Starting phenix.real_space_refine on Sun Oct 13 19:20:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/10_2024/8sgc_40454.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 412 5.16 5 C 41697 2.51 5 N 11602 2.21 5 O 12914 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 66737 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 264 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain breaks: 2 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1339 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 34.32, per 1000 atoms: 0.51 Number of scatterers: 66737 At special positions: 0 Unit cell: (181.976, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 412 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12914 8.00 N 11602 7.00 C 41697 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 Atom "HETATM66260 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66644 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66516 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66324 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 7.8 seconds 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16150 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 98 sheets defined 56.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.528A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 109 removed outlier: 3.593A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.313A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.805A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 432 through 445 removed outlier: 4.190A pdb=" N LEU A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.647A pdb=" N ALA A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 5.168A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.389A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.586A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.590A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.145A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.624A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.423A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 4.037A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.627A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.750A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 4.016A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.077A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.739A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.544A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 50 removed outlier: 4.189A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 105 through 126 removed outlier: 4.280A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.629A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 removed outlier: 3.512A pdb=" N VAL E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.841A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 438 Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.858A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.723A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.774A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 115 removed outlier: 3.576A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.577A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.529A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.653A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.551A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.943A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.687A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.001A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.747A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.534A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.565A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.189A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 4.091A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 removed outlier: 3.512A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.886A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.708A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.269A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.649A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.558A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.757A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.100A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.647A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 Processing helix chain 'Z' and resid 252 through 264 removed outlier: 4.069A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.631A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.834A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.165A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.688A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.569A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 4.003A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.869A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.213A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.753A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 433 through 445 removed outlier: 3.898A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.473A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.615A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.153A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.718A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 removed outlier: 3.579A pdb=" N GLN d 32 " --> pdb=" O ASP d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.611A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.652A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 173 removed outlier: 3.611A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 178 removed outlier: 4.257A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix removed outlier: 3.502A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE d 195 " --> pdb=" O VAL d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.920A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.793A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.564A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.912A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.610A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 126 removed outlier: 4.274A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.630A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 205 through 207 No H-bonds generated for 'chain 'e' and resid 205 through 207' Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 295 removed outlier: 3.774A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.998A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.899A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.684A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 37 removed outlier: 3.693A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 69 removed outlier: 3.735A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 4.018A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.613A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.832A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.570A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.595A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.718A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.158A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.733A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 171 through 185 removed outlier: 3.596A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 removed outlier: 3.576A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 removed outlier: 3.824A pdb=" N LEU h 342 " --> pdb=" O ALA h 339 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.511A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.132A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 168 removed outlier: 4.302A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 removed outlier: 3.508A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 4.865A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.788A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.275A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.592A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.744A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.633A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.547A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.825A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.234A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.577A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.681A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.660A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.807A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.709A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 431 No H-bonds generated for 'chain 'z' and resid 430 through 431' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.160A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.597A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 56 through 62 removed outlier: 4.573A pdb=" N LYS P 60 " --> pdb=" O ASN P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.720A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 195 through 209 Processing helix chain 'P' and resid 219 through 223 Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 251 through 256 Processing helix chain 'P' and resid 260 through 271 removed outlier: 4.052A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 220 through 222 removed outlier: 3.513A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 253 through 255 removed outlier: 3.698A pdb=" N PHE N 254 " --> pdb=" O TRP N 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.315A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.107A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.774A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.382A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.571A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.571A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.222A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.411A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.148A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.722A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.471A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 478 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.415A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.542A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.712A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.672A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.421A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.520A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.192A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 205 removed outlier: 7.036A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD3, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.653A pdb=" N VAL G 290 " --> pdb=" O ILE G 312 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 407 through 409 Processing sheet with id=AD5, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD6, first strand: chain 'H' and resid 14 through 17 removed outlier: 4.459A pdb=" N VAL H 516 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET Q 55 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU H 518 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE Q 57 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE H 520 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Q 66 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.724A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD9, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AE2, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE3, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.020A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.949A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.329A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE7, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE8, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AE9, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF1, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.191A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF3, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.446A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.643A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.547A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 52 through 55 removed outlier: 7.154A pdb=" N ASP a 42 " --> pdb=" O ASP g 521 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N VAL g 523 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET a 44 " --> pdb=" O VAL g 523 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY g 525 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL a 46 " --> pdb=" O GLY g 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF8, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AF9, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.327A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.549A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.549A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.231A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG5, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.386A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 61 through 64 removed outlier: 5.910A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG8, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.865A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.307A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU b 350 " --> pdb=" O ARG b 231 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG b 231 " --> pdb=" O GLU b 350 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH2, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH3, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.542A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.526A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.526A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH7, first strand: chain 'e' and resid 28 through 29 removed outlier: 4.519A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH9, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.866A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.464A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.228A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI4, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI5, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.912A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI7, first strand: chain 'g' and resid 238 through 241 Processing sheet with id=AI8, first strand: chain 'g' and resid 478 through 480 removed outlier: 3.537A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.482A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.806A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ3, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ4, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ5, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ6, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.186A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.879A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.569A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK1, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK2, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK3, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK4, first strand: chain 'z' and resid 192 through 196 Processing sheet with id=AK5, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK6, first strand: chain 'z' and resid 310 through 313 removed outlier: 6.625A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK8, first strand: chain 'P' and resid 215 through 218 removed outlier: 6.394A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 4056 hydrogen bonds defined for protein. 11598 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: 30.99 Time building geometry restraints manager: 15.12 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: 22417 1.34 - 1.46: 7414 1.46 - 1.57: 36881 1.57 - 1.69: 48 1.69 - 1.81: 730 Bond restraints: 67490 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 b 603 " pdb="AL AF3 b 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 e 603 " pdb="AL AF3 e 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 67485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 90150 2.05 - 4.10: 734 4.10 - 6.15: 225 6.15 - 8.20: 15 8.20 - 10.25: 1 Bond angle restraints: 91125 Sorted by residual: angle pdb=" C GLY h 18 " pdb=" N ILE h 19 " pdb=" CA ILE h 19 " ideal model delta sigma weight residual 120.24 123.99 -3.75 6.30e-01 2.52e+00 3.55e+01 angle pdb=" C LYS P 176 " pdb=" N GLU P 177 " pdb=" CA GLU P 177 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 angle pdb=" N ILE G 165 " pdb=" CA ILE G 165 " pdb=" C ILE G 165 " ideal model delta sigma weight residual 112.29 108.99 3.30 9.40e-01 1.13e+00 1.23e+01 angle pdb=" CA MET E 4 " pdb=" CB MET E 4 " pdb=" CG MET E 4 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.64e+00 angle pdb=" N GLU z 121 " pdb=" CA GLU z 121 " pdb=" CB GLU z 121 " ideal model delta sigma weight residual 110.12 114.58 -4.46 1.47e+00 4.63e-01 9.20e+00 ... (remaining 91120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 41021 34.69 - 69.38: 638 69.38 - 104.07: 55 104.07 - 138.76: 9 138.76 - 173.45: 8 Dihedral angle restraints: 41731 sinusoidal: 16798 harmonic: 24933 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.45 -173.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.38 172.63 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.29 -170.29 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7177 0.031 - 0.062: 2346 0.062 - 0.092: 704 0.092 - 0.123: 592 0.123 - 0.154: 41 Chirality restraints: 10860 Sorted by residual: chirality pdb=" CA ILE B 11 " pdb=" N ILE B 11 " pdb=" C ILE B 11 " pdb=" CB ILE B 11 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA GLU A 77 " pdb=" N GLU A 77 " pdb=" C GLU A 77 " pdb=" CB GLU A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 10857 not shown) Planarity restraints: 11630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 7 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 8 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 73 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C LYS A 73 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS A 73 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 74 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO e 441 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 ... (remaining 11627 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 659 2.56 - 3.15: 53098 3.15 - 3.73: 106027 3.73 - 4.32: 145940 4.32 - 4.90: 250117 Nonbonded interactions: 555841 Sorted by model distance: nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.975 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.975 2.120 nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.980 2.170 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.982 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.984 2.120 ... (remaining 555836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.050 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 127.800 Find NCS groups from input model: 5.740 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 67490 Z= 0.258 Angle : 0.514 10.248 91125 Z= 0.251 Chirality : 0.040 0.154 10860 Planarity : 0.003 0.068 11630 Dihedral : 14.017 173.453 25581 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.09), residues: 8626 helix: 2.51 (0.08), residues: 4455 sheet: 0.34 (0.16), residues: 1141 loop : -0.23 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 266 HIS 0.004 0.001 HIS G 470 PHE 0.017 0.001 PHE e 386 TYR 0.019 0.001 TYR G 274 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 7.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 268 MET cc_start: 0.8401 (pmm) cc_final: 0.8091 (pmm) REVERT: A 51 ASP cc_start: 0.8550 (m-30) cc_final: 0.7431 (m-30) REVERT: D 25 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8351 (tp-100) REVERT: D 67 ASP cc_start: 0.8537 (m-30) cc_final: 0.8288 (m-30) REVERT: D 307 ASP cc_start: 0.8372 (t0) cc_final: 0.8139 (t0) REVERT: E 39 MET cc_start: 0.8891 (ttm) cc_final: 0.8628 (ttp) REVERT: E 474 MET cc_start: 0.8199 (tmm) cc_final: 0.7951 (tmm) REVERT: G 21 LYS cc_start: 0.8418 (tptp) cc_final: 0.8111 (tptt) REVERT: Q 42 THR cc_start: 0.8017 (m) cc_final: 0.7707 (m) REVERT: Q 200 ASP cc_start: 0.8800 (m-30) cc_final: 0.8571 (t0) REVERT: Q 357 ASP cc_start: 0.8478 (t0) cc_final: 0.8218 (t0) REVERT: Z 238 GLU cc_start: 0.8969 (pt0) cc_final: 0.8565 (pt0) REVERT: b 13 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8310 (mtpp) REVERT: d 192 MET cc_start: 0.9124 (mmm) cc_final: 0.8854 (mmm) REVERT: d 232 LYS cc_start: 0.8877 (pttp) cc_final: 0.8596 (ptmm) REVERT: g 47 MET cc_start: 0.9098 (mmp) cc_final: 0.8856 (mmp) REVERT: h 324 MET cc_start: 0.9120 (mmm) cc_final: 0.8849 (mmm) REVERT: h 440 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8925 (tppp) REVERT: q 41 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8538 (tp-100) REVERT: q 130 GLU cc_start: 0.8346 (tp30) cc_final: 0.7861 (tp30) REVERT: z 17 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8429 (mp10) outliers start: 0 outliers final: 2 residues processed: 554 average time/residue: 1.5616 time to fit residues: 1112.5938 Evaluate side-chains 437 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain h residue 81 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 725 optimal weight: 9.9990 chunk 651 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 439 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 673 optimal weight: 20.0000 chunk 260 optimal weight: 0.9980 chunk 409 optimal weight: 0.9980 chunk 501 optimal weight: 0.9990 chunk 780 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 502 ASN G 526 HIS H 283 HIS ** H 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 386 GLN a 103 ASN b 227 ASN z 161 HIS z 218 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 67490 Z= 0.153 Angle : 0.539 11.362 91125 Z= 0.268 Chirality : 0.041 0.152 10860 Planarity : 0.003 0.054 11630 Dihedral : 7.442 169.765 9375 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.82 % Favored : 97.17 % Rotamer: Outliers : 0.64 % Allowed : 5.96 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.09), residues: 8626 helix: 2.52 (0.08), residues: 4516 sheet: 0.24 (0.16), residues: 1113 loop : -0.31 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.012 0.001 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.015 0.001 TYR Q 505 ARG 0.008 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 486 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8407 (m-30) cc_final: 0.8115 (m-30) REVERT: D 24 TYR cc_start: 0.8403 (t80) cc_final: 0.8194 (t80) REVERT: D 25 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8426 (tp-100) REVERT: D 28 ASP cc_start: 0.8021 (t70) cc_final: 0.7632 (t70) REVERT: D 67 ASP cc_start: 0.8656 (m-30) cc_final: 0.8450 (m-30) REVERT: D 307 ASP cc_start: 0.8497 (t0) cc_final: 0.8126 (t0) REVERT: E 39 MET cc_start: 0.8871 (ttm) cc_final: 0.8594 (ttp) REVERT: E 448 MET cc_start: 0.8995 (mtt) cc_final: 0.8713 (mtm) REVERT: E 474 MET cc_start: 0.8338 (tmm) cc_final: 0.7972 (tmm) REVERT: H 14 ASP cc_start: 0.8704 (t0) cc_final: 0.8240 (t0) REVERT: H 70 ASP cc_start: 0.7804 (t0) cc_final: 0.7122 (t0) REVERT: Q 357 ASP cc_start: 0.8466 (t0) cc_final: 0.8218 (t0) REVERT: Q 526 MET cc_start: 0.9119 (mtm) cc_final: 0.8894 (mtm) REVERT: Z 238 GLU cc_start: 0.8971 (pt0) cc_final: 0.8543 (pt0) REVERT: Z 357 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8364 (mm-30) REVERT: b 13 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8751 (mttp) REVERT: d 192 MET cc_start: 0.9123 (mmm) cc_final: 0.8868 (mmm) REVERT: d 232 LYS cc_start: 0.8860 (pttp) cc_final: 0.8561 (ptmm) REVERT: d 261 ASP cc_start: 0.8095 (p0) cc_final: 0.7710 (p0) REVERT: e 80 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8778 (mtm) REVERT: e 526 MET cc_start: 0.9289 (ttt) cc_final: 0.8810 (ttt) REVERT: g 47 MET cc_start: 0.9116 (mmp) cc_final: 0.8894 (mmp) REVERT: g 133 MET cc_start: 0.9133 (mtp) cc_final: 0.8931 (mtp) REVERT: g 437 TYR cc_start: 0.8774 (t80) cc_final: 0.8449 (t80) REVERT: h 324 MET cc_start: 0.9138 (mmm) cc_final: 0.8857 (mmm) REVERT: q 41 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8552 (tp-100) REVERT: q 130 GLU cc_start: 0.8308 (tp30) cc_final: 0.7822 (tp30) REVERT: z 17 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8419 (mp10) REVERT: z 194 MET cc_start: 0.9223 (tpp) cc_final: 0.8676 (tpp) REVERT: P 196 GLU cc_start: 0.5279 (pt0) cc_final: 0.3941 (tm-30) outliers start: 46 outliers final: 10 residues processed: 503 average time/residue: 1.5319 time to fit residues: 1001.4623 Evaluate side-chains 447 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 436 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 358 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 433 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 649 optimal weight: 6.9990 chunk 531 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 781 optimal weight: 0.9980 chunk 844 optimal weight: 7.9990 chunk 695 optimal weight: 3.9990 chunk 774 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 626 optimal weight: 6.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 386 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 67490 Z= 0.246 Angle : 0.547 9.337 91125 Z= 0.270 Chirality : 0.042 0.153 10860 Planarity : 0.003 0.057 11630 Dihedral : 7.303 171.759 9373 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 1.08 % Allowed : 7.68 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.09), residues: 8626 helix: 2.52 (0.08), residues: 4522 sheet: 0.09 (0.16), residues: 1123 loop : -0.38 (0.11), residues: 2981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.011 0.001 HIS z 161 PHE 0.018 0.001 PHE e 386 TYR 0.014 0.001 TYR Z 353 ARG 0.007 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 453 time to evaluate : 6.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 268 MET cc_start: 0.8102 (pmt) cc_final: 0.7676 (pmm) REVERT: A 51 ASP cc_start: 0.8491 (m-30) cc_final: 0.8244 (m-30) REVERT: D 25 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8472 (tp-100) REVERT: D 28 ASP cc_start: 0.8057 (t70) cc_final: 0.7390 (t0) REVERT: D 67 ASP cc_start: 0.8630 (m-30) cc_final: 0.8426 (m-30) REVERT: D 248 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9147 (tt) REVERT: D 307 ASP cc_start: 0.8575 (t0) cc_final: 0.8134 (t0) REVERT: E 39 MET cc_start: 0.8911 (ttm) cc_final: 0.8637 (ttp) REVERT: E 448 MET cc_start: 0.9047 (mtt) cc_final: 0.8761 (mtm) REVERT: G 21 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7963 (tptt) REVERT: G 167 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7652 (mtp-110) REVERT: H 2 MET cc_start: 0.7072 (mmt) cc_final: 0.6584 (mmt) REVERT: H 14 ASP cc_start: 0.8757 (t0) cc_final: 0.8218 (t0) REVERT: H 70 ASP cc_start: 0.7858 (t0) cc_final: 0.7175 (t0) REVERT: H 283 HIS cc_start: 0.8145 (m90) cc_final: 0.7894 (m-70) REVERT: H 497 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7770 (ppp) REVERT: Q 357 ASP cc_start: 0.8456 (t0) cc_final: 0.8252 (t0) REVERT: Z 238 GLU cc_start: 0.8992 (pt0) cc_final: 0.8576 (pt0) REVERT: Z 357 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8387 (mm-30) REVERT: a 106 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7984 (tp30) REVERT: d 192 MET cc_start: 0.9157 (mmm) cc_final: 0.8898 (mmm) REVERT: d 232 LYS cc_start: 0.8857 (pttp) cc_final: 0.8609 (ptmm) REVERT: d 261 ASP cc_start: 0.8085 (p0) cc_final: 0.7742 (p0) REVERT: g 47 MET cc_start: 0.9095 (mmp) cc_final: 0.8845 (mmp) REVERT: g 133 MET cc_start: 0.9146 (mtp) cc_final: 0.8935 (mtp) REVERT: h 324 MET cc_start: 0.9150 (mmm) cc_final: 0.8844 (mmm) REVERT: h 440 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8877 (tppp) REVERT: q 41 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8562 (tp-100) REVERT: q 130 GLU cc_start: 0.8368 (tp30) cc_final: 0.7823 (tp30) REVERT: z 17 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8432 (mp10) REVERT: z 194 MET cc_start: 0.9268 (tpp) cc_final: 0.8767 (tpp) REVERT: P 196 GLU cc_start: 0.5372 (pt0) cc_final: 0.3867 (tm-30) outliers start: 78 outliers final: 21 residues processed: 487 average time/residue: 1.5113 time to fit residues: 957.3677 Evaluate side-chains 456 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 431 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 167 ARG Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 7 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 772 optimal weight: 2.9990 chunk 587 optimal weight: 6.9990 chunk 405 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 372 optimal weight: 0.9990 chunk 524 optimal weight: 7.9990 chunk 784 optimal weight: 9.9990 chunk 830 optimal weight: 1.9990 chunk 409 optimal weight: 0.9990 chunk 743 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 69 HIS e 139 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 67490 Z= 0.260 Angle : 0.548 10.429 91125 Z= 0.270 Chirality : 0.042 0.168 10860 Planarity : 0.003 0.057 11630 Dihedral : 7.245 173.679 9373 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.33 % Favored : 96.66 % Rotamer: Outliers : 0.93 % Allowed : 9.40 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.09), residues: 8626 helix: 2.51 (0.08), residues: 4518 sheet: 0.00 (0.16), residues: 1127 loop : -0.38 (0.11), residues: 2981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.012 0.001 HIS Z 161 PHE 0.014 0.001 PHE e 386 TYR 0.012 0.001 TYR Q 505 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 446 time to evaluate : 6.211 Fit side-chains revert: symmetry clash REVERT: N 268 MET cc_start: 0.8150 (pmt) cc_final: 0.7867 (pmm) REVERT: A 51 ASP cc_start: 0.8483 (m-30) cc_final: 0.8175 (m-30) REVERT: A 306 MET cc_start: 0.8882 (mtp) cc_final: 0.8247 (mtm) REVERT: D 25 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8475 (tp-100) REVERT: D 28 ASP cc_start: 0.8076 (t70) cc_final: 0.7687 (t70) REVERT: D 67 ASP cc_start: 0.8621 (m-30) cc_final: 0.8385 (m-30) REVERT: D 307 ASP cc_start: 0.8588 (t0) cc_final: 0.8088 (t0) REVERT: E 39 MET cc_start: 0.8901 (ttm) cc_final: 0.8625 (ttp) REVERT: E 448 MET cc_start: 0.9054 (mtt) cc_final: 0.8777 (mtm) REVERT: G 17 GLU cc_start: 0.7025 (tp30) cc_final: 0.6753 (tp30) REVERT: G 20 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7504 (ttp-170) REVERT: G 21 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8011 (tptt) REVERT: G 219 MET cc_start: 0.8993 (ttp) cc_final: 0.8791 (ppp) REVERT: H 2 MET cc_start: 0.7201 (mmt) cc_final: 0.6941 (mmt) REVERT: H 14 ASP cc_start: 0.8739 (t0) cc_final: 0.8221 (t0) REVERT: H 70 ASP cc_start: 0.7874 (t0) cc_final: 0.7171 (t0) REVERT: Q 526 MET cc_start: 0.9136 (mtm) cc_final: 0.8924 (mtm) REVERT: Z 238 GLU cc_start: 0.9000 (pt0) cc_final: 0.8612 (pt0) REVERT: Z 357 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8421 (mm-30) REVERT: a 39 VAL cc_start: 0.9202 (m) cc_final: 0.8921 (t) REVERT: a 106 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7969 (tp30) REVERT: a 156 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: b 139 GLU cc_start: 0.8076 (mp0) cc_final: 0.7638 (mp0) REVERT: b 415 MET cc_start: 0.9352 (mmm) cc_final: 0.9006 (mmp) REVERT: d 192 MET cc_start: 0.9146 (mmm) cc_final: 0.8861 (mmm) REVERT: d 261 ASP cc_start: 0.8092 (p0) cc_final: 0.7754 (p0) REVERT: e 526 MET cc_start: 0.9290 (ttt) cc_final: 0.8808 (ttt) REVERT: g 47 MET cc_start: 0.9110 (mmp) cc_final: 0.8908 (mmp) REVERT: h 251 ASP cc_start: 0.8580 (p0) cc_final: 0.8367 (p0) REVERT: h 324 MET cc_start: 0.9156 (mmm) cc_final: 0.8842 (mmm) REVERT: q 41 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8567 (tp-100) REVERT: q 130 GLU cc_start: 0.8378 (tp30) cc_final: 0.7863 (tp30) REVERT: z 17 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8426 (mp10) REVERT: z 194 MET cc_start: 0.9270 (tpp) cc_final: 0.8786 (tpp) outliers start: 67 outliers final: 25 residues processed: 476 average time/residue: 1.5518 time to fit residues: 959.4987 Evaluate side-chains 448 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 421 time to evaluate : 6.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 7 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 691 optimal weight: 0.7980 chunk 471 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 618 optimal weight: 0.9990 chunk 342 optimal weight: 9.9990 chunk 708 optimal weight: 8.9990 chunk 573 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 423 optimal weight: 0.9980 chunk 745 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS h 25 ASN q 53 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67490 Z= 0.169 Angle : 0.521 12.017 91125 Z= 0.255 Chirality : 0.041 0.157 10860 Planarity : 0.003 0.056 11630 Dihedral : 7.097 177.983 9371 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 0.98 % Allowed : 10.09 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.09), residues: 8626 helix: 2.57 (0.08), residues: 4522 sheet: -0.02 (0.16), residues: 1106 loop : -0.37 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.012 0.001 PHE g 362 TYR 0.017 0.001 TYR D 24 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 462 time to evaluate : 6.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8492 (m-30) cc_final: 0.8151 (m-30) REVERT: A 242 GLN cc_start: 0.8911 (mt0) cc_final: 0.8487 (mt0) REVERT: A 306 MET cc_start: 0.8845 (mtp) cc_final: 0.8301 (mtm) REVERT: B 48 MET cc_start: 0.8811 (mmp) cc_final: 0.8560 (mmt) REVERT: D 25 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8459 (tp-100) REVERT: D 28 ASP cc_start: 0.7992 (t70) cc_final: 0.7320 (t0) REVERT: D 67 ASP cc_start: 0.8605 (m-30) cc_final: 0.8379 (m-30) REVERT: D 307 ASP cc_start: 0.8596 (t0) cc_final: 0.8075 (t0) REVERT: E 39 MET cc_start: 0.8868 (ttm) cc_final: 0.8568 (ttp) REVERT: G 20 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7529 (ttp-170) REVERT: G 21 LYS cc_start: 0.8419 (tmtt) cc_final: 0.7997 (tptt) REVERT: H 14 ASP cc_start: 0.8744 (t0) cc_final: 0.8219 (t0) REVERT: H 70 ASP cc_start: 0.7868 (t0) cc_final: 0.7176 (t0) REVERT: H 283 HIS cc_start: 0.8225 (m-70) cc_final: 0.7803 (m-70) REVERT: H 497 MET cc_start: 0.8031 (ptp) cc_final: 0.7747 (ppp) REVERT: Q 526 MET cc_start: 0.9114 (mtm) cc_final: 0.8912 (mtm) REVERT: Z 238 GLU cc_start: 0.8977 (pt0) cc_final: 0.8593 (pt0) REVERT: Z 357 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8405 (mm-30) REVERT: Z 415 GLU cc_start: 0.8825 (mp0) cc_final: 0.8352 (mp0) REVERT: a 39 VAL cc_start: 0.9164 (m) cc_final: 0.8900 (t) REVERT: a 106 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7954 (tp30) REVERT: a 344 MET cc_start: 0.8838 (mtm) cc_final: 0.8576 (mtm) REVERT: b 415 MET cc_start: 0.9405 (mmm) cc_final: 0.9120 (mmp) REVERT: d 192 MET cc_start: 0.9143 (mmm) cc_final: 0.8880 (mmm) REVERT: d 261 ASP cc_start: 0.8066 (p0) cc_final: 0.7732 (p0) REVERT: e 288 MET cc_start: 0.9012 (ptp) cc_final: 0.8702 (ptp) REVERT: e 526 MET cc_start: 0.9293 (ttt) cc_final: 0.8859 (ttt) REVERT: h 251 ASP cc_start: 0.8553 (p0) cc_final: 0.8331 (p0) REVERT: h 324 MET cc_start: 0.9151 (mmm) cc_final: 0.8841 (mmm) REVERT: q 41 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8563 (tp-100) REVERT: q 130 GLU cc_start: 0.8361 (tp30) cc_final: 0.7820 (tp30) REVERT: z 194 MET cc_start: 0.9238 (tpp) cc_final: 0.8757 (tpp) REVERT: P 196 GLU cc_start: 0.5165 (pt0) cc_final: 0.4038 (tm-30) outliers start: 71 outliers final: 30 residues processed: 501 average time/residue: 1.4839 time to fit residues: 972.2660 Evaluate side-chains 470 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 439 time to evaluate : 6.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 279 optimal weight: 0.0980 chunk 747 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 831 optimal weight: 6.9990 chunk 689 optimal weight: 4.9990 chunk 384 optimal weight: 0.0570 chunk 69 optimal weight: 0.9990 chunk 274 optimal weight: 7.9990 chunk 436 optimal weight: 9.9990 overall best weight: 1.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 67490 Z= 0.150 Angle : 0.521 10.433 91125 Z= 0.255 Chirality : 0.041 0.181 10860 Planarity : 0.003 0.056 11630 Dihedral : 6.941 175.334 9371 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.10 % Favored : 96.89 % Rotamer: Outliers : 0.95 % Allowed : 10.59 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.09), residues: 8626 helix: 2.62 (0.08), residues: 4514 sheet: -0.04 (0.16), residues: 1121 loop : -0.36 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.013 0.001 HIS Z 161 PHE 0.012 0.001 PHE g 362 TYR 0.019 0.001 TYR D 24 ARG 0.005 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 455 time to evaluate : 6.193 Fit side-chains revert: symmetry clash REVERT: A 164 ASN cc_start: 0.6780 (m-40) cc_final: 0.6515 (m-40) REVERT: A 242 GLN cc_start: 0.8875 (mt0) cc_final: 0.8427 (mt0) REVERT: D 25 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8443 (tp-100) REVERT: D 28 ASP cc_start: 0.7914 (t70) cc_final: 0.7163 (t0) REVERT: D 67 ASP cc_start: 0.8588 (m-30) cc_final: 0.8362 (m-30) REVERT: D 307 ASP cc_start: 0.8580 (t0) cc_final: 0.8000 (t0) REVERT: E 39 MET cc_start: 0.8853 (ttm) cc_final: 0.8585 (ttp) REVERT: E 48 MET cc_start: 0.9304 (tpp) cc_final: 0.9091 (mmm) REVERT: E 379 ASN cc_start: 0.9033 (t0) cc_final: 0.8812 (t0) REVERT: G 21 LYS cc_start: 0.8314 (tmtt) cc_final: 0.8024 (tptt) REVERT: H 14 ASP cc_start: 0.8746 (t0) cc_final: 0.8221 (t0) REVERT: H 114 GLU cc_start: 0.8388 (pt0) cc_final: 0.8159 (pt0) REVERT: H 283 HIS cc_start: 0.8185 (m-70) cc_final: 0.7864 (m-70) REVERT: H 497 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7738 (ppp) REVERT: Q 357 ASP cc_start: 0.8283 (t0) cc_final: 0.8053 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9117 (mtm) cc_final: 0.8880 (mtm) REVERT: Z 238 GLU cc_start: 0.8961 (pt0) cc_final: 0.8580 (pt0) REVERT: Z 357 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8399 (mm-30) REVERT: a 39 VAL cc_start: 0.9113 (m) cc_final: 0.8847 (t) REVERT: a 106 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7933 (tp30) REVERT: a 306 MET cc_start: 0.8361 (mtt) cc_final: 0.7914 (mtt) REVERT: b 415 MET cc_start: 0.9418 (mmm) cc_final: 0.9036 (mmp) REVERT: d 192 MET cc_start: 0.9145 (mmm) cc_final: 0.8876 (mmm) REVERT: d 232 LYS cc_start: 0.8918 (ptmm) cc_final: 0.8677 (pttm) REVERT: d 261 ASP cc_start: 0.8017 (p0) cc_final: 0.7686 (p0) REVERT: e 288 MET cc_start: 0.8993 (ptp) cc_final: 0.8693 (ptp) REVERT: h 251 ASP cc_start: 0.8532 (p0) cc_final: 0.8317 (p0) REVERT: h 324 MET cc_start: 0.9145 (mmm) cc_final: 0.8843 (mmm) REVERT: q 41 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8548 (tp-100) REVERT: q 130 GLU cc_start: 0.8356 (tp30) cc_final: 0.7807 (tp30) REVERT: z 194 MET cc_start: 0.9237 (tpp) cc_final: 0.8745 (tpp) REVERT: P 198 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.5321 (mmp) outliers start: 69 outliers final: 32 residues processed: 496 average time/residue: 1.5106 time to fit residues: 979.9029 Evaluate side-chains 466 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 433 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 801 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 473 optimal weight: 10.0000 chunk 606 optimal weight: 5.9990 chunk 470 optimal weight: 9.9990 chunk 699 optimal weight: 6.9990 chunk 464 optimal weight: 0.9980 chunk 827 optimal weight: 9.9990 chunk 518 optimal weight: 2.9990 chunk 504 optimal weight: 4.9990 chunk 382 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN H 283 HIS H 501 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS d 172 ASN z 84 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 67490 Z= 0.316 Angle : 0.581 14.653 91125 Z= 0.284 Chirality : 0.043 0.210 10860 Planarity : 0.003 0.057 11630 Dihedral : 7.003 171.436 9371 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 1.05 % Allowed : 10.92 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.09), residues: 8626 helix: 2.54 (0.08), residues: 4513 sheet: -0.12 (0.16), residues: 1125 loop : -0.39 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.013 0.001 HIS Z 161 PHE 0.013 0.001 PHE e 386 TYR 0.013 0.001 TYR E 420 ARG 0.005 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 434 time to evaluate : 6.219 Fit side-chains revert: symmetry clash REVERT: D 25 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8532 (tp-100) REVERT: D 28 ASP cc_start: 0.8087 (t0) cc_final: 0.7393 (t0) REVERT: D 67 ASP cc_start: 0.8575 (m-30) cc_final: 0.8334 (m-30) REVERT: D 307 ASP cc_start: 0.8654 (t0) cc_final: 0.8113 (t0) REVERT: E 39 MET cc_start: 0.8853 (ttm) cc_final: 0.8586 (ttp) REVERT: G 20 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: G 21 LYS cc_start: 0.8449 (tmtt) cc_final: 0.8059 (tptt) REVERT: H 14 ASP cc_start: 0.8752 (t0) cc_final: 0.8239 (t0) REVERT: H 70 ASP cc_start: 0.7861 (t0) cc_final: 0.7157 (t0) REVERT: Q 357 ASP cc_start: 0.8381 (t0) cc_final: 0.8105 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9137 (mtm) cc_final: 0.8907 (mtm) REVERT: Z 238 GLU cc_start: 0.8994 (pt0) cc_final: 0.8625 (pt0) REVERT: Z 357 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8417 (mm-30) REVERT: a 39 VAL cc_start: 0.9169 (m) cc_final: 0.8896 (t) REVERT: a 106 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7974 (tp30) REVERT: a 156 MET cc_start: 0.8697 (mtp) cc_final: 0.8446 (mtp) REVERT: b 415 MET cc_start: 0.9469 (mmm) cc_final: 0.9083 (mmp) REVERT: d 192 MET cc_start: 0.9164 (mmm) cc_final: 0.8867 (mmm) REVERT: d 261 ASP cc_start: 0.8084 (p0) cc_final: 0.7776 (p0) REVERT: e 29 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7841 (mtp) REVERT: e 526 MET cc_start: 0.9305 (ttt) cc_final: 0.8742 (ttt) REVERT: g 133 MET cc_start: 0.8960 (mtp) cc_final: 0.8753 (mtp) REVERT: h 251 ASP cc_start: 0.8518 (p0) cc_final: 0.8314 (p0) REVERT: h 324 MET cc_start: 0.9162 (mmm) cc_final: 0.8854 (mmm) REVERT: h 440 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8867 (tppp) REVERT: q 41 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8258 (tp40) REVERT: q 55 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8246 (tpp) REVERT: q 127 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: q 130 GLU cc_start: 0.8401 (tp30) cc_final: 0.7895 (tp30) REVERT: z 17 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: z 194 MET cc_start: 0.9271 (tpp) cc_final: 0.8800 (tpp) REVERT: P 84 MET cc_start: 0.4824 (tmm) cc_final: 0.4465 (tpp) REVERT: P 198 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.5357 (mmp) outliers start: 76 outliers final: 39 residues processed: 479 average time/residue: 1.4890 time to fit residues: 936.0433 Evaluate side-chains 466 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 421 time to evaluate : 6.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 482 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain P residue 180 SER Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 512 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 494 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 526 optimal weight: 5.9990 chunk 564 optimal weight: 2.9990 chunk 409 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 650 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS d 172 ASN z 23 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 67490 Z= 0.259 Angle : 0.561 13.085 91125 Z= 0.276 Chirality : 0.042 0.269 10860 Planarity : 0.003 0.057 11630 Dihedral : 6.971 169.572 9371 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.31 % Favored : 96.68 % Rotamer: Outliers : 0.87 % Allowed : 11.35 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8626 helix: 2.53 (0.08), residues: 4508 sheet: -0.17 (0.15), residues: 1131 loop : -0.40 (0.11), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.020 0.001 HIS z 161 PHE 0.012 0.001 PHE g 362 TYR 0.012 0.001 TYR Q 505 ARG 0.005 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 433 time to evaluate : 6.077 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8479 (ttp) cc_final: 0.8257 (ttm) REVERT: D 25 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8535 (tp-100) REVERT: D 28 ASP cc_start: 0.8102 (t0) cc_final: 0.7697 (t70) REVERT: D 67 ASP cc_start: 0.8594 (m-30) cc_final: 0.8349 (m-30) REVERT: D 307 ASP cc_start: 0.8642 (t0) cc_final: 0.8091 (t0) REVERT: E 39 MET cc_start: 0.8836 (ttm) cc_final: 0.8575 (ttp) REVERT: G 20 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (ttp-170) REVERT: G 21 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8062 (tptt) REVERT: H 14 ASP cc_start: 0.8763 (t0) cc_final: 0.8233 (t0) REVERT: H 70 ASP cc_start: 0.7866 (t0) cc_final: 0.7162 (t0) REVERT: H 283 HIS cc_start: 0.8285 (m-70) cc_final: 0.7886 (m-70) REVERT: H 497 MET cc_start: 0.8074 (ptp) cc_final: 0.7785 (ppp) REVERT: Q 357 ASP cc_start: 0.8439 (t0) cc_final: 0.8162 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9139 (mtm) cc_final: 0.8910 (mtm) REVERT: Z 46 MET cc_start: 0.8521 (tpp) cc_final: 0.7954 (ttm) REVERT: Z 238 GLU cc_start: 0.8994 (pt0) cc_final: 0.8631 (pt0) REVERT: Z 357 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8408 (mm-30) REVERT: a 39 VAL cc_start: 0.9167 (m) cc_final: 0.8894 (t) REVERT: a 106 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7969 (tp30) REVERT: a 156 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8469 (mtp) REVERT: b 353 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7769 (tmm) REVERT: b 415 MET cc_start: 0.9466 (mmm) cc_final: 0.9085 (mmp) REVERT: d 192 MET cc_start: 0.9160 (mmm) cc_final: 0.8886 (mmm) REVERT: d 261 ASP cc_start: 0.8091 (p0) cc_final: 0.7792 (p0) REVERT: e 288 MET cc_start: 0.9065 (ptp) cc_final: 0.8834 (ptp) REVERT: e 526 MET cc_start: 0.9328 (ttt) cc_final: 0.8778 (ttt) REVERT: h 251 ASP cc_start: 0.8473 (p0) cc_final: 0.8271 (p0) REVERT: h 324 MET cc_start: 0.9158 (mmm) cc_final: 0.8847 (mmm) REVERT: q 41 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8594 (tp-100) REVERT: q 55 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8142 (tpp) REVERT: q 127 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: q 130 GLU cc_start: 0.8396 (tp30) cc_final: 0.7889 (tp30) REVERT: z 17 GLN cc_start: 0.8233 (mp-120) cc_final: 0.7922 (mp10) REVERT: z 194 MET cc_start: 0.9264 (tpp) cc_final: 0.8799 (tpp) REVERT: P 84 MET cc_start: 0.4699 (tmm) cc_final: 0.4284 (tpp) REVERT: P 93 MET cc_start: 0.3850 (mmp) cc_final: 0.2888 (ptt) REVERT: P 198 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.5346 (mmp) outliers start: 63 outliers final: 41 residues processed: 469 average time/residue: 1.5236 time to fit residues: 936.4141 Evaluate side-chains 466 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 420 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 753 optimal weight: 2.9990 chunk 793 optimal weight: 6.9990 chunk 723 optimal weight: 3.9990 chunk 771 optimal weight: 7.9990 chunk 792 optimal weight: 0.9990 chunk 464 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 605 optimal weight: 0.0980 chunk 236 optimal weight: 7.9990 chunk 697 optimal weight: 0.7980 chunk 729 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS d 172 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 67490 Z= 0.173 Angle : 0.545 13.451 91125 Z= 0.266 Chirality : 0.041 0.218 10860 Planarity : 0.003 0.056 11630 Dihedral : 6.828 168.174 9371 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.30 % Favored : 96.69 % Rotamer: Outliers : 0.80 % Allowed : 11.62 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.09), residues: 8626 helix: 2.59 (0.08), residues: 4512 sheet: -0.16 (0.15), residues: 1142 loop : -0.38 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.017 0.001 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.013 0.001 TYR Q 505 ARG 0.005 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 444 time to evaluate : 6.128 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8475 (mpp) REVERT: D 25 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8496 (tp-100) REVERT: D 28 ASP cc_start: 0.7986 (t0) cc_final: 0.7283 (t0) REVERT: D 67 ASP cc_start: 0.8584 (m-30) cc_final: 0.8344 (m-30) REVERT: D 307 ASP cc_start: 0.8613 (t0) cc_final: 0.8043 (t0) REVERT: E 39 MET cc_start: 0.8828 (ttm) cc_final: 0.8526 (ttt) REVERT: G 21 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8030 (tptt) REVERT: G 52 ASP cc_start: 0.8321 (t70) cc_final: 0.7738 (t0) REVERT: G 54 MET cc_start: 0.8722 (pmm) cc_final: 0.8470 (pmm) REVERT: H 14 ASP cc_start: 0.8762 (t0) cc_final: 0.8223 (t0) REVERT: H 70 ASP cc_start: 0.7869 (t0) cc_final: 0.7187 (t0) REVERT: H 114 GLU cc_start: 0.8395 (pt0) cc_final: 0.8183 (pt0) REVERT: H 283 HIS cc_start: 0.8215 (m-70) cc_final: 0.7873 (m-70) REVERT: H 497 MET cc_start: 0.8005 (ptp) cc_final: 0.7746 (ppp) REVERT: Q 357 ASP cc_start: 0.8443 (t0) cc_final: 0.8150 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9120 (mtm) cc_final: 0.8887 (mtm) REVERT: Z 238 GLU cc_start: 0.8982 (pt0) cc_final: 0.8620 (pt0) REVERT: Z 357 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8406 (mm-30) REVERT: a 39 VAL cc_start: 0.9129 (m) cc_final: 0.8841 (t) REVERT: a 106 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7947 (tp30) REVERT: b 139 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: b 353 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: b 415 MET cc_start: 0.9460 (mmm) cc_final: 0.9084 (mmp) REVERT: d 60 MET cc_start: 0.9028 (ttm) cc_final: 0.8738 (tpp) REVERT: d 232 LYS cc_start: 0.8926 (ptmm) cc_final: 0.8659 (pttm) REVERT: d 261 ASP cc_start: 0.8045 (p0) cc_final: 0.7758 (p0) REVERT: e 58 ASP cc_start: 0.8341 (m-30) cc_final: 0.8140 (m-30) REVERT: h 324 MET cc_start: 0.9147 (mmm) cc_final: 0.8866 (mmm) REVERT: q 41 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8548 (tp-100) REVERT: q 55 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8204 (tpp) REVERT: q 127 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: q 130 GLU cc_start: 0.8371 (tp30) cc_final: 0.7842 (tp30) REVERT: z 17 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: z 194 MET cc_start: 0.9241 (tpp) cc_final: 0.8769 (tpp) REVERT: P 84 MET cc_start: 0.4588 (tmm) cc_final: 0.4174 (tpp) REVERT: P 93 MET cc_start: 0.3743 (mmp) cc_final: 0.2785 (ptt) REVERT: P 198 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.5309 (mmp) outliers start: 58 outliers final: 37 residues processed: 479 average time/residue: 1.5219 time to fit residues: 955.9470 Evaluate side-chains 471 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 428 time to evaluate : 6.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 768 optimal weight: 9.9990 chunk 506 optimal weight: 9.9990 chunk 815 optimal weight: 2.9990 chunk 497 optimal weight: 9.9990 chunk 387 optimal weight: 7.9990 chunk 567 optimal weight: 7.9990 chunk 855 optimal weight: 10.0000 chunk 787 optimal weight: 7.9990 chunk 681 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 526 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS d 172 ASN q 53 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 67490 Z= 0.462 Angle : 0.656 14.298 91125 Z= 0.324 Chirality : 0.045 0.245 10860 Planarity : 0.004 0.058 11630 Dihedral : 7.100 170.983 9371 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.84 % Favored : 96.15 % Rotamer: Outliers : 0.94 % Allowed : 11.48 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8626 helix: 2.39 (0.08), residues: 4503 sheet: -0.18 (0.15), residues: 1126 loop : -0.48 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 304 HIS 0.016 0.001 HIS z 161 PHE 0.019 0.002 PHE H 220 TYR 0.029 0.002 TYR D 24 ARG 0.007 0.000 ARG E 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 416 time to evaluate : 6.164 Fit side-chains revert: symmetry clash REVERT: D 28 ASP cc_start: 0.8228 (t0) cc_final: 0.7796 (t70) REVERT: D 67 ASP cc_start: 0.8568 (m-30) cc_final: 0.8288 (m-30) REVERT: D 307 ASP cc_start: 0.8653 (t0) cc_final: 0.8147 (t0) REVERT: D 467 GLU cc_start: 0.8504 (tp30) cc_final: 0.8096 (tp30) REVERT: G 20 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7755 (ttp-170) REVERT: G 21 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8091 (tptt) REVERT: H 11 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8132 (tm-30) REVERT: H 14 ASP cc_start: 0.8808 (t0) cc_final: 0.8304 (t0) REVERT: H 70 ASP cc_start: 0.7896 (t0) cc_final: 0.7188 (t0) REVERT: H 283 HIS cc_start: 0.8310 (m-70) cc_final: 0.7920 (m-70) REVERT: Q 357 ASP cc_start: 0.8536 (t0) cc_final: 0.8299 (t0) REVERT: Q 526 MET cc_start: 0.9151 (mtm) cc_final: 0.8918 (mtm) REVERT: Z 238 GLU cc_start: 0.9007 (pt0) cc_final: 0.8676 (pt0) REVERT: Z 357 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8413 (mm-30) REVERT: a 106 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8009 (tp30) REVERT: a 344 MET cc_start: 0.8892 (mtm) cc_final: 0.8424 (pmm) REVERT: b 139 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: b 353 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: b 415 MET cc_start: 0.9477 (mmm) cc_final: 0.9075 (mmp) REVERT: d 172 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8678 (m110) REVERT: d 261 ASP cc_start: 0.8136 (p0) cc_final: 0.7861 (p0) REVERT: d 263 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: e 288 MET cc_start: 0.9106 (ptp) cc_final: 0.8871 (ptp) REVERT: h 324 MET cc_start: 0.9186 (mmm) cc_final: 0.8957 (mmm) REVERT: h 440 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8907 (tppp) REVERT: q 41 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8338 (tp40) REVERT: q 127 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: q 130 GLU cc_start: 0.8425 (tp30) cc_final: 0.7923 (tp30) REVERT: z 17 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: P 84 MET cc_start: 0.4633 (tmm) cc_final: 0.4183 (tpp) REVERT: P 93 MET cc_start: 0.3778 (mmp) cc_final: 0.2838 (ptt) REVERT: P 196 GLU cc_start: 0.5326 (pt0) cc_final: 0.4522 (mp0) REVERT: P 198 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.5309 (mmp) outliers start: 68 outliers final: 33 residues processed: 458 average time/residue: 1.5843 time to fit residues: 944.2680 Evaluate side-chains 452 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 410 time to evaluate : 6.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 172 ASN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 263 GLN Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain P residue 180 SER Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 417 optimal weight: 3.9990 chunk 541 optimal weight: 8.9990 chunk 725 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 628 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 682 optimal weight: 0.7980 chunk 285 optimal weight: 7.9990 chunk 700 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS d 172 ASN q 53 ASN q 383 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.054481 restraints weight = 190739.123| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.08 r_work: 0.2512 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 67490 Z= 0.198 Angle : 0.580 13.463 91125 Z= 0.284 Chirality : 0.042 0.231 10860 Planarity : 0.003 0.058 11630 Dihedral : 7.023 169.677 9371 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.24 % Favored : 96.75 % Rotamer: Outliers : 0.75 % Allowed : 11.96 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8626 helix: 2.46 (0.08), residues: 4504 sheet: -0.22 (0.15), residues: 1130 loop : -0.47 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.017 0.001 HIS Z 161 PHE 0.014 0.001 PHE a 167 TYR 0.027 0.001 TYR D 24 ARG 0.006 0.000 ARG Z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16053.75 seconds wall clock time: 282 minutes 4.44 seconds (16924.44 seconds total)