (tm-30) REVERT: Z 653 GLN cc_start: 0.4594 (OUTLIER) cc_final: 0.4156 (tm130) REVERT: Z 1141 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8031 (mt-10) outliers start: 130 outliers final: 65 residues processed: 373 average time/residue: 0.6391 time to fit residues: 279.6848 Evaluate side-chains 367 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 281 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 154 ILE Chi-restraints excluded: chain Z residue 170 THR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 201 VAL Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 249 VAL Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 457 THR Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 551 ILE Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 981 GLN Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1114 GLU Chi-restraints excluded: chain Z residue 1124 VAL Chi-restraints excluded: chain Z residue 1140 VAL Chi-restraints excluded: chain Z residue 1211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 173 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 chunk 291 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 325 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 610 GLN C 778 ASN D 526 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128952 restraints weight = 34833.955| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.94 r_work: 0.2984 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31053 Z= 0.168 Angle : 0.574 8.940 42560 Z= 0.307 Chirality : 0.045 0.180 4905 Planarity : 0.005 0.053 5204 Dihedral : 16.412 175.712 5189 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.00 % Allowed : 16.70 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 3665 helix: 1.01 (0.15), residues: 1213 sheet: -0.32 (0.21), residues: 571 loop : -1.49 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 48 TYR 0.018 0.002 TYR Z 6 PHE 0.022 0.002 PHE A 174 TRP 0.009 0.001 TRP C 732 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00403 (31046) covalent geometry : angle 0.57404 (42554) hydrogen bonds : bond 0.05247 ( 1231) hydrogen bonds : angle 4.44530 ( 3403) metal coordination : bond 0.00236 ( 7) metal coordination : angle 0.99712 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 295 time to evaluate : 1.158 Fit side-chains REVERT: A 48 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 92 ASP cc_start: 0.7272 (t0) cc_final: 0.6998 (t0) REVERT: A 137 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 138 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8992 (ttp) REVERT: B 14 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7360 (mtm180) REVERT: B 87 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8379 (pt) REVERT: B 136 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7125 (tp) REVERT: B 143 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: C 78 TYR cc_start: 0.8016 (m-80) cc_final: 0.7770 (m-80) REVERT: C 82 ARG cc_start: 0.6313 (ttp80) cc_final: 0.5918 (mtm180) REVERT: C 158 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: C 326 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: C 330 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6370 (ttp-170) REVERT: C 358 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8042 (tp30) REVERT: C 466 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7783 (pp20) REVERT: C 467 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5640 (mp0) REVERT: C 497 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: C 505 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: C 646 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: C 697 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6623 (mmm160) REVERT: C 698 GLN cc_start: 0.7658 (mt0) cc_final: 0.6986 (pt0) REVERT: C 758 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (mt) REVERT: C 949 MET cc_start: 0.9274 (mmt) cc_final: 0.8943 (mmm) REVERT: D 23 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7993 (mtp85) REVERT: D 41 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8669 (mtpp) REVERT: D 49 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7686 (p) REVERT: D 406 LYS cc_start: 0.8471 (tttt) cc_final: 0.7974 (ttmp) REVERT: D 506 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8596 (pt) REVERT: D 578 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6270 (mm-30) REVERT: D 622 GLU cc_start: 0.7725 (pt0) cc_final: 0.7425 (pp20) REVERT: E 17 GLU cc_start: 0.8284 (tp30) cc_final: 0.7583 (tm-30) REVERT: E 24 SER cc_start: 0.7755 (p) cc_final: 0.7350 (t) REVERT: F 301 MET cc_start: 0.7019 (mmm) cc_final: 0.6617 (mmm) REVERT: F 347 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7482 (mm-30) REVERT: F 367 ARG cc_start: 0.6956 (ttt180) cc_final: 0.6452 (tpp80) REVERT: Z 365 LYS cc_start: 0.6197 (pttp) cc_final: 0.4301 (mtpm) REVERT: Z 368 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.5096 (p) REVERT: Z 447 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4141 (mt) REVERT: Z 452 VAL cc_start: 0.5572 (OUTLIER) cc_final: 0.5084 (p) REVERT: Z 454 GLU cc_start: 0.4899 (OUTLIER) cc_final: 0.4441 (tm-30) REVERT: Z 653 GLN cc_start: 0.4582 (OUTLIER) cc_final: 0.4141 (tm130) REVERT: Z 1141 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8023 (mt-10) outliers start: 117 outliers final: 61 residues processed: 374 average time/residue: 0.5777 time to fit residues: 253.3768 Evaluate side-chains 369 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 154 ILE Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 249 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 457 THR Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 551 ILE Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1124 VAL Chi-restraints excluded: chain Z residue 1211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN C 778 ASN D 526 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 370 HIS Z 482 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126667 restraints weight = 35067.235| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.41 r_work: 0.2922 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31053 Z= 0.192 Angle : 0.601 8.868 42560 Z= 0.320 Chirality : 0.046 0.195 4905 Planarity : 0.005 0.059 5204 Dihedral : 16.457 176.080 5189 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.11 % Allowed : 17.21 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.13), residues: 3665 helix: 0.97 (0.15), residues: 1214 sheet: -0.35 (0.21), residues: 582 loop : -1.48 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 210 TYR 0.020 0.002 TYR C 680 PHE 0.024 0.002 PHE A 174 TRP 0.011 0.002 TRP C 732 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00464 (31046) covalent geometry : angle 0.60078 (42554) hydrogen bonds : bond 0.05544 ( 1231) hydrogen bonds : angle 4.46321 ( 3403) metal coordination : bond 0.00260 ( 7) metal coordination : angle 0.97013 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 288 time to evaluate : 0.823 Fit side-chains REVERT: A 48 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 92 ASP cc_start: 0.7064 (t0) cc_final: 0.6818 (t0) REVERT: A 95 GLN cc_start: 0.7862 (mm110) cc_final: 0.7628 (mm-40) REVERT: A 137 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: A 138 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8997 (ttp) REVERT: B 14 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7346 (mtm180) REVERT: B 113 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5313 (pm20) REVERT: B 136 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7272 (tp) REVERT: B 143 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: C 78 TYR cc_start: 0.7982 (m-80) cc_final: 0.7717 (m-80) REVERT: C 82 ARG cc_start: 0.6365 (ttp80) cc_final: 0.5972 (mtm180) REVERT: C 170 ASP cc_start: 0.4578 (OUTLIER) cc_final: 0.4029 (p0) REVERT: C 330 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6345 (ttp-170) REVERT: C 358 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7833 (tp30) REVERT: C 466 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: C 467 GLU cc_start: 0.6369 (mm-30) cc_final: 0.5576 (mp0) REVERT: C 497 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: C 505 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: C 646 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8275 (pp20) REVERT: C 697 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6644 (mmm160) REVERT: C 698 GLN cc_start: 0.7674 (mt0) cc_final: 0.7021 (pt0) REVERT: C 949 MET cc_start: 0.9216 (mmt) cc_final: 0.8790 (mmm) REVERT: D 23 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7929 (mtp85) REVERT: D 41 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8564 (mtpp) REVERT: D 95 GLU cc_start: 0.8140 (pt0) cc_final: 0.7649 (pm20) REVERT: D 406 LYS cc_start: 0.8463 (tttt) cc_final: 0.7973 (ttmp) REVERT: D 506 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8535 (pt) REVERT: D 578 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: E 17 GLU cc_start: 0.8117 (tp30) cc_final: 0.7513 (tm-30) REVERT: E 24 SER cc_start: 0.7582 (p) cc_final: 0.7191 (t) REVERT: F 301 MET cc_start: 0.7060 (mmm) cc_final: 0.6792 (mmm) REVERT: F 347 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7319 (mm-30) REVERT: F 367 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6459 (tpp80) REVERT: F 391 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6188 (mp10) REVERT: F 402 GLN cc_start: 0.7262 (mt0) cc_final: 0.6616 (mt0) REVERT: Z 365 LYS cc_start: 0.6292 (pttp) cc_final: 0.4418 (mtpm) REVERT: Z 368 THR cc_start: 0.5426 (OUTLIER) cc_final: 0.5130 (p) REVERT: Z 447 LEU cc_start: 0.4612 (OUTLIER) cc_final: 0.4100 (mt) REVERT: Z 452 VAL cc_start: 0.5706 (OUTLIER) cc_final: 0.5190 (p) REVERT: Z 454 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.4544 (tm-30) REVERT: Z 653 GLN cc_start: 0.4591 (OUTLIER) cc_final: 0.4197 (tm130) REVERT: Z 1141 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 120 outliers final: 68 residues processed: 374 average time/residue: 0.5805 time to fit residues: 254.3394 Evaluate side-chains 377 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 286 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 367 ARG Chi-restraints excluded: chain F residue 391 GLN Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 154 ILE Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 201 VAL Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 249 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 457 THR Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 551 ILE Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 1042 VAL Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1114 GLU Chi-restraints excluded: chain Z residue 1124 VAL Chi-restraints excluded: chain Z residue 1140 VAL Chi-restraints excluded: chain Z residue 1166 LEU Chi-restraints excluded: chain Z residue 1211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 265 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 286 optimal weight: 0.0980 chunk 238 optimal weight: 0.5980 chunk 330 optimal weight: 0.1980 chunk 357 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 246 optimal weight: 0.3980 chunk 270 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 408 HIS C 610 GLN C 616 ASN C 778 ASN D 526 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 327 GLN Z 370 HIS Z 482 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134206 restraints weight = 35229.392| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.20 r_work: 0.3023 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31053 Z= 0.102 Angle : 0.507 8.321 42560 Z= 0.271 Chirality : 0.042 0.196 4905 Planarity : 0.004 0.052 5204 Dihedral : 16.145 176.702 5189 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.26 % Allowed : 19.34 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3665 helix: 1.36 (0.15), residues: 1224 sheet: -0.26 (0.21), residues: 590 loop : -1.30 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 409 TYR 0.012 0.001 TYR B 20 PHE 0.019 0.001 PHE Z 339 TRP 0.016 0.001 TRP D 25 HIS 0.002 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00220 (31046) covalent geometry : angle 0.50712 (42554) hydrogen bonds : bond 0.04083 ( 1231) hydrogen bonds : angle 4.12068 ( 3403) metal coordination : bond 0.00170 ( 7) metal coordination : angle 1.16590 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 324 time to evaluate : 1.180 Fit side-chains REVERT: A 92 ASP cc_start: 0.7070 (t0) cc_final: 0.6843 (t0) REVERT: A 139 GLU cc_start: 0.8699 (tt0) cc_final: 0.8093 (pt0) REVERT: B 143 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: C 82 ARG cc_start: 0.6218 (ttp80) cc_final: 0.5888 (mtm180) REVERT: C 170 ASP cc_start: 0.4448 (OUTLIER) cc_final: 0.3906 (p0) REVERT: C 358 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7804 (tp30) REVERT: C 467 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5421 (mp0) REVERT: C 497 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6434 (tp30) REVERT: C 541 MET cc_start: 0.8451 (mtt) cc_final: 0.8237 (mtp) REVERT: C 646 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8111 (pp20) REVERT: C 697 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6540 (mmm160) REVERT: C 698 GLN cc_start: 0.7583 (mt0) cc_final: 0.7061 (pt0) REVERT: C 936 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8642 (mm-30) REVERT: C 949 MET cc_start: 0.9014 (mmt) cc_final: 0.8684 (mmm) REVERT: D 23 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7908 (mtp85) REVERT: D 41 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8501 (mtpp) REVERT: D 88 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7634 (ttm-80) REVERT: D 95 GLU cc_start: 0.8110 (pt0) cc_final: 0.7642 (pm20) REVERT: D 382 GLU cc_start: 0.8460 (tp30) cc_final: 0.8236 (tp30) REVERT: D 406 LYS cc_start: 0.8473 (tttt) cc_final: 0.7952 (ttmp) REVERT: D 578 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: E 17 GLU cc_start: 0.8093 (tp30) cc_final: 0.7536 (tm-30) REVERT: E 24 SER cc_start: 0.7646 (p) cc_final: 0.7302 (t) REVERT: F 301 MET cc_start: 0.7108 (mmm) cc_final: 0.6796 (mmm) REVERT: F 347 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7279 (mm-30) REVERT: F 367 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6506 (tpp80) REVERT: F 391 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: Z 34 ASP cc_start: 0.8288 (t70) cc_final: 0.7912 (t0) REVERT: Z 311 GLU cc_start: 0.8068 (tt0) cc_final: 0.7816 (tp30) REVERT: Z 365 LYS cc_start: 0.6103 (pttp) cc_final: 0.4553 (mtpm) REVERT: Z 375 GLU cc_start: 0.5236 (mt-10) cc_final: 0.4854 (tt0) REVERT: Z 452 VAL cc_start: 0.5616 (OUTLIER) cc_final: 0.5159 (p) REVERT: Z 454 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4630 (tm-30) REVERT: Z 653 GLN cc_start: 0.4498 (OUTLIER) cc_final: 0.4149 (tm130) REVERT: Z 1141 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7852 (mt-10) outliers start: 66 outliers final: 26 residues processed: 370 average time/residue: 0.7031 time to fit residues: 302.8314 Evaluate side-chains 344 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain F residue 391 GLN Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 154 ILE Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 201 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 457 THR Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 551 ILE Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 290 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 135 optimal weight: 0.0070 chunk 213 optimal weight: 0.7980 chunk 159 optimal weight: 0.0670 chunk 202 optimal weight: 0.2980 chunk 214 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 610 GLN C 778 ASN ** D 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN F 402 GLN Z 370 HIS ** Z 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133720 restraints weight = 35018.780| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.46 r_work: 0.3026 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31053 Z= 0.100 Angle : 0.504 9.390 42560 Z= 0.268 Chirality : 0.042 0.182 4905 Planarity : 0.004 0.079 5204 Dihedral : 16.026 177.791 5189 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.51 % Allowed : 20.47 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.14), residues: 3665 helix: 1.56 (0.15), residues: 1225 sheet: -0.14 (0.21), residues: 594 loop : -1.15 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.014 0.001 TYR C 998 PHE 0.019 0.001 PHE Z 91 TRP 0.010 0.001 TRP D 25 HIS 0.004 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00218 (31046) covalent geometry : angle 0.50388 (42554) hydrogen bonds : bond 0.03939 ( 1231) hydrogen bonds : angle 3.98270 ( 3403) metal coordination : bond 0.00138 ( 7) metal coordination : angle 1.05004 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 1.190 Fit side-chains REVERT: A 139 GLU cc_start: 0.8651 (tt0) cc_final: 0.8146 (pt0) REVERT: B 143 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: C 82 ARG cc_start: 0.6195 (ttp80) cc_final: 0.5868 (mtm180) REVERT: C 137 LYS cc_start: 0.2433 (OUTLIER) cc_final: 0.1861 (mmtt) REVERT: C 358 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7835 (tp30) REVERT: C 467 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5446 (mp0) REVERT: C 497 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6364 (tp30) REVERT: C 697 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.6486 (mmm160) REVERT: C 698 GLN cc_start: 0.7646 (mt0) cc_final: 0.7171 (pt0) REVERT: C 936 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8551 (mm-30) REVERT: C 949 MET cc_start: 0.8778 (mmt) cc_final: 0.8513 (mmm) REVERT: D 23 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7842 (mtp85) REVERT: D 41 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8518 (mtpp) REVERT: D 48 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8035 (ttp80) REVERT: D 88 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7629 (ttm-80) REVERT: D 382 GLU cc_start: 0.8416 (tp30) cc_final: 0.8159 (tp30) REVERT: D 406 LYS cc_start: 0.8415 (tttt) cc_final: 0.7884 (ttmm) REVERT: E 17 GLU cc_start: 0.8090 (tp30) cc_final: 0.7527 (tm-30) REVERT: E 24 SER cc_start: 0.7664 (p) cc_final: 0.7330 (t) REVERT: F 301 MET cc_start: 0.7182 (mmm) cc_final: 0.6826 (mmm) REVERT: F 347 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7192 (mm-30) REVERT: F 367 ARG cc_start: 0.7031 (ttt180) cc_final: 0.6450 (tpp80) REVERT: F 391 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6253 (mp10) REVERT: Z 34 ASP cc_start: 0.8261 (t70) cc_final: 0.7887 (t0) REVERT: Z 55 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7435 (t70) REVERT: Z 311 GLU cc_start: 0.8025 (tt0) cc_final: 0.7745 (tp30) REVERT: Z 365 LYS cc_start: 0.6003 (pttp) cc_final: 0.4481 (mtpm) REVERT: Z 375 GLU cc_start: 0.5146 (mt-10) cc_final: 0.4766 (tt0) REVERT: Z 447 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.4492 (mt) REVERT: Z 452 VAL cc_start: 0.5819 (OUTLIER) cc_final: 0.5379 (p) REVERT: Z 454 GLU cc_start: 0.5138 (OUTLIER) cc_final: 0.4640 (pt0) REVERT: Z 653 GLN cc_start: 0.4471 (OUTLIER) cc_final: 0.4196 (tm130) REVERT: Z 1141 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7811 (mt-10) outliers start: 44 outliers final: 23 residues processed: 347 average time/residue: 0.5597 time to fit residues: 227.8189 Evaluate side-chains 332 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 911 GLN Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain F residue 391 GLN Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 55 ASP Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 457 THR Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 551 ILE Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 653 GLN Chi-restraints excluded: chain Z residue 655 SER Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 263 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 348 optimal weight: 0.2980 chunk 339 optimal weight: 7.9990 chunk 104 optimal weight: 0.0040 chunk 249 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 355 optimal weight: 0.9990 chunk 279 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 overall best weight: 2.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 111 GLN C 778 ASN ** D 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN Z 370 HIS ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126624 restraints weight = 35181.862| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.46 r_work: 0.2941 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31053 Z= 0.183 Angle : 0.584 9.170 42560 Z= 0.310 Chirality : 0.045 0.182 4905 Planarity : 0.005 0.079 5204 Dihedral : 16.263 177.697 5189 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.26 % Allowed : 19.95 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3665 helix: 1.34 (0.15), residues: 1223 sheet: -0.16 (0.21), residues: 586 loop : -1.26 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 72 TYR 0.021 0.002 TYR C 680 PHE 0.035 0.002 PHE A 174 TRP 0.009 0.001 TRP C 732 HIS 0.005 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00441 (31046) covalent geometry : angle 0.58402 (42554) hydrogen bonds : bond 0.05188 ( 1231) hydrogen bonds : angle 4.21978 ( 3403) metal coordination : bond 0.00230 ( 7) metal coordination : angle 0.81090 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10683.84 seconds wall clock time: 182 minutes 5.12 seconds (10925.12 seconds total)