Starting phenix.real_space_refine on Tue Aug 26 22:51:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jas_36133/08_2025/8jas_36133.map" } resolution = 3.54 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= 0.001 sd= 0.018 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 4754 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 233 5.16 5 C 25086 2.51 5 N 6680 2.21 5 O 7280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 39287 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1726 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "S" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "R" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 661 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "J" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4619 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 565} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "L" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1161 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "V" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 666 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 410 SG CYS A 54 79.387 76.055 82.159 1.00 48.45 S ATOM 8298 SG CYS B 54 82.965 74.924 83.333 1.00 22.68 S ATOM 19558 SG CYS R 53 91.244 85.385 170.851 1.00 95.08 S ATOM 19581 SG CYS R 56 91.965 81.756 169.966 1.00 99.71 S ATOM 19665 SG CYS R 68 92.364 82.919 173.544 1.00104.08 S ATOM 19472 SG CYS R 42 91.989 91.961 174.593 1.00 72.41 S ATOM 19491 SG CYS R 45 88.723 90.255 173.625 1.00 76.06 S ATOM 19786 SG CYS R 83 91.695 89.936 171.305 1.00 90.39 S ATOM 19715 SG CYS R 75 100.483 98.979 178.115 1.00 94.65 S ATOM 19882 SG CYS R 94 98.738 99.483 175.506 1.00 95.50 S ATOM 20411 SG CYS J 54 78.627 127.958 172.425 1.00 31.80 S ATOM 25030 SG CYS K 54 80.731 130.845 170.692 1.00 82.03 S ATOM 33576 SG CYS V 53 74.957 120.453 83.550 1.00 86.52 S ATOM 33599 SG CYS V 56 74.273 124.182 83.750 1.00 93.30 S ATOM 33683 SG CYS V 68 74.867 122.478 80.293 1.00 91.40 S ATOM 33490 SG CYS V 42 77.362 114.544 79.060 1.00 74.59 S ATOM 33509 SG CYS V 45 74.090 114.967 80.805 1.00 75.04 S ATOM 33804 SG CYS V 83 77.046 116.472 82.479 1.00 78.48 S ATOM 33733 SG CYS V 75 87.754 111.147 73.596 1.00 88.96 S ATOM 33900 SG CYS V 94 86.186 110.386 76.387 1.00 78.50 S Time building chain proxies: 7.36, per 1000 atoms: 0.19 Number of scatterers: 39287 At special positions: 0 Unit cell: (151.7, 195.16, 248.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 233 16.00 O 7280 8.00 N 6680 7.00 C 25086 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 54 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 54 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 89 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS J 89 " pdb="ZN ZN K 601 " - pdb=" SG CYS J 54 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 54 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb=" ZN V 200 " pdb="ZN ZN V 200 " - pdb=" ND1 HIS V 82 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 53 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 56 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 68 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 80 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 83 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 42 " pdb=" ZN V 202 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 94 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 75 " pdb="ZN ZN V 202 " - pdb=" ND1 HIS V 77 " Number of angles added : 16 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9266 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 19 sheets defined 71.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.686A pdb=" N ILE A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 33' Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.786A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.611A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.914A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 72 No H-bonds generated for 'chain 'A' and resid 71 through 72' Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.782A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 Processing helix chain 'A' and resid 135 through 152 removed outlier: 3.848A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 176 removed outlier: 3.569A pdb=" N VAL A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.590A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.678A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 241 through 258 removed outlier: 3.688A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.972A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 309 removed outlier: 4.515A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.914A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.705A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.814A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.738A pdb=" N GLU A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.788A pdb=" N SER A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 4.761A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.505A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.272A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.823A pdb=" N THR E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 53 through 78 removed outlier: 3.581A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.909A pdb=" N ARG E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.934A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET E 151 " --> pdb=" O TRP E 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 168 removed outlier: 4.238A pdb=" N LEU E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 186 removed outlier: 3.759A pdb=" N VAL E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 200 through 220 removed outlier: 4.909A pdb=" N SER E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Proline residue: E 210 - end of helix removed outlier: 3.897A pdb=" N THR E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 removed outlier: 3.510A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.852A pdb=" N ALA D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.715A pdb=" N ASP B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.071A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.918A pdb=" N PHE B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.254A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.663A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.886A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 139 through 152 removed outlier: 3.600A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.689A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 234 Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.597A pdb=" N VAL B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.522A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.619A pdb=" N PHE B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 350 through 368 removed outlier: 3.547A pdb=" N ALA B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.517A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.649A pdb=" N GLU B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 removed outlier: 3.630A pdb=" N GLU B 492 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 527 removed outlier: 4.275A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.785A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 4.542A pdb=" N GLY G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.325A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.628A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.611A pdb=" N THR I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.511A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 79 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.651A pdb=" N GLU I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.277A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 172 removed outlier: 3.618A pdb=" N LEU I 159 " --> pdb=" O LEU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.517A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 201 through 207 removed outlier: 3.577A pdb=" N PHE I 207 " --> pdb=" O TYR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 230 Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.838A pdb=" N MET I 236 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP I 245 " --> pdb=" O GLY I 241 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 Processing helix chain 'I' and resid 274 through 287 removed outlier: 4.223A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 removed outlier: 3.644A pdb=" N LEU I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA I 303 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 327 removed outlier: 3.843A pdb=" N MET I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU I 324 " --> pdb=" O HIS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'I' and resid 334 through 357 removed outlier: 4.105A pdb=" N GLN I 352 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 357 " --> pdb=" O LEU I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 377 Processing helix chain 'I' and resid 386 through 400 removed outlier: 3.550A pdb=" N LEU I 390 " --> pdb=" O LYS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 423 removed outlier: 3.511A pdb=" N ASP I 413 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER I 417 " --> pdb=" O ASP I 413 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE I 419 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR I 420 " --> pdb=" O THR I 416 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL I 421 " --> pdb=" O SER I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 445 removed outlier: 3.608A pdb=" N PHE I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 465 Processing helix chain 'I' and resid 470 through 477 removed outlier: 3.571A pdb=" N ARG I 475 " --> pdb=" O SER I 471 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 4.051A pdb=" N ASP I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 495 " --> pdb=" O ASN I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 548 removed outlier: 4.399A pdb=" N LYS I 535 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER I 536 " --> pdb=" O GLU I 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE I 540 " --> pdb=" O SER I 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU I 541 " --> pdb=" O VAL I 537 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 579 through 591 removed outlier: 3.808A pdb=" N ALA I 583 " --> pdb=" O THR I 579 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL I 584 " --> pdb=" O TYR I 580 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN I 590 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER I 591 " --> pdb=" O ALA I 587 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 603 removed outlier: 3.594A pdb=" N ASP I 601 " --> pdb=" O LYS I 597 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR I 603 " --> pdb=" O LEU I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 606 through 620 removed outlier: 4.399A pdb=" N LEU I 610 " --> pdb=" O ASN I 606 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS I 612 " --> pdb=" O LYS I 608 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE I 614 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS I 615 " --> pdb=" O THR I 611 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 617 " --> pdb=" O THR I 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 68 Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 31 through 35 removed outlier: 3.655A pdb=" N SER J 34 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 50 removed outlier: 4.081A pdb=" N PHE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 removed outlier: 3.935A pdb=" N SER J 58 " --> pdb=" O CYS J 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 removed outlier: 4.209A pdb=" N LYS J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.578A pdb=" N HIS J 81 " --> pdb=" O HIS J 77 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET J 87 " --> pdb=" O PHE J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 110 removed outlier: 3.577A pdb=" N SER J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 134 Processing helix chain 'J' and resid 135 through 153 removed outlier: 4.263A pdb=" N LYS J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 150 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 170 removed outlier: 4.021A pdb=" N PHE J 160 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU J 170 " --> pdb=" O CYS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 175 removed outlier: 3.671A pdb=" N GLY J 175 " --> pdb=" O HIS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 199 removed outlier: 4.156A pdb=" N GLU J 184 " --> pdb=" O HIS J 180 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 removed outlier: 4.219A pdb=" N ALA J 214 " --> pdb=" O GLY J 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 235 removed outlier: 3.529A pdb=" N LYS J 227 " --> pdb=" O ASP J 223 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU J 231 " --> pdb=" O LYS J 227 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 259 removed outlier: 3.656A pdb=" N VAL J 258 " --> pdb=" O LYS J 254 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS J 259 " --> pdb=" O ALA J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 279 removed outlier: 3.520A pdb=" N GLU J 266 " --> pdb=" O PHE J 262 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE J 269 " --> pdb=" O ALA J 265 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 301 removed outlier: 3.833A pdb=" N ASN J 300 " --> pdb=" O PHE J 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL J 301 " --> pdb=" O TYR J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 321 removed outlier: 3.545A pdb=" N ALA J 309 " --> pdb=" O CYS J 305 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA J 313 " --> pdb=" O ALA J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 344 removed outlier: 3.581A pdb=" N TYR J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 368 removed outlier: 3.510A pdb=" N HIS J 366 " --> pdb=" O GLY J 362 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE J 367 " --> pdb=" O ILE J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 393 removed outlier: 3.653A pdb=" N SER J 377 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL J 381 " --> pdb=" O SER J 377 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA J 390 " --> pdb=" O LEU J 386 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE J 391 " --> pdb=" O GLU J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 422 removed outlier: 3.547A pdb=" N GLU J 399 " --> pdb=" O ASN J 395 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN J 400 " --> pdb=" O LYS J 396 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 403 " --> pdb=" O GLU J 399 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA J 420 " --> pdb=" O LEU J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 442 removed outlier: 3.603A pdb=" N ASN J 434 " --> pdb=" O LYS J 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 437 " --> pdb=" O GLY J 433 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER J 441 " --> pdb=" O ARG J 437 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET J 442 " --> pdb=" O LEU J 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 463 removed outlier: 3.816A pdb=" N GLU J 449 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS J 452 " --> pdb=" O ALA J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 484 removed outlier: 3.738A pdb=" N LEU J 472 " --> pdb=" O TYR J 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 484 " --> pdb=" O LEU J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 506 removed outlier: 5.159A pdb=" N LYS J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 496 " --> pdb=" O GLU J 492 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER J 498 " --> pdb=" O LEU J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 526 removed outlier: 3.706A pdb=" N ASP J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 551 removed outlier: 3.830A pdb=" N VAL J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP J 548 " --> pdb=" O ASN J 544 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG J 549 " --> pdb=" O ARG J 545 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN J 550 " --> pdb=" O LEU J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 562 removed outlier: 3.848A pdb=" N THR J 562 " --> pdb=" O GLU J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 578 removed outlier: 4.297A pdb=" N LEU J 575 " --> pdb=" O VAL J 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN J 578 " --> pdb=" O PHE J 574 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 23 Processing helix chain 'K' and resid 28 through 33 removed outlier: 4.152A pdb=" N ARG K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 removed outlier: 3.810A pdb=" N ASP K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.932A pdb=" N GLU K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS K 61 " --> pdb=" O GLY K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 71 through 72 No H-bonds generated for 'chain 'K' and resid 71 through 72' Processing helix chain 'K' and resid 73 through 74 No H-bonds generated for 'chain 'K' and resid 73 through 74' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.693A pdb=" N HIS K 81 " --> pdb=" O HIS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 106 removed outlier: 3.698A pdb=" N SER K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 112 through 134 removed outlier: 3.829A pdb=" N LYS K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 119 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 4.250A pdb=" N LYS K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR K 151 " --> pdb=" O LEU K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 173 removed outlier: 4.066A pdb=" N GLU K 164 " --> pdb=" O PHE K 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 199 removed outlier: 3.602A pdb=" N GLU K 183 " --> pdb=" O TYR K 179 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 219 removed outlier: 4.105A pdb=" N LEU K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS K 213 " --> pdb=" O TYR K 209 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA K 214 " --> pdb=" O GLY K 210 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE K 217 " --> pdb=" O CYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 235 removed outlier: 3.972A pdb=" N GLU K 235 " --> pdb=" O GLU K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 259 removed outlier: 3.676A pdb=" N ALA K 255 " --> pdb=" O GLN K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 280 removed outlier: 3.747A pdb=" N GLN K 267 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS K 271 " --> pdb=" O GLN K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 301 removed outlier: 3.550A pdb=" N ASP K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 322 removed outlier: 3.587A pdb=" N VAL K 308 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA K 309 " --> pdb=" O CYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 344 Processing helix chain 'K' and resid 350 through 368 removed outlier: 3.715A pdb=" N LEU K 354 " --> pdb=" O PHE K 350 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE K 367 " --> pdb=" O ILE K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 393 removed outlier: 4.016A pdb=" N ALA K 376 " --> pdb=" O HIS K 372 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL K 381 " --> pdb=" O SER K 377 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 382 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 422 removed outlier: 3.655A pdb=" N ARG K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN K 404 " --> pdb=" O GLN K 400 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU K 411 " --> pdb=" O HIS K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 442 Processing helix chain 'K' and resid 444 through 464 removed outlier: 3.605A pdb=" N LYS K 459 " --> pdb=" O ALA K 455 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU K 460 " --> pdb=" O ILE K 456 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN K 461 " --> pdb=" O GLN K 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 462 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 484 removed outlier: 3.934A pdb=" N TYR K 483 " --> pdb=" O SER K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 506 removed outlier: 3.609A pdb=" N ALA K 491 " --> pdb=" O GLN K 487 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS K 493 " --> pdb=" O GLU K 489 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU K 505 " --> pdb=" O ILE K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 527 removed outlier: 4.024A pdb=" N TYR K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY K 519 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 526 " --> pdb=" O LYS K 522 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE K 527 " --> pdb=" O LEU K 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 551 removed outlier: 3.955A pdb=" N ARG K 547 " --> pdb=" O TRP K 543 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP K 548 " --> pdb=" O ASN K 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN K 550 " --> pdb=" O LEU K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 561 removed outlier: 3.536A pdb=" N SER K 561 " --> pdb=" O LEU K 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 566 through 577 removed outlier: 3.741A pdb=" N VAL K 571 " --> pdb=" O THR K 567 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER K 573 " --> pdb=" O GLU K 569 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 577 " --> pdb=" O SER K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.671A pdb=" N THR L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE L 21 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 25 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 47 removed outlier: 3.525A pdb=" N ARG L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE L 39 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER L 40 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 79 removed outlier: 4.249A pdb=" N ARG L 75 " --> pdb=" O HIS L 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 77 " --> pdb=" O HIS L 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 105 removed outlier: 4.266A pdb=" N GLU L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 138 through 151 removed outlier: 3.706A pdb=" N ALA L 143 " --> pdb=" O ILE L 139 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET L 151 " --> pdb=" O TRP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'M' and resid 26 through 36 removed outlier: 4.003A pdb=" N ILE M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 37 removed outlier: 3.679A pdb=" N LEU N 37 " --> pdb=" O GLU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 34 through 37' Processing helix chain 'N' and resid 39 through 47 removed outlier: 3.773A pdb=" N LYS N 43 " --> pdb=" O SER N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 51 removed outlier: 3.596A pdb=" N GLN N 51 " --> pdb=" O GLY N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 48 through 51' Processing helix chain 'N' and resid 66 through 83 removed outlier: 3.942A pdb=" N LYS N 72 " --> pdb=" O HIS N 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET N 75 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE N 77 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR N 78 " --> pdb=" O CYS N 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR N 79 " --> pdb=" O MET N 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR N 83 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 111 removed outlier: 3.511A pdb=" N MET N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.824A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 47 Processing helix chain 'T' and resid 48 through 52 removed outlier: 3.603A pdb=" N GLN T 51 " --> pdb=" O GLY T 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 48 through 52' Processing helix chain 'T' and resid 66 through 84 removed outlier: 3.547A pdb=" N THR T 78 " --> pdb=" O CYS T 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL T 81 " --> pdb=" O PHE T 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR T 83 " --> pdb=" O TYR T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 111 removed outlier: 4.279A pdb=" N LEU T 101 " --> pdb=" O PRO T 97 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN T 108 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.614A pdb=" N ASN V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 89 removed outlier: 3.511A pdb=" N LYS V 89 " --> pdb=" O SER V 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 25 removed outlier: 3.693A pdb=" N THR U 13 " --> pdb=" O ASP U 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR U 19 " --> pdb=" O ASN U 15 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL U 25 " --> pdb=" O ILE U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 4.108A pdb=" N ILE U 42 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR U 43 " --> pdb=" O PHE U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 79 removed outlier: 3.574A pdb=" N ARG U 70 " --> pdb=" O GLU U 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS U 71 " --> pdb=" O ASN U 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 92 Processing helix chain 'U' and resid 94 through 105 Processing helix chain 'U' and resid 105 through 112 Processing helix chain 'U' and resid 138 through 151 removed outlier: 3.609A pdb=" N LEU U 144 " --> pdb=" O GLY U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 172 removed outlier: 3.534A pdb=" N LEU U 159 " --> pdb=" O LEU U 155 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE U 160 " --> pdb=" O GLN U 156 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG U 161 " --> pdb=" O ALA U 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET U 162 " --> pdb=" O ILE U 158 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG U 165 " --> pdb=" O ARG U 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 186 Processing helix chain 'U' and resid 186 through 191 Processing helix chain 'U' and resid 200 through 207 Processing helix chain 'U' and resid 207 through 230 removed outlier: 3.576A pdb=" N GLN U 228 " --> pdb=" O SER U 224 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU U 229 " --> pdb=" O ASN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 254 removed outlier: 3.743A pdb=" N MET U 236 " --> pdb=" O CYS U 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU U 237 " --> pdb=" O SER U 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR U 253 " --> pdb=" O ARG U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 258 through 269 removed outlier: 3.810A pdb=" N ARG U 269 " --> pdb=" O GLU U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 281 removed outlier: 3.952A pdb=" N LEU U 278 " --> pdb=" O HIS U 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS U 279 " --> pdb=" O LEU U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 289 removed outlier: 3.704A pdb=" N ILE U 285 " --> pdb=" O GLU U 281 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE U 286 " --> pdb=" O CYS U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 304 removed outlier: 3.895A pdb=" N ASN U 296 " --> pdb=" O ASN U 292 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET U 297 " --> pdb=" O ASP U 293 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA U 303 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL U 304 " --> pdb=" O LEU U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 329 removed outlier: 3.682A pdb=" N MET U 311 " --> pdb=" O GLY U 307 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG U 325 " --> pdb=" O ASP U 321 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA U 326 " --> pdb=" O GLU U 322 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN U 329 " --> pdb=" O ARG U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 334 through 357 Processing helix chain 'U' and resid 361 through 377 Processing helix chain 'U' and resid 386 through 400 removed outlier: 3.681A pdb=" N ALA U 392 " --> pdb=" O PRO U 388 " (cutoff:3.500A) Processing helix chain 'U' and resid 401 through 404 removed outlier: 3.845A pdb=" N LYS U 404 " --> pdb=" O LYS U 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 401 through 404' Processing helix chain 'U' and resid 407 through 423 removed outlier: 3.521A pdb=" N GLU U 412 " --> pdb=" O GLU U 408 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP U 413 " --> pdb=" O ASN U 409 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR U 420 " --> pdb=" O THR U 416 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL U 421 " --> pdb=" O SER U 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 427 through 445 removed outlier: 3.851A pdb=" N PHE U 431 " --> pdb=" O ASP U 427 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET U 438 " --> pdb=" O PHE U 434 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS U 441 " --> pdb=" O ARG U 437 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS U 445 " --> pdb=" O LYS U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 470 removed outlier: 7.303A pdb=" N TYR U 467 " --> pdb=" O GLN U 463 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLU U 468 " --> pdb=" O ALA U 464 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE U 469 " --> pdb=" O CYS U 465 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR U 470 " --> pdb=" O GLY U 466 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 477 Processing helix chain 'U' and resid 479 through 496 removed outlier: 3.749A pdb=" N ALA U 484 " --> pdb=" O MET U 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP U 485 " --> pdb=" O SER U 481 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS U 489 " --> pdb=" O ASP U 485 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 548 removed outlier: 3.987A pdb=" N LYS U 535 " --> pdb=" O GLN U 531 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER U 536 " --> pdb=" O GLU U 532 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE U 540 " --> pdb=" O SER U 536 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU U 541 " --> pdb=" O VAL U 537 " (cutoff:3.500A) Processing helix chain 'U' and resid 579 through 587 removed outlier: 3.664A pdb=" N VAL U 584 " --> pdb=" O TYR U 580 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 603 removed outlier: 3.540A pdb=" N ASP U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR U 603 " --> pdb=" O LEU U 599 " (cutoff:3.500A) Processing helix chain 'U' and resid 607 through 620 removed outlier: 4.261A pdb=" N LYS U 612 " --> pdb=" O LYS U 608 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE U 614 " --> pdb=" O LEU U 610 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS U 615 " --> pdb=" O THR U 611 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER U 616 " --> pdb=" O LYS U 612 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU U 617 " --> pdb=" O THR U 613 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL U 620 " --> pdb=" O SER U 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 removed outlier: 3.763A pdb=" N THR C 16 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 5 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.879A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AA7, first strand: chain 'I' and resid 508 through 513 removed outlier: 6.371A pdb=" N GLN I 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA R 31 " --> pdb=" O GLN I 508 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR I 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP R 33 " --> pdb=" O TYR I 510 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU I 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 561 through 562 removed outlier: 3.755A pdb=" N VAL I 577 " --> pdb=" O GLY I 562 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL I 574 " --> pdb=" O PHE I 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 593 through 595 removed outlier: 3.901A pdb=" N VAL I 594 " --> pdb=" O PHE I 638 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE I 638 " --> pdb=" O VAL I 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.723A pdb=" N THR M 16 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M 5 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE M 4 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL M 75 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N MET M 6 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU M 77 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG M 8 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'Q' and resid 3 through 5 removed outlier: 3.609A pdb=" N LEU Q 5 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR Q 16 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 42 through 45 removed outlier: 3.514A pdb=" N ALA Q 78 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 20 through 22 removed outlier: 6.138A pdb=" N LYS T 20 " --> pdb=" O VAL T 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 508 through 513 removed outlier: 3.606A pdb=" N TYR U 510 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA V 31 " --> pdb=" O TYR U 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'U' and resid 561 through 566 removed outlier: 4.312A pdb=" N VAL U 577 " --> pdb=" O GLY U 562 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL U 564 " --> pdb=" O ALA U 575 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA U 575 " --> pdb=" O VAL U 564 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET U 566 " --> pdb=" O TYR U 573 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 593 through 594 removed outlier: 3.629A pdb=" N VAL U 594 " --> pdb=" O PHE U 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE U 638 " --> pdb=" O VAL U 594 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER U 639 " --> pdb=" O ASN U 624 " (cutoff:3.500A) 2191 hydrogen bonds defined for protein. 6510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12706 1.34 - 1.46: 6569 1.46 - 1.58: 20497 1.58 - 1.70: 0 1.70 - 1.82: 354 Bond restraints: 40126 Sorted by residual: bond pdb=" CA ASP V 51 " pdb=" C ASP V 51 " ideal model delta sigma weight residual 1.528 1.501 0.027 1.34e-02 5.57e+03 3.99e+00 bond pdb=" C MET I 335 " pdb=" N PRO I 336 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" CA ASP R 51 " pdb=" C ASP R 51 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.35e-02 5.49e+03 2.33e+00 bond pdb=" C ASP V 51 " pdb=" O ASP V 51 " ideal model delta sigma weight residual 1.234 1.219 0.015 1.07e-02 8.73e+03 2.02e+00 bond pdb=" CG1 ILE A 385 " pdb=" CD1 ILE A 385 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.66e+00 ... (remaining 40121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 53013 1.57 - 3.14: 978 3.14 - 4.72: 130 4.72 - 6.29: 37 6.29 - 7.86: 9 Bond angle restraints: 54167 Sorted by residual: angle pdb=" N ILE B 39 " pdb=" CA ILE B 39 " pdb=" C ILE B 39 " ideal model delta sigma weight residual 112.96 108.88 4.08 1.00e+00 1.00e+00 1.67e+01 angle pdb=" N VAL U 191 " pdb=" CA VAL U 191 " pdb=" C VAL U 191 " ideal model delta sigma weight residual 112.80 108.12 4.68 1.15e+00 7.56e-01 1.66e+01 angle pdb=" C ASP Q 47 " pdb=" N ASP Q 48 " pdb=" CA ASP Q 48 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N ILE E 206 " pdb=" CA ILE E 206 " pdb=" C ILE E 206 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" C LYS C 46 " pdb=" N ASP C 47 " pdb=" CA ASP C 47 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.88e+00 ... (remaining 54162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 21644 17.98 - 35.95: 2013 35.95 - 53.93: 376 53.93 - 71.91: 71 71.91 - 89.88: 48 Dihedral angle restraints: 24152 sinusoidal: 9826 harmonic: 14326 Sorted by residual: dihedral pdb=" CA VAL B 301 " pdb=" C VAL B 301 " pdb=" N ASP B 302 " pdb=" CA ASP B 302 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA MET I 26 " pdb=" C MET I 26 " pdb=" N LEU I 27 " pdb=" CA LEU I 27 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL I 24 " pdb=" C VAL I 24 " pdb=" N VAL I 25 " pdb=" CA VAL I 25 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 24149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4419 0.041 - 0.082: 1265 0.082 - 0.122: 232 0.122 - 0.163: 18 0.163 - 0.204: 5 Chirality restraints: 5939 Sorted by residual: chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE N 30 " pdb=" CA ILE N 30 " pdb=" CG1 ILE N 30 " pdb=" CG2 ILE N 30 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB ILE D 99 " pdb=" CA ILE D 99 " pdb=" CG1 ILE D 99 " pdb=" CG2 ILE D 99 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 5936 not shown) Planarity restraints: 6903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE U 529 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO U 530 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO U 530 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO U 530 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 0 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO F 1 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 1 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 1 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 529 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO I 530 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO I 530 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 530 " 0.028 5.00e-02 4.00e+02 ... (remaining 6900 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 357 2.61 - 3.18: 34247 3.18 - 3.75: 64901 3.75 - 4.33: 87052 4.33 - 4.90: 141351 Nonbonded interactions: 327908 Sorted by model distance: nonbonded pdb=" OD1 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.033 2.230 nonbonded pdb=" OD1 ASP V 97 " pdb="ZN ZN V 202 " model vdw 2.138 2.230 nonbonded pdb=" OG SER A 566 " pdb=" OE1 GLU A 569 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR M 23 " pdb=" OE1 GLU M 26 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR I 219 " pdb=" OE1 GLU I 246 " model vdw 2.216 3.040 ... (remaining 327903 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 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'B' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'J' and resid 7 through 577) selection = (chain 'K' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) } ncs_group { reference = (chain 'C' and resid 2 through 100) selection = (chain 'G' and (resid 2 through 79 or resid 88 through 100)) selection = (chain 'M' and resid 2 through 100) } ncs_group { reference = (chain 'D' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'H' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'N' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'T' and (resid 17 through 50 or resid 58 through 112)) } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'R' selection = (chain 'V' and (resid 27 through 107 or resid 200 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.860 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 : 0.002 0.050 40156 Z= 0.117 Angle : 0.539 7.862 54183 Z= 0.296 Chirality : 0.038 0.204 5939 Planarity : 0.004 0.057 6903 Dihedral : 14.772 89.882 14886 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.12), residues: 4782 helix: -0.56 (0.09), residues: 3080 sheet: -1.34 (0.50), residues: 115 loop : -1.07 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 32 TYR 0.025 0.001 TYR D 76 PHE 0.025 0.001 PHE B 322 TRP 0.014 0.001 TRP E 91 HIS 0.005 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00243 (40126) covalent geometry : angle 0.53724 (54167) hydrogen bonds : bond 0.24227 ( 2189) hydrogen bonds : angle 7.60427 ( 6510) metal coordination : bond 0.00618 ( 30) metal coordination : angle 2.63077 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 853 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8092 (m-30) cc_final: 0.7851 (m-30) REVERT: A 160 PHE cc_start: 0.8171 (m-80) cc_final: 0.7945 (m-80) REVERT: A 194 ASP cc_start: 0.8609 (t70) cc_final: 0.8148 (t70) REVERT: A 263 LYS cc_start: 0.8449 (tptp) cc_final: 0.8220 (mtmt) REVERT: A 407 HIS cc_start: 0.8503 (t-90) cc_final: 0.8282 (t-90) REVERT: A 416 LEU cc_start: 0.8473 (mm) cc_final: 0.8225 (mm) REVERT: E 37 ASP cc_start: 0.7342 (m-30) cc_final: 0.6893 (m-30) REVERT: C 53 ASP cc_start: 0.7112 (t70) cc_final: 0.6815 (t0) REVERT: C 56 THR cc_start: 0.6819 (m) cc_final: 0.6535 (m) REVERT: B 31 ASP cc_start: 0.8397 (t0) cc_final: 0.8159 (m-30) REVERT: B 138 ASP cc_start: 0.7748 (m-30) cc_final: 0.7375 (m-30) REVERT: B 539 VAL cc_start: 0.8010 (t) cc_final: 0.7702 (p) REVERT: G 32 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8057 (tt0) REVERT: I 527 PHE cc_start: 0.6316 (t80) cc_final: 0.6026 (t80) REVERT: I 548 PHE cc_start: 0.7584 (m-80) cc_final: 0.7091 (m-80) REVERT: I 553 LEU cc_start: 0.9134 (mt) cc_final: 0.8863 (mt) REVERT: J 389 ILE cc_start: 0.8267 (mm) cc_final: 0.8058 (mt) REVERT: J 411 LEU cc_start: 0.8008 (mm) cc_final: 0.7770 (pp) REVERT: K 132 ASP cc_start: 0.7755 (m-30) cc_final: 0.7380 (m-30) REVERT: K 387 GLU cc_start: 0.7581 (tt0) cc_final: 0.7170 (tp30) REVERT: K 451 MET cc_start: 0.7858 (mmp) cc_final: 0.7460 (mmm) REVERT: K 468 TYR cc_start: 0.7746 (t80) cc_final: 0.7267 (t80) REVERT: K 469 GLU cc_start: 0.8401 (tp30) cc_final: 0.8036 (mm-30) REVERT: L 86 MET cc_start: 0.0254 (tmm) cc_final: -0.0063 (tmm) REVERT: M 9 ARG cc_start: 0.5948 (tpt90) cc_final: 0.5563 (tpt90) REVERT: M 32 GLU cc_start: 0.7307 (tt0) cc_final: 0.7092 (tp30) REVERT: M 53 ASP cc_start: 0.6748 (m-30) cc_final: 0.6244 (m-30) REVERT: N 65 ILE cc_start: 0.8258 (mp) cc_final: 0.8058 (mp) REVERT: U 141 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7464 (tm-30) REVERT: U 201 LYS cc_start: 0.8397 (tptp) cc_final: 0.8025 (ptmt) REVERT: U 542 LEU cc_start: 0.8223 (mp) cc_final: 0.7635 (tt) outliers start: 1 outliers final: 0 residues processed: 853 average time/residue: 0.2254 time to fit residues: 309.9179 Evaluate side-chains 502 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 190 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 415 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN J 50 GLN J 84 GLN J 427 GLN ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 525 ASN M 70 GLN N 108 ASN V 76 ASN U 377 ASN U 624 ASN U 641 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.140159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092499 restraints weight = 89713.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093407 restraints weight = 49013.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093579 restraints weight = 32187.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094047 restraints weight = 30941.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094277 restraints weight = 26852.854| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40156 Z= 0.163 Angle : 0.607 10.406 54183 Z= 0.326 Chirality : 0.040 0.255 5939 Planarity : 0.004 0.064 6903 Dihedral : 4.368 72.880 5292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.12 % Allowed : 10.52 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: -0.67 (0.12), residues: 4782 helix: 0.02 (0.09), residues: 3202 sheet: -1.69 (0.45), residues: 114 loop : -1.13 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 32 TYR 0.026 0.002 TYR I 49 PHE 0.028 0.002 PHE N 77 TRP 0.026 0.002 TRP U 517 HIS 0.009 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00353 (40126) covalent geometry : angle 0.60566 (54167) hydrogen bonds : bond 0.05671 ( 2189) hydrogen bonds : angle 5.04039 ( 6510) metal coordination : bond 0.01239 ( 30) metal coordination : angle 2.58193 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 582 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8007 (m-30) cc_final: 0.7698 (m-30) REVERT: A 411 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7999 (mm) REVERT: A 416 LEU cc_start: 0.8493 (mm) cc_final: 0.8231 (mt) REVERT: A 568 GLU cc_start: 0.8290 (mp0) cc_final: 0.8043 (mp0) REVERT: E 109 ASN cc_start: 0.8834 (t0) cc_final: 0.8632 (t0) REVERT: C 53 ASP cc_start: 0.7033 (t70) cc_final: 0.6771 (t0) REVERT: C 106 GLN cc_start: 0.7115 (mp10) cc_final: 0.6889 (mp10) REVERT: B 31 ASP cc_start: 0.8870 (t0) cc_final: 0.8351 (m-30) REVERT: B 138 ASP cc_start: 0.7855 (m-30) cc_final: 0.7502 (m-30) REVERT: B 468 TYR cc_start: 0.8389 (t80) cc_final: 0.8041 (t80) REVERT: B 510 TYR cc_start: 0.7640 (t80) cc_final: 0.7229 (t80) REVERT: B 539 VAL cc_start: 0.7915 (t) cc_final: 0.7409 (p) REVERT: G 32 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8002 (tt0) REVERT: I 270 MET cc_start: 0.8653 (tmm) cc_final: 0.8390 (ttt) REVERT: I 378 TYR cc_start: 0.8208 (t80) cc_final: 0.7842 (t80) REVERT: I 548 PHE cc_start: 0.7498 (m-80) cc_final: 0.7027 (m-80) REVERT: I 622 MET cc_start: 0.6262 (tpp) cc_final: 0.5947 (tpp) REVERT: J 228 TRP cc_start: 0.8307 (m100) cc_final: 0.7875 (m100) REVERT: J 233 MET cc_start: 0.8297 (ttp) cc_final: 0.8009 (ttp) REVERT: J 411 LEU cc_start: 0.8317 (mm) cc_final: 0.8085 (pp) REVERT: J 515 TYR cc_start: 0.1227 (OUTLIER) cc_final: 0.0389 (m-80) REVERT: K 132 ASP cc_start: 0.7952 (m-30) cc_final: 0.7600 (m-30) REVERT: K 224 GLU cc_start: 0.8795 (tp30) cc_final: 0.8524 (tp30) REVERT: K 451 MET cc_start: 0.7941 (mmp) cc_final: 0.7582 (mmm) REVERT: K 468 TYR cc_start: 0.8020 (t80) cc_final: 0.7645 (t80) REVERT: K 545 ARG cc_start: 0.8167 (mmp80) cc_final: 0.7845 (mmp80) REVERT: K 569 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8643 (mp0) REVERT: L 22 LYS cc_start: 0.8034 (tptp) cc_final: 0.7359 (tppt) REVERT: L 68 HIS cc_start: 0.4950 (t70) cc_final: 0.4162 (p-80) REVERT: L 70 ARG cc_start: 0.7845 (mmt-90) cc_final: 0.6785 (ppt170) REVERT: L 115 LYS cc_start: 0.7914 (tppt) cc_final: 0.7578 (tppt) REVERT: M 32 GLU cc_start: 0.7954 (tt0) cc_final: 0.7660 (tp30) REVERT: M 53 ASP cc_start: 0.6908 (m-30) cc_final: 0.6284 (m-30) REVERT: M 70 GLN cc_start: 0.8215 (mm110) cc_final: 0.6761 (pp30) REVERT: N 64 GLU cc_start: 0.6581 (pm20) cc_final: 0.6079 (pm20) REVERT: Q 29 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6527 (mmm160) REVERT: T 64 GLU cc_start: 0.7386 (pm20) cc_final: 0.7139 (pm20) REVERT: T 80 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7943 (ttmm) REVERT: V 50 MET cc_start: 0.8472 (mmm) cc_final: 0.7972 (mmm) REVERT: U 141 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7444 (tm-30) REVERT: U 201 LYS cc_start: 0.8418 (tptp) cc_final: 0.7998 (ptmt) REVERT: U 217 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8593 (pp20) REVERT: U 297 MET cc_start: 0.8790 (tmm) cc_final: 0.8394 (tmm) REVERT: U 335 MET cc_start: 0.8721 (tpp) cc_final: 0.8440 (tpp) REVERT: U 345 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: U 406 MET cc_start: 0.8335 (mtp) cc_final: 0.7305 (tpp) REVERT: U 434 PHE cc_start: 0.8282 (t80) cc_final: 0.8059 (t80) REVERT: U 539 MET cc_start: 0.8848 (tpp) cc_final: 0.8560 (tpp) outliers start: 48 outliers final: 30 residues processed: 616 average time/residue: 0.2481 time to fit residues: 251.5452 Evaluate side-chains 528 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 494 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 515 TYR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain Q residue 55 LYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 306 THR Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain U residue 546 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 380 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 297 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 461 optimal weight: 0.9980 chunk 351 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN A 461 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 300 ASN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 578 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 GLN K 40 GLN K 81 HIS K 180 HIS K 326 ASN K 415 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 HIS V 76 ASN U 625 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090724 restraints weight = 89999.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090589 restraints weight = 46278.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091222 restraints weight = 34098.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091484 restraints weight = 34518.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091575 restraints weight = 29331.940| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 40156 Z= 0.215 Angle : 0.608 11.396 54183 Z= 0.323 Chirality : 0.041 0.193 5939 Planarity : 0.004 0.061 6903 Dihedral : 4.400 75.652 5292 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.03 % Allowed : 12.39 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: -0.48 (0.12), residues: 4782 helix: 0.18 (0.09), residues: 3205 sheet: -1.68 (0.43), residues: 130 loop : -1.09 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 106 TYR 0.025 0.002 TYR K 338 PHE 0.024 0.002 PHE B 534 TRP 0.037 0.002 TRP U 517 HIS 0.007 0.001 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00495 (40126) covalent geometry : angle 0.60671 (54167) hydrogen bonds : bond 0.04863 ( 2189) hydrogen bonds : angle 4.71759 ( 6510) metal coordination : bond 0.01967 ( 30) metal coordination : angle 2.77289 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 534 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 138 ASP cc_start: 0.7999 (m-30) cc_final: 0.7694 (m-30) REVERT: A 380 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7283 (ttm110) REVERT: A 411 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 415 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7402 (tp40) REVERT: A 416 LEU cc_start: 0.8549 (mm) cc_final: 0.8327 (mt) REVERT: A 568 GLU cc_start: 0.8399 (mp0) cc_final: 0.8125 (mp0) REVERT: E 37 ASP cc_start: 0.7609 (m-30) cc_final: 0.6942 (m-30) REVERT: E 196 LYS cc_start: 0.8297 (mptt) cc_final: 0.8097 (ptmm) REVERT: C 53 ASP cc_start: 0.6926 (t70) cc_final: 0.6677 (t0) REVERT: D 85 ASN cc_start: 0.8818 (m-40) cc_final: 0.8310 (t0) REVERT: B 31 ASP cc_start: 0.9001 (t0) cc_final: 0.8265 (t0) REVERT: B 138 ASP cc_start: 0.7857 (m-30) cc_final: 0.7548 (m-30) REVERT: B 156 MET cc_start: 0.6864 (mmp) cc_final: 0.6176 (tmm) REVERT: B 233 MET cc_start: 0.8422 (mtp) cc_final: 0.8143 (mtp) REVERT: B 468 TYR cc_start: 0.8461 (t80) cc_final: 0.7923 (t80) REVERT: B 510 TYR cc_start: 0.7699 (t80) cc_final: 0.7331 (t80) REVERT: G 32 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8072 (tt0) REVERT: H 17 MET cc_start: 0.7660 (tpp) cc_final: 0.7452 (tpt) REVERT: I 270 MET cc_start: 0.8749 (tmm) cc_final: 0.8504 (ttt) REVERT: I 378 TYR cc_start: 0.8283 (t80) cc_final: 0.7950 (t80) REVERT: I 527 PHE cc_start: 0.6100 (t80) cc_final: 0.5799 (t80) REVERT: I 548 PHE cc_start: 0.7603 (m-80) cc_final: 0.7161 (m-80) REVERT: I 622 MET cc_start: 0.6415 (tpp) cc_final: 0.6115 (tpp) REVERT: J 228 TRP cc_start: 0.8320 (m100) cc_final: 0.7715 (m100) REVERT: J 233 MET cc_start: 0.8475 (ttp) cc_final: 0.8225 (ttp) REVERT: J 411 LEU cc_start: 0.8432 (mm) cc_final: 0.8140 (pp) REVERT: J 515 TYR cc_start: 0.1237 (OUTLIER) cc_final: 0.0451 (m-80) REVERT: K 132 ASP cc_start: 0.8020 (m-30) cc_final: 0.7614 (m-30) REVERT: K 251 GLN cc_start: 0.7941 (mt0) cc_final: 0.7568 (pt0) REVERT: K 294 TYR cc_start: 0.8914 (t80) cc_final: 0.8645 (t80) REVERT: K 442 MET cc_start: 0.6821 (mmt) cc_final: 0.6415 (mmt) REVERT: K 444 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8742 (mttp) REVERT: K 451 MET cc_start: 0.7947 (mmp) cc_final: 0.7616 (mmm) REVERT: K 545 ARG cc_start: 0.8293 (mmp80) cc_final: 0.7905 (mmp80) REVERT: K 569 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8677 (mp0) REVERT: L 43 TYR cc_start: 0.8309 (t80) cc_final: 0.8077 (t80) REVERT: L 68 HIS cc_start: 0.4530 (t70) cc_final: 0.4130 (t-170) REVERT: M 23 THR cc_start: 0.7090 (t) cc_final: 0.6865 (m) REVERT: M 53 ASP cc_start: 0.7000 (m-30) cc_final: 0.6478 (m-30) REVERT: N 17 MET cc_start: 0.6723 (tmm) cc_final: 0.5116 (pmm) REVERT: N 18 TYR cc_start: 0.5955 (m-10) cc_final: 0.5227 (m-80) REVERT: N 62 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8008 (t80) REVERT: T 64 GLU cc_start: 0.7493 (pm20) cc_final: 0.7128 (pm20) REVERT: T 80 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7754 (ttmm) REVERT: U 201 LYS cc_start: 0.8462 (tptp) cc_final: 0.7927 (ptmt) REVERT: U 206 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6812 (mp) REVERT: U 217 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8591 (pp20) REVERT: U 335 MET cc_start: 0.8836 (tpp) cc_final: 0.8510 (tpp) REVERT: U 345 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: U 406 MET cc_start: 0.8275 (mtp) cc_final: 0.7300 (tpp) REVERT: U 539 MET cc_start: 0.8962 (tpp) cc_final: 0.8698 (tpp) outliers start: 87 outliers final: 49 residues processed: 587 average time/residue: 0.2456 time to fit residues: 238.0475 Evaluate side-chains 525 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 468 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain J residue 515 TYR Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 542 LEU Chi-restraints excluded: chain U residue 546 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 60 optimal weight: 0.9990 chunk 389 optimal weight: 8.9990 chunk 306 optimal weight: 0.6980 chunk 430 optimal weight: 0.6980 chunk 374 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 445 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 581 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 GLN K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN U 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092883 restraints weight = 88871.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092987 restraints weight = 46259.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.093819 restraints weight = 36151.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094394 restraints weight = 31087.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094303 restraints weight = 28169.353| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40156 Z= 0.135 Angle : 0.543 12.043 54183 Z= 0.288 Chirality : 0.038 0.198 5939 Planarity : 0.004 0.056 6903 Dihedral : 4.288 76.921 5292 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: -0.22 (0.12), residues: 4782 helix: 0.42 (0.09), residues: 3203 sheet: -1.66 (0.41), residues: 138 loop : -1.06 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 161 TYR 0.019 0.001 TYR D 76 PHE 0.018 0.001 PHE E 39 TRP 0.035 0.001 TRP I 517 HIS 0.005 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00297 (40126) covalent geometry : angle 0.54214 (54167) hydrogen bonds : bond 0.04273 ( 2189) hydrogen bonds : angle 4.49344 ( 6510) metal coordination : bond 0.00831 ( 30) metal coordination : angle 2.08583 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 520 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7834 (m-30) cc_final: 0.7581 (m-30) REVERT: A 411 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7904 (mm) REVERT: A 415 GLN cc_start: 0.7523 (tp40) cc_final: 0.7300 (tp40) REVERT: A 568 GLU cc_start: 0.8242 (mp0) cc_final: 0.8039 (mp0) REVERT: E 99 ASP cc_start: 0.7648 (m-30) cc_final: 0.7238 (t0) REVERT: E 146 MET cc_start: 0.7037 (ttm) cc_final: 0.6819 (ttm) REVERT: E 196 LYS cc_start: 0.8312 (mptt) cc_final: 0.7946 (pptt) REVERT: E 207 PHE cc_start: 0.8081 (t80) cc_final: 0.7105 (t80) REVERT: C 53 ASP cc_start: 0.6959 (t70) cc_final: 0.6720 (t0) REVERT: D 85 ASN cc_start: 0.8696 (m-40) cc_final: 0.8345 (t0) REVERT: B 31 ASP cc_start: 0.8879 (t0) cc_final: 0.8110 (t0) REVERT: B 138 ASP cc_start: 0.7825 (m-30) cc_final: 0.7527 (m-30) REVERT: B 156 MET cc_start: 0.6724 (mmp) cc_final: 0.6224 (tmm) REVERT: B 468 TYR cc_start: 0.8343 (t80) cc_final: 0.7822 (t80) REVERT: B 506 PHE cc_start: 0.7833 (m-10) cc_final: 0.7422 (m-10) REVERT: B 510 TYR cc_start: 0.7647 (t80) cc_final: 0.7342 (t80) REVERT: G 32 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8058 (tt0) REVERT: I 270 MET cc_start: 0.8683 (tmm) cc_final: 0.8474 (ttt) REVERT: I 304 VAL cc_start: 0.8233 (t) cc_final: 0.7995 (m) REVERT: I 378 TYR cc_start: 0.8222 (t80) cc_final: 0.7897 (t80) REVERT: I 410 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: I 527 PHE cc_start: 0.6140 (t80) cc_final: 0.5736 (t80) REVERT: I 548 PHE cc_start: 0.7531 (m-80) cc_final: 0.7051 (m-80) REVERT: I 622 MET cc_start: 0.6506 (tpp) cc_final: 0.6178 (tpp) REVERT: J 228 TRP cc_start: 0.8164 (m100) cc_final: 0.7605 (m100) REVERT: J 233 MET cc_start: 0.8457 (ttp) cc_final: 0.8226 (ttp) REVERT: J 411 LEU cc_start: 0.8466 (mm) cc_final: 0.8175 (pp) REVERT: K 132 ASP cc_start: 0.7924 (m-30) cc_final: 0.7564 (m-30) REVERT: K 442 MET cc_start: 0.7115 (mmt) cc_final: 0.6894 (mmt) REVERT: K 485 MET cc_start: 0.6464 (mmt) cc_final: 0.6090 (mtm) REVERT: K 545 ARG cc_start: 0.8255 (mmp80) cc_final: 0.7839 (mmp80) REVERT: L 43 TYR cc_start: 0.8215 (t80) cc_final: 0.7982 (t80) REVERT: L 101 MET cc_start: 0.6753 (mmt) cc_final: 0.6120 (ptp) REVERT: M 23 THR cc_start: 0.6984 (t) cc_final: 0.6741 (m) REVERT: M 53 ASP cc_start: 0.6994 (m-30) cc_final: 0.6484 (m-30) REVERT: M 65 GLN cc_start: 0.8422 (pp30) cc_final: 0.8220 (pp30) REVERT: M 70 GLN cc_start: 0.8352 (mm-40) cc_final: 0.6555 (pp30) REVERT: N 62 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8084 (t80) REVERT: Q 27 LEU cc_start: 0.8384 (mm) cc_final: 0.7741 (pp) REVERT: T 37 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7525 (mm) REVERT: T 38 THR cc_start: 0.8102 (t) cc_final: 0.7880 (t) REVERT: T 64 GLU cc_start: 0.7428 (pm20) cc_final: 0.7047 (pm20) REVERT: T 80 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: U 94 TYR cc_start: 0.7685 (t80) cc_final: 0.7397 (t80) REVERT: U 201 LYS cc_start: 0.8497 (tptp) cc_final: 0.7956 (ptmt) REVERT: U 206 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6932 (mp) REVERT: U 335 MET cc_start: 0.8789 (tpp) cc_final: 0.8478 (tpp) REVERT: U 345 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: U 406 MET cc_start: 0.8137 (mtp) cc_final: 0.7295 (tpp) REVERT: U 539 MET cc_start: 0.8925 (tpp) cc_final: 0.8689 (tpp) outliers start: 67 outliers final: 37 residues processed: 564 average time/residue: 0.2201 time to fit residues: 206.7061 Evaluate side-chains 508 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 464 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 410 GLU Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 82 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 465 optimal weight: 0.5980 chunk 269 optimal weight: 10.0000 chunk 387 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN J 50 GLN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN K 180 HIS K 300 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN M 70 GLN Q 49 GLN V 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.140041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096567 restraints weight = 89025.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094031 restraints weight = 53446.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094936 restraints weight = 42498.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095198 restraints weight = 35622.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097625 restraints weight = 34211.150| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40156 Z= 0.134 Angle : 0.540 10.243 54183 Z= 0.284 Chirality : 0.038 0.178 5939 Planarity : 0.004 0.055 6903 Dihedral : 4.239 76.806 5292 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.92 % Allowed : 15.55 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: -0.06 (0.12), residues: 4782 helix: 0.54 (0.09), residues: 3213 sheet: -1.63 (0.42), residues: 131 loop : -1.02 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 106 TYR 0.022 0.001 TYR K 338 PHE 0.031 0.001 PHE B 186 TRP 0.026 0.001 TRP I 517 HIS 0.005 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00301 (40126) covalent geometry : angle 0.53865 (54167) hydrogen bonds : bond 0.04048 ( 2189) hydrogen bonds : angle 4.36732 ( 6510) metal coordination : bond 0.00897 ( 30) metal coordination : angle 1.98042 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 507 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6951 (p) REVERT: A 138 ASP cc_start: 0.7933 (m-30) cc_final: 0.7665 (m-30) REVERT: A 411 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 415 GLN cc_start: 0.7495 (tp40) cc_final: 0.7277 (tp40) REVERT: E 37 ASP cc_start: 0.7531 (m-30) cc_final: 0.6848 (m-30) REVERT: E 93 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: E 99 ASP cc_start: 0.7672 (m-30) cc_final: 0.7449 (m-30) REVERT: E 146 MET cc_start: 0.7179 (ttm) cc_final: 0.6957 (ttm) REVERT: E 196 LYS cc_start: 0.8170 (mptt) cc_final: 0.7884 (pptt) REVERT: C 53 ASP cc_start: 0.7040 (t70) cc_final: 0.6809 (t0) REVERT: D 85 ASN cc_start: 0.8615 (m-40) cc_final: 0.8305 (t0) REVERT: D 98 GLU cc_start: 0.7706 (pm20) cc_final: 0.7400 (pm20) REVERT: B 31 ASP cc_start: 0.8901 (t0) cc_final: 0.8167 (t0) REVERT: B 138 ASP cc_start: 0.7824 (m-30) cc_final: 0.7541 (m-30) REVERT: B 156 MET cc_start: 0.6735 (mmp) cc_final: 0.6255 (tmm) REVERT: B 233 MET cc_start: 0.8267 (mtp) cc_final: 0.8060 (mtp) REVERT: B 262 PHE cc_start: 0.8364 (m-10) cc_final: 0.8108 (m-10) REVERT: B 468 TYR cc_start: 0.8279 (t80) cc_final: 0.7797 (t80) REVERT: B 506 PHE cc_start: 0.7754 (m-10) cc_final: 0.7537 (m-10) REVERT: B 510 TYR cc_start: 0.7582 (t80) cc_final: 0.7346 (t80) REVERT: G 32 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8024 (tt0) REVERT: I 270 MET cc_start: 0.8688 (tmm) cc_final: 0.8462 (ttt) REVERT: I 304 VAL cc_start: 0.8216 (t) cc_final: 0.8003 (m) REVERT: I 378 TYR cc_start: 0.8181 (t80) cc_final: 0.7877 (t80) REVERT: I 435 TYR cc_start: 0.9162 (t80) cc_final: 0.8830 (t80) REVERT: I 469 PHE cc_start: 0.8591 (t80) cc_final: 0.8389 (t80) REVERT: I 527 PHE cc_start: 0.6056 (t80) cc_final: 0.5642 (t80) REVERT: I 548 PHE cc_start: 0.7455 (m-80) cc_final: 0.7016 (m-80) REVERT: I 622 MET cc_start: 0.6459 (tpp) cc_final: 0.6162 (tpp) REVERT: J 228 TRP cc_start: 0.7987 (m100) cc_final: 0.7449 (m100) REVERT: J 233 MET cc_start: 0.8479 (ttp) cc_final: 0.8264 (ttp) REVERT: J 411 LEU cc_start: 0.8402 (mm) cc_final: 0.8146 (pp) REVERT: K 132 ASP cc_start: 0.7798 (m-30) cc_final: 0.7489 (m-30) REVERT: K 545 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7806 (mmp80) REVERT: L 26 MET cc_start: 0.7036 (mtm) cc_final: 0.5434 (tpt) REVERT: L 101 MET cc_start: 0.6469 (mmt) cc_final: 0.6071 (ptp) REVERT: M 23 THR cc_start: 0.6858 (t) cc_final: 0.6600 (m) REVERT: M 53 ASP cc_start: 0.7009 (m-30) cc_final: 0.5957 (t0) REVERT: M 65 GLN cc_start: 0.8408 (pp30) cc_final: 0.8127 (mp10) REVERT: N 17 MET cc_start: 0.5953 (tmm) cc_final: 0.4707 (pmm) REVERT: N 33 ARG cc_start: 0.6167 (tpp-160) cc_final: 0.5966 (tpp-160) REVERT: N 62 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7872 (t80) REVERT: Q 27 LEU cc_start: 0.8419 (mm) cc_final: 0.7741 (pp) REVERT: T 37 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7560 (mm) REVERT: T 80 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: V 32 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8823 (mp) REVERT: U 9 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7575 (p0) REVERT: U 94 TYR cc_start: 0.7772 (t80) cc_final: 0.7512 (t80) REVERT: U 141 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7463 (tm-30) REVERT: U 201 LYS cc_start: 0.8509 (tptp) cc_final: 0.7982 (ptmt) REVERT: U 206 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6965 (mp) REVERT: U 270 MET cc_start: 0.7609 (tmm) cc_final: 0.7228 (tmm) REVERT: U 335 MET cc_start: 0.8793 (tpp) cc_final: 0.8491 (tpp) REVERT: U 345 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: U 406 MET cc_start: 0.7971 (mtp) cc_final: 0.7170 (tpp) outliers start: 82 outliers final: 51 residues processed: 554 average time/residue: 0.2063 time to fit residues: 188.8236 Evaluate side-chains 524 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 463 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain F residue -1 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 410 HIS Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 42 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 296 optimal weight: 0.2980 chunk 397 optimal weight: 7.9990 chunk 447 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 396 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Q 49 GLN V 76 ASN U 513 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094612 restraints weight = 89144.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094244 restraints weight = 47843.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094631 restraints weight = 35479.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095033 restraints weight = 34249.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095084 restraints weight = 30444.211| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40156 Z= 0.130 Angle : 0.539 10.417 54183 Z= 0.282 Chirality : 0.038 0.209 5939 Planarity : 0.004 0.054 6903 Dihedral : 4.202 76.072 5292 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.08 % Allowed : 16.34 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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 (0.12), residues: 4782 helix: 0.66 (0.09), residues: 3207 sheet: -1.59 (0.43), residues: 124 loop : -0.99 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 106 TYR 0.019 0.001 TYR K 338 PHE 0.020 0.001 PHE B 186 TRP 0.020 0.001 TRP R 35 HIS 0.004 0.001 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00291 (40126) covalent geometry : angle 0.53826 (54167) hydrogen bonds : bond 0.03904 ( 2189) hydrogen bonds : angle 4.27142 ( 6510) metal coordination : bond 0.00898 ( 30) metal coordination : angle 1.81335 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 497 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6983 (p) REVERT: A 138 ASP cc_start: 0.7848 (m-30) cc_final: 0.7601 (m-30) REVERT: A 385 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 415 GLN cc_start: 0.7521 (tp40) cc_final: 0.7308 (tp40) REVERT: E 37 ASP cc_start: 0.7527 (m-30) cc_final: 0.6876 (m-30) REVERT: E 93 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: E 99 ASP cc_start: 0.7706 (m-30) cc_final: 0.7496 (m-30) REVERT: E 146 MET cc_start: 0.7178 (ttm) cc_final: 0.6945 (ttm) REVERT: E 196 LYS cc_start: 0.8255 (mptt) cc_final: 0.7922 (pptt) REVERT: D 85 ASN cc_start: 0.8670 (m-40) cc_final: 0.8333 (t0) REVERT: B 31 ASP cc_start: 0.8901 (t0) cc_final: 0.8171 (t0) REVERT: B 138 ASP cc_start: 0.7846 (m-30) cc_final: 0.7548 (m-30) REVERT: B 156 MET cc_start: 0.6884 (mmp) cc_final: 0.6211 (tmm) REVERT: B 233 MET cc_start: 0.8260 (mtp) cc_final: 0.8043 (mtp) REVERT: B 262 PHE cc_start: 0.8458 (m-10) cc_final: 0.8194 (m-10) REVERT: B 468 TYR cc_start: 0.8475 (t80) cc_final: 0.7887 (t80) REVERT: B 506 PHE cc_start: 0.7764 (m-10) cc_final: 0.7518 (m-10) REVERT: B 510 TYR cc_start: 0.7638 (t80) cc_final: 0.7397 (t80) REVERT: B 539 VAL cc_start: 0.7521 (t) cc_final: 0.7247 (p) REVERT: G 32 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8080 (tt0) REVERT: I 146 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7111 (mmp) REVERT: I 246 GLU cc_start: 0.8227 (tp30) cc_final: 0.7986 (tp30) REVERT: I 270 MET cc_start: 0.8712 (tmm) cc_final: 0.8464 (ttt) REVERT: I 297 MET cc_start: 0.8490 (mmm) cc_final: 0.8264 (tpp) REVERT: I 304 VAL cc_start: 0.8229 (t) cc_final: 0.8002 (m) REVERT: I 378 TYR cc_start: 0.8234 (t80) cc_final: 0.7915 (t80) REVERT: I 435 TYR cc_start: 0.9168 (t80) cc_final: 0.8799 (t80) REVERT: I 527 PHE cc_start: 0.6013 (t80) cc_final: 0.5573 (t80) REVERT: I 548 PHE cc_start: 0.7465 (m-80) cc_final: 0.7009 (m-80) REVERT: I 622 MET cc_start: 0.6534 (tpp) cc_final: 0.6203 (tpp) REVERT: J 228 TRP cc_start: 0.8034 (m100) cc_final: 0.7398 (m100) REVERT: J 411 LEU cc_start: 0.8447 (mm) cc_final: 0.8161 (pp) REVERT: K 132 ASP cc_start: 0.7838 (m-30) cc_final: 0.7553 (m-30) REVERT: K 224 GLU cc_start: 0.8805 (tp30) cc_final: 0.8347 (tp30) REVERT: K 545 ARG cc_start: 0.8231 (mmp80) cc_final: 0.7827 (mmp80) REVERT: L 26 MET cc_start: 0.7050 (mtm) cc_final: 0.5550 (tpt) REVERT: M 53 ASP cc_start: 0.6962 (m-30) cc_final: 0.5843 (t0) REVERT: M 65 GLN cc_start: 0.8381 (pp30) cc_final: 0.8129 (mp10) REVERT: N 17 MET cc_start: 0.6000 (tmm) cc_final: 0.4639 (pmm) REVERT: N 62 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7597 (t80) REVERT: Q 27 LEU cc_start: 0.8444 (mm) cc_final: 0.7763 (pp) REVERT: T 37 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7556 (mm) REVERT: T 64 GLU cc_start: 0.7332 (pm20) cc_final: 0.7015 (pm20) REVERT: T 80 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7797 (ttmm) REVERT: V 32 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8801 (mp) REVERT: V 50 MET cc_start: 0.8386 (mmm) cc_final: 0.8109 (tpp) REVERT: U 9 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7600 (p0) REVERT: U 94 TYR cc_start: 0.7767 (t80) cc_final: 0.7495 (t80) REVERT: U 141 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7503 (tm-30) REVERT: U 201 LYS cc_start: 0.8519 (tptp) cc_final: 0.7934 (ptmt) REVERT: U 206 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6989 (mp) REVERT: U 297 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (ppp) REVERT: U 335 MET cc_start: 0.8802 (tpp) cc_final: 0.8490 (tpp) REVERT: U 345 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: U 406 MET cc_start: 0.7874 (mtp) cc_final: 0.7019 (tpp) REVERT: U 539 MET cc_start: 0.8907 (tpp) cc_final: 0.8595 (tpp) outliers start: 89 outliers final: 57 residues processed: 549 average time/residue: 0.2187 time to fit residues: 198.8569 Evaluate side-chains 532 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 463 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain F residue -1 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 297 MET Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 23 optimal weight: 0.0050 chunk 306 optimal weight: 0.0770 chunk 252 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 404 optimal weight: 4.9990 chunk 468 optimal weight: 8.9990 chunk 389 optimal weight: 0.0370 chunk 427 optimal weight: 9.9990 chunk 217 optimal weight: 0.0050 chunk 332 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 overall best weight: 0.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 204 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS M 49 GLN Q 49 GLN V 76 ASN U 156 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.141627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096084 restraints weight = 89105.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095870 restraints weight = 46325.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096406 restraints weight = 33587.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096843 restraints weight = 32114.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096779 restraints weight = 28799.387| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40156 Z= 0.112 Angle : 0.543 10.690 54183 Z= 0.282 Chirality : 0.038 0.208 5939 Planarity : 0.003 0.071 6903 Dihedral : 4.164 75.462 5292 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.94 % Allowed : 16.81 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.17 (0.12), residues: 4782 helix: 0.75 (0.09), residues: 3202 sheet: -1.50 (0.42), residues: 133 loop : -1.01 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 161 TYR 0.022 0.001 TYR I 558 PHE 0.043 0.001 PHE I 469 TRP 0.054 0.001 TRP I 517 HIS 0.007 0.001 HIS K 410 Details of bonding type rmsd covalent geometry : bond 0.00237 (40126) covalent geometry : angle 0.54273 (54167) hydrogen bonds : bond 0.03729 ( 2189) hydrogen bonds : angle 4.18480 ( 6510) metal coordination : bond 0.00406 ( 30) metal coordination : angle 1.62357 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 513 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6967 (p) REVERT: A 138 ASP cc_start: 0.7880 (m-30) cc_final: 0.7613 (m-30) REVERT: A 193 MET cc_start: 0.8005 (mtp) cc_final: 0.7792 (mtp) REVERT: A 385 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 415 GLN cc_start: 0.7515 (tp40) cc_final: 0.7299 (tp40) REVERT: A 568 GLU cc_start: 0.8205 (mp0) cc_final: 0.8004 (mm-30) REVERT: E 37 ASP cc_start: 0.7556 (m-30) cc_final: 0.6866 (m-30) REVERT: E 93 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: E 146 MET cc_start: 0.7191 (ttm) cc_final: 0.6962 (ttm) REVERT: E 196 LYS cc_start: 0.8236 (mptt) cc_final: 0.7922 (pptt) REVERT: E 204 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7429 (mm110) REVERT: D 85 ASN cc_start: 0.8679 (m-40) cc_final: 0.8306 (t0) REVERT: D 98 GLU cc_start: 0.7802 (pm20) cc_final: 0.7552 (pm20) REVERT: B 31 ASP cc_start: 0.8878 (t0) cc_final: 0.8453 (t0) REVERT: B 138 ASP cc_start: 0.7741 (m-30) cc_final: 0.7480 (m-30) REVERT: B 156 MET cc_start: 0.6861 (mmp) cc_final: 0.6229 (tmm) REVERT: B 233 MET cc_start: 0.8257 (mtp) cc_final: 0.8023 (mtp) REVERT: B 468 TYR cc_start: 0.8430 (t80) cc_final: 0.7809 (t80) REVERT: B 506 PHE cc_start: 0.7699 (m-10) cc_final: 0.7487 (m-10) REVERT: B 539 VAL cc_start: 0.7480 (t) cc_final: 0.7219 (p) REVERT: G 32 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8038 (tt0) REVERT: I 146 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6950 (mmp) REVERT: I 246 GLU cc_start: 0.8146 (tp30) cc_final: 0.7900 (tp30) REVERT: I 270 MET cc_start: 0.8700 (tmm) cc_final: 0.8467 (ttt) REVERT: I 304 VAL cc_start: 0.8194 (t) cc_final: 0.7968 (m) REVERT: I 378 TYR cc_start: 0.8241 (t80) cc_final: 0.7887 (t80) REVERT: I 457 MET cc_start: 0.9222 (tpp) cc_final: 0.8819 (tpp) REVERT: I 527 PHE cc_start: 0.6036 (t80) cc_final: 0.5594 (t80) REVERT: I 548 PHE cc_start: 0.7504 (m-80) cc_final: 0.7064 (m-80) REVERT: I 622 MET cc_start: 0.6528 (tpp) cc_final: 0.6193 (tpp) REVERT: J 228 TRP cc_start: 0.8026 (m100) cc_final: 0.7393 (m100) REVERT: J 411 LEU cc_start: 0.8436 (mm) cc_final: 0.8158 (pp) REVERT: K 132 ASP cc_start: 0.7797 (m-30) cc_final: 0.7551 (m-30) REVERT: K 224 GLU cc_start: 0.8667 (tp30) cc_final: 0.8307 (tp30) REVERT: K 545 ARG cc_start: 0.8205 (mmp80) cc_final: 0.7821 (mmp80) REVERT: L 26 MET cc_start: 0.6995 (mtm) cc_final: 0.5282 (tpt) REVERT: L 106 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6894 (ttp80) REVERT: M 53 ASP cc_start: 0.7022 (m-30) cc_final: 0.5923 (t0) REVERT: N 17 MET cc_start: 0.5951 (tmm) cc_final: 0.4647 (pmm) REVERT: N 75 MET cc_start: 0.6401 (tpt) cc_final: 0.6180 (tpt) REVERT: Q 27 LEU cc_start: 0.8444 (mm) cc_final: 0.7761 (pp) REVERT: T 37 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7515 (mm) REVERT: T 64 GLU cc_start: 0.7274 (pm20) cc_final: 0.6955 (pm20) REVERT: T 80 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7922 (ttmm) REVERT: V 32 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8793 (mp) REVERT: V 50 MET cc_start: 0.8399 (mmm) cc_final: 0.8144 (tpp) REVERT: U 9 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7659 (p0) REVERT: U 26 MET cc_start: 0.7752 (ppp) cc_final: 0.7543 (ppp) REVERT: U 94 TYR cc_start: 0.7806 (t80) cc_final: 0.7560 (t80) REVERT: U 206 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6959 (mp) REVERT: U 270 MET cc_start: 0.7708 (tmm) cc_final: 0.7466 (tmm) REVERT: U 335 MET cc_start: 0.8807 (tpp) cc_final: 0.8512 (tpp) REVERT: U 345 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: U 406 MET cc_start: 0.7801 (mtp) cc_final: 0.7042 (tpp) REVERT: U 517 TRP cc_start: 0.8814 (m-10) cc_final: 0.8456 (m-10) outliers start: 83 outliers final: 54 residues processed: 562 average time/residue: 0.2356 time to fit residues: 218.9270 Evaluate side-chains 529 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 465 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 647 LYS Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 366 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 244 optimal weight: 0.3980 chunk 452 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 195 optimal weight: 0.0170 chunk 308 optimal weight: 4.9990 chunk 423 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** I 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN V 48 HIS V 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.141177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096014 restraints weight = 89505.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095228 restraints weight = 49427.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095584 restraints weight = 41145.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095931 restraints weight = 34555.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.096074 restraints weight = 30819.691| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40156 Z= 0.124 Angle : 0.554 10.360 54183 Z= 0.288 Chirality : 0.038 0.184 5939 Planarity : 0.004 0.067 6903 Dihedral : 4.190 75.730 5292 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.99 % Allowed : 17.35 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.24 (0.12), residues: 4782 helix: 0.79 (0.09), residues: 3200 sheet: -1.42 (0.43), residues: 133 loop : -0.98 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 82 TYR 0.041 0.001 TYR K 345 PHE 0.032 0.001 PHE I 469 TRP 0.045 0.001 TRP I 517 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00277 (40126) covalent geometry : angle 0.55306 (54167) hydrogen bonds : bond 0.03716 ( 2189) hydrogen bonds : angle 4.15548 ( 6510) metal coordination : bond 0.00727 ( 30) metal coordination : angle 1.79136 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 490 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7006 (p) REVERT: A 138 ASP cc_start: 0.7877 (m-30) cc_final: 0.7592 (m-30) REVERT: A 385 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 415 GLN cc_start: 0.7537 (tp40) cc_final: 0.7327 (tp40) REVERT: A 568 GLU cc_start: 0.8208 (mp0) cc_final: 0.7985 (mm-30) REVERT: E 93 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: E 99 ASP cc_start: 0.7623 (m-30) cc_final: 0.7353 (t0) REVERT: E 146 MET cc_start: 0.7191 (ttm) cc_final: 0.6938 (ttm) REVERT: E 196 LYS cc_start: 0.8284 (mptt) cc_final: 0.7947 (pptt) REVERT: D 85 ASN cc_start: 0.8701 (m-40) cc_final: 0.8316 (t0) REVERT: B 31 ASP cc_start: 0.8926 (t0) cc_final: 0.8221 (t0) REVERT: B 138 ASP cc_start: 0.7739 (m-30) cc_final: 0.7498 (m-30) REVERT: B 156 MET cc_start: 0.6908 (mmp) cc_final: 0.6234 (tmm) REVERT: B 233 MET cc_start: 0.8250 (mtp) cc_final: 0.8027 (mtp) REVERT: G 32 GLU cc_start: 0.8742 (tm-30) cc_final: 0.7998 (tt0) REVERT: I 146 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6954 (mmp) REVERT: I 246 GLU cc_start: 0.8185 (tp30) cc_final: 0.7900 (tp30) REVERT: I 270 MET cc_start: 0.8748 (tmm) cc_final: 0.8476 (ttt) REVERT: I 304 VAL cc_start: 0.8167 (t) cc_final: 0.7932 (m) REVERT: I 378 TYR cc_start: 0.8274 (t80) cc_final: 0.7909 (t80) REVERT: I 435 TYR cc_start: 0.9204 (t80) cc_final: 0.8965 (t80) REVERT: I 527 PHE cc_start: 0.6113 (t80) cc_final: 0.5640 (t80) REVERT: I 548 PHE cc_start: 0.7546 (m-80) cc_final: 0.7056 (m-80) REVERT: I 622 MET cc_start: 0.6641 (tpp) cc_final: 0.6279 (tpp) REVERT: J 228 TRP cc_start: 0.8149 (m100) cc_final: 0.7501 (m100) REVERT: J 411 LEU cc_start: 0.8525 (mm) cc_final: 0.8205 (pp) REVERT: K 132 ASP cc_start: 0.7794 (m-30) cc_final: 0.7565 (m-30) REVERT: K 224 GLU cc_start: 0.8687 (tp30) cc_final: 0.8373 (tp30) REVERT: K 545 ARG cc_start: 0.8237 (mmp80) cc_final: 0.7868 (mmp80) REVERT: L 22 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8611 (mmtt) REVERT: L 26 MET cc_start: 0.7017 (mtm) cc_final: 0.5537 (tpt) REVERT: M 32 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7231 (tp30) REVERT: M 53 ASP cc_start: 0.7034 (m-30) cc_final: 0.5931 (t0) REVERT: N 17 MET cc_start: 0.6184 (tmm) cc_final: 0.4818 (pmm) REVERT: N 33 ARG cc_start: 0.6194 (tpp-160) cc_final: 0.5964 (tpp-160) REVERT: Q 27 LEU cc_start: 0.8413 (mm) cc_final: 0.7787 (pp) REVERT: Q 49 GLN cc_start: 0.5806 (pp30) cc_final: 0.5598 (pp30) REVERT: T 37 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7523 (mm) REVERT: T 64 GLU cc_start: 0.7319 (pm20) cc_final: 0.6952 (pm20) REVERT: T 80 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7896 (ttmm) REVERT: V 32 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8778 (mp) REVERT: V 50 MET cc_start: 0.8414 (mmm) cc_final: 0.8197 (tpp) REVERT: U 9 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7654 (p0) REVERT: U 94 TYR cc_start: 0.7759 (t80) cc_final: 0.7547 (t80) REVERT: U 141 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7640 (tm-30) REVERT: U 206 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6946 (mp) REVERT: U 335 MET cc_start: 0.8859 (tpp) cc_final: 0.8573 (tpp) REVERT: U 345 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: U 406 MET cc_start: 0.7790 (mtp) cc_final: 0.7027 (tpp) REVERT: U 517 TRP cc_start: 0.8849 (m-10) cc_final: 0.8530 (m-10) outliers start: 85 outliers final: 56 residues processed: 540 average time/residue: 0.2291 time to fit residues: 204.7066 Evaluate side-chains 535 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 469 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 608 LYS Chi-restraints excluded: chain I residue 647 LYS Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 387 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 146 MET Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 445 optimal weight: 3.9990 chunk 386 optimal weight: 20.0000 chunk 397 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 463 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 428 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 153 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 HIS K 180 HIS K 344 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN N 61 ASN V 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088903 restraints weight = 89722.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088370 restraints weight = 46636.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.089326 restraints weight = 34800.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089443 restraints weight = 34280.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089449 restraints weight = 29595.939| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 40156 Z= 0.241 Angle : 0.646 11.691 54183 Z= 0.335 Chirality : 0.042 0.196 5939 Planarity : 0.004 0.070 6903 Dihedral : 4.394 73.813 5292 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.06 % Allowed : 17.47 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: -0.05 (0.12), residues: 4782 helix: 0.57 (0.09), residues: 3196 sheet: -1.61 (0.48), residues: 114 loop : -1.06 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 106 TYR 0.024 0.002 TYR K 345 PHE 0.030 0.002 PHE I 469 TRP 0.037 0.002 TRP I 517 HIS 0.008 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00561 (40126) covalent geometry : angle 0.64373 (54167) hydrogen bonds : bond 0.04081 ( 2189) hydrogen bonds : angle 4.30395 ( 6510) metal coordination : bond 0.02305 ( 30) metal coordination : angle 2.93532 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 481 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7252 (p) REVERT: A 138 ASP cc_start: 0.7982 (m-30) cc_final: 0.7655 (m-30) REVERT: A 385 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 415 GLN cc_start: 0.7625 (tp40) cc_final: 0.7399 (tp40) REVERT: E 37 ASP cc_start: 0.7531 (m-30) cc_final: 0.6850 (m-30) REVERT: E 99 ASP cc_start: 0.7704 (m-30) cc_final: 0.7392 (t0) REVERT: E 146 MET cc_start: 0.7295 (ttm) cc_final: 0.7040 (ttm) REVERT: E 153 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7022 (tp30) REVERT: E 196 LYS cc_start: 0.8276 (mptt) cc_final: 0.7968 (pptt) REVERT: D 20 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8047 (ptpt) REVERT: D 85 ASN cc_start: 0.8794 (m-40) cc_final: 0.8374 (t0) REVERT: B 31 ASP cc_start: 0.9080 (t0) cc_final: 0.8236 (t0) REVERT: B 138 ASP cc_start: 0.7947 (m-30) cc_final: 0.7650 (m-30) REVERT: B 233 MET cc_start: 0.8372 (mtp) cc_final: 0.8125 (mtp) REVERT: B 399 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: G 32 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8041 (tt0) REVERT: I 270 MET cc_start: 0.8880 (tmm) cc_final: 0.8513 (ttt) REVERT: I 297 MET cc_start: 0.8553 (mmm) cc_final: 0.8177 (tpp) REVERT: I 304 VAL cc_start: 0.8319 (t) cc_final: 0.8102 (m) REVERT: I 378 TYR cc_start: 0.8380 (t80) cc_final: 0.8001 (t80) REVERT: I 435 TYR cc_start: 0.9265 (t80) cc_final: 0.9050 (t80) REVERT: I 457 MET cc_start: 0.9254 (tpp) cc_final: 0.8833 (tpp) REVERT: I 527 PHE cc_start: 0.6215 (t80) cc_final: 0.5759 (t80) REVERT: I 548 PHE cc_start: 0.7592 (m-80) cc_final: 0.7077 (m-80) REVERT: I 622 MET cc_start: 0.6663 (tpp) cc_final: 0.6288 (tpp) REVERT: R 47 ASN cc_start: 0.8450 (m-40) cc_final: 0.7867 (m-40) REVERT: J 228 TRP cc_start: 0.8176 (m100) cc_final: 0.7479 (m100) REVERT: J 411 LEU cc_start: 0.8589 (mm) cc_final: 0.8204 (pp) REVERT: K 132 ASP cc_start: 0.8023 (m-30) cc_final: 0.7602 (m-30) REVERT: K 485 MET cc_start: 0.7604 (mpp) cc_final: 0.7019 (pmm) REVERT: K 545 ARG cc_start: 0.8259 (mmp80) cc_final: 0.7874 (mmp80) REVERT: L 26 MET cc_start: 0.7434 (mtm) cc_final: 0.6270 (tpt) REVERT: L 106 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6935 (ttp80) REVERT: M 32 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7329 (tp30) REVERT: M 37 ARG cc_start: 0.5702 (mmm160) cc_final: 0.5403 (mmm160) REVERT: M 53 ASP cc_start: 0.7194 (m-30) cc_final: 0.6118 (t0) REVERT: M 103 MET cc_start: 0.3690 (tpp) cc_final: 0.3356 (ttm) REVERT: Q 27 LEU cc_start: 0.8440 (mm) cc_final: 0.7834 (pp) REVERT: T 37 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7594 (mm) REVERT: T 80 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7949 (ttmm) REVERT: T 89 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8122 (tm-30) REVERT: V 32 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8868 (mp) REVERT: V 50 MET cc_start: 0.8447 (mmm) cc_final: 0.8189 (tpp) REVERT: U 9 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7635 (p0) REVERT: U 94 TYR cc_start: 0.7736 (t80) cc_final: 0.7422 (t80) REVERT: U 206 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6898 (mp) REVERT: U 270 MET cc_start: 0.7603 (tmm) cc_final: 0.7356 (tmm) REVERT: U 335 MET cc_start: 0.8888 (tpp) cc_final: 0.8593 (tpp) REVERT: U 345 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7539 (mp0) outliers start: 88 outliers final: 59 residues processed: 531 average time/residue: 0.2486 time to fit residues: 217.9797 Evaluate side-chains 528 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 459 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 1 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 452 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 146 MET Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 297 MET Chi-restraints excluded: chain U residue 345 GLU Chi-restraints excluded: chain U residue 411 VAL Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 447 optimal weight: 3.9990 chunk 430 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 362 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 323 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 204 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 300 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 600 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN V 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.139909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093342 restraints weight = 88785.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093021 restraints weight = 50417.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093388 restraints weight = 37945.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093883 restraints weight = 38568.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093997 restraints weight = 31396.388| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40156 Z= 0.140 Angle : 0.601 12.013 54183 Z= 0.309 Chirality : 0.039 0.296 5939 Planarity : 0.004 0.066 6903 Dihedral : 4.344 74.539 5292 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.71 % Allowed : 18.17 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.15 (0.12), residues: 4782 helix: 0.72 (0.09), residues: 3194 sheet: -1.61 (0.47), residues: 114 loop : -0.98 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 106 TYR 0.029 0.001 TYR A 209 PHE 0.023 0.001 PHE I 469 TRP 0.034 0.002 TRP I 517 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00321 (40126) covalent geometry : angle 0.60008 (54167) hydrogen bonds : bond 0.03806 ( 2189) hydrogen bonds : angle 4.18694 ( 6510) metal coordination : bond 0.00859 ( 30) metal coordination : angle 2.09144 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 481 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7164 (p) REVERT: A 138 ASP cc_start: 0.7845 (m-30) cc_final: 0.7558 (m-30) REVERT: A 233 MET cc_start: 0.8881 (mmm) cc_final: 0.8658 (tpt) REVERT: A 385 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 37 ASP cc_start: 0.7429 (m-30) cc_final: 0.6762 (m-30) REVERT: E 146 MET cc_start: 0.7225 (ttm) cc_final: 0.6986 (ttm) REVERT: E 196 LYS cc_start: 0.8350 (mptt) cc_final: 0.7990 (pptt) REVERT: D 20 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (ptpt) REVERT: D 85 ASN cc_start: 0.8722 (m-40) cc_final: 0.8330 (t0) REVERT: D 98 GLU cc_start: 0.7882 (pm20) cc_final: 0.7599 (pm20) REVERT: B 31 ASP cc_start: 0.8939 (t0) cc_final: 0.8174 (t0) REVERT: B 138 ASP cc_start: 0.7855 (m-30) cc_final: 0.7532 (m-30) REVERT: B 233 MET cc_start: 0.8296 (mtp) cc_final: 0.8063 (mtp) REVERT: B 399 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: G 32 GLU cc_start: 0.8810 (tm-30) cc_final: 0.7989 (tt0) REVERT: G 37 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6727 (mmm-85) REVERT: I 270 MET cc_start: 0.8815 (tmm) cc_final: 0.8555 (ttt) REVERT: I 297 MET cc_start: 0.8522 (mmm) cc_final: 0.8196 (tpp) REVERT: I 304 VAL cc_start: 0.8265 (t) cc_final: 0.8027 (m) REVERT: I 378 TYR cc_start: 0.8343 (t80) cc_final: 0.7965 (t80) REVERT: I 457 MET cc_start: 0.9235 (tpp) cc_final: 0.8825 (tpp) REVERT: I 527 PHE cc_start: 0.6242 (t80) cc_final: 0.5679 (t80) REVERT: I 548 PHE cc_start: 0.7644 (m-80) cc_final: 0.7077 (m-80) REVERT: I 558 TYR cc_start: 0.8615 (p90) cc_final: 0.8403 (p90) REVERT: I 622 MET cc_start: 0.6708 (tpp) cc_final: 0.6321 (tpp) REVERT: R 47 ASN cc_start: 0.8392 (m-40) cc_final: 0.7859 (m-40) REVERT: R 50 MET cc_start: 0.8333 (mmm) cc_final: 0.7895 (tpp) REVERT: R 67 GLU cc_start: 0.7715 (pm20) cc_final: 0.6928 (pm20) REVERT: J 228 TRP cc_start: 0.8299 (m100) cc_final: 0.7557 (m100) REVERT: J 411 LEU cc_start: 0.8627 (mm) cc_final: 0.8225 (pp) REVERT: K 132 ASP cc_start: 0.7964 (m-30) cc_final: 0.7588 (m-30) REVERT: K 180 HIS cc_start: 0.7966 (m-70) cc_final: 0.7746 (m90) REVERT: K 224 GLU cc_start: 0.8929 (tp30) cc_final: 0.8593 (tp30) REVERT: K 485 MET cc_start: 0.7508 (mpp) cc_final: 0.6947 (pmm) REVERT: K 545 ARG cc_start: 0.8305 (mmp80) cc_final: 0.7944 (mmp80) REVERT: L 22 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8556 (mmtt) REVERT: L 26 MET cc_start: 0.7534 (mtm) cc_final: 0.6361 (tpt) REVERT: L 106 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6889 (ttp80) REVERT: L 107 TYR cc_start: 0.8598 (t80) cc_final: 0.8308 (t80) REVERT: M 53 ASP cc_start: 0.7219 (m-30) cc_final: 0.6117 (t0) REVERT: M 103 MET cc_start: 0.3711 (tpp) cc_final: 0.3371 (ttm) REVERT: N 17 MET cc_start: 0.5956 (tmm) cc_final: 0.4926 (pmm) REVERT: N 98 GLU cc_start: 0.7695 (tt0) cc_final: 0.7483 (tt0) REVERT: N 102 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8289 (mt-10) REVERT: Q 27 LEU cc_start: 0.8429 (mm) cc_final: 0.7837 (pp) REVERT: T 37 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7510 (mm) REVERT: T 80 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7954 (ttmm) REVERT: T 89 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8123 (tm-30) REVERT: V 32 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8801 (mp) REVERT: V 50 MET cc_start: 0.8399 (mmm) cc_final: 0.8152 (tpp) REVERT: U 9 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7571 (p0) REVERT: U 94 TYR cc_start: 0.7672 (t80) cc_final: 0.7346 (t80) REVERT: U 206 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6980 (mp) REVERT: U 270 MET cc_start: 0.7467 (tmm) cc_final: 0.7215 (tmm) REVERT: U 335 MET cc_start: 0.8860 (tpp) cc_final: 0.8562 (tpp) REVERT: U 406 MET cc_start: 0.7861 (mtp) cc_final: 0.7030 (tpp) REVERT: U 517 TRP cc_start: 0.8845 (m-10) cc_final: 0.8566 (m-10) outliers start: 73 outliers final: 55 residues processed: 521 average time/residue: 0.2511 time to fit residues: 216.4843 Evaluate side-chains 526 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 462 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 480 MET Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 556 LEU Chi-restraints excluded: chain I residue 600 GLN Chi-restraints excluded: chain J residue 279 HIS Chi-restraints excluded: chain J residue 534 PHE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 112 CYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 80 LYS Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 146 MET Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 266 CYS Chi-restraints excluded: chain U residue 411 VAL Chi-restraints excluded: chain U residue 426 ASP Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 169 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 452 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 473 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 300 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 600 GLN ** I 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN V 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.139530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092206 restraints weight = 88902.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092951 restraints weight = 49129.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092527 restraints weight = 33812.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093195 restraints weight = 37326.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093332 restraints weight = 31576.158| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 40156 Z= 0.203 Angle : 0.681 59.198 54183 Z= 0.373 Chirality : 0.041 0.496 5939 Planarity : 0.004 0.066 6903 Dihedral : 4.351 74.508 5292 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.57 % Allowed : 18.21 % Favored : 80.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.20 % 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: 0.12 (0.12), residues: 4782 helix: 0.70 (0.09), residues: 3194 sheet: -1.62 (0.47), residues: 114 loop : -0.98 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 518 TYR 0.038 0.001 TYR I 580 PHE 0.018 0.001 PHE I 469 TRP 0.029 0.002 TRP I 517 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00443 (40126) covalent geometry : angle 0.67998 (54167) hydrogen bonds : bond 0.03842 ( 2189) hydrogen bonds : angle 4.18718 ( 6510) metal coordination : bond 0.01021 ( 30) metal coordination : angle 2.11689 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8774.18 seconds wall clock time: 152 minutes 8.20 seconds (9128.20 seconds total)