Starting phenix.real_space_refine on Fri Sep 27 20:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/09_2024/8sha_40482.cif" } resolution = 3.0 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= 0.052 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 416 5.16 5 C 41964 2.51 5 N 11677 2.21 5 O 12986 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 46 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67155 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 428 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 5 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: 4094 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} Conformer: "C" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} bond proxies already assigned to first conformer: 4120 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: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1631 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 3 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: 35.15, per 1000 atoms: 0.52 Number of scatterers: 67155 At special positions: 0 Unit cell: (180.918, 176.686, 181.976, 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 416 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12986 8.00 N 11677 7.00 C 41964 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 "HETATM67062 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66806 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66710 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 7.6 seconds 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16246 Finding SS restraints... Secondary structure from input PDB file: 371 helices and 101 sheets defined 56.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.541A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.687A 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 removed outlier: 3.732A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 3.787A 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 144 through 157 removed outlier: 3.944A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.174A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.575A 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 258 through 280 removed outlier: 4.397A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.084A 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 433 through 445 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 removed outlier: 3.958A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.318A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.672A 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: 3.545A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.724A 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 49 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' 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: 3.633A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.664A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.967A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.923A 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 removed outlier: 3.532A pdb=" N MET D 355 " --> pdb=" O THR D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.860A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.998A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.769A 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 504 through 507 Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.502A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.828A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.531A 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: 4.226A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (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: 6.621A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.859A 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: 3.529A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.837A 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: 3.590A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.901A 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: 3.555A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.510A 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 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' 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 306 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.587A pdb=" N ARG G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.593A 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 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.681A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.030A 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: 3.682A 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 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 338 through 342 removed outlier: 3.555A 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: 3.936A 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 516 removed outlier: 3.570A pdb=" N VAL H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.342A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.383A 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 156 through 168 removed outlier: 4.220A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 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: 3.574A pdb=" N LEU Q 265 " --> pdb=" O THR Q 261 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.695A 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: 3.612A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.220A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.752A 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 'Q' and resid 535 through 539 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.674A 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: 3.631A 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: 4.188A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.806A 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 Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.581A 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: 3.665A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.381A 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 432 through 445 removed outlier: 4.167A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.596A 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 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.714A 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 91 through 110 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 144 through 157 removed outlier: 3.724A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.312A 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: 3.867A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 removed outlier: 3.669A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.674A pdb=" N MET a 344 " --> pdb=" O GLU a 341 " (cutoff:3.500A) 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: 3.626A 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 478 through 484 removed outlier: 3.705A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (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 151 through 169 removed outlier: 4.466A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 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: 3.544A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) 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 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.742A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 471 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 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: 3.768A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.889A 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 172 removed outlier: 3.632A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.653A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix 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: 4.024A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.872A 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 removed outlier: 3.556A pdb=" N MET d 355 " --> pdb=" O THR d 352 " (cutoff:3.500A) Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 441 Processing helix chain 'd' and resid 442 through 444 No H-bonds generated for 'chain 'd' and resid 442 through 444' Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.662A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.864A 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 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.908A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.545A 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 107 through 126 removed outlier: 3.612A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (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: 6.572A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.935A 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: 3.545A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.616A 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: 3.551A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 41 removed outlier: 3.892A pdb=" N LEU g 41 " --> pdb=" O ARG g 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 38 through 41' Processing helix chain 'g' and resid 62 through 68 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.572A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.560A 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: 3.807A 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: 3.680A 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 339 through 343 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 470 removed outlier: 3.604A 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: 3.549A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.565A pdb=" N THR h 39 " --> pdb=" O VAL h 36 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 36 through 40' Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.600A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.237A 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: 3.628A 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 186 removed outlier: 3.694A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (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 338 through 340 No H-bonds generated for 'chain 'h' and resid 338 through 340' 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: 3.723A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.143A 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 516 removed outlier: 3.655A pdb=" N VAL h 516 " --> pdb=" O LEU h 512 " (cutoff:3.500A) Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 3.939A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.576A 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 156 through 168 removed outlier: 4.371A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 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: 4.731A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.816A 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 340 through 344 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.909A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS q 430 " --> pdb=" O TYR q 426 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.418A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.817A 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 removed outlier: 3.508A 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 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.754A 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: 3.586A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.792A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.122A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.663A 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 removed outlier: 3.738A 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: 3.558A 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: 3.633A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.224A 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 432 through 445 removed outlier: 4.163A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.698A 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 498 through 517 Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.511A pdb=" N GLY P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 84 removed outlier: 3.510A pdb=" N TRP P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 141 through 152 removed outlier: 4.137A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU P 152 " --> pdb=" O MET P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 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 250 through 255 removed outlier: 4.210A pdb=" N GLN P 254 " --> pdb=" O ARG P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 271 removed outlier: 3.789A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 200 through 203 removed outlier: 4.157A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER N 202 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 253 through 254 removed outlier: 6.589A pdb=" N VAL N 265 " --> pdb=" O VAL N 274 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN N 272 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.609A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.437A 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: 6.040A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.435A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.680A 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: 6.552A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.719A 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: 6.552A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.481A 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: 9.137A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.479A 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: 4.252A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.319A 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: 6.818A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.739A 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: 6.443A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.392A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 289 " --> pdb=" O LYS B 236 " (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: 3.851A pdb=" N GLY D 392 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 5.945A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 5.945A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AC5, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.316A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.725A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.564A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 299 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.564A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.213A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.799A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD8, first strand: chain 'H' and resid 14 through 17 Processing sheet with id=AD9, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.493A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE3, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.030A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 149 through 150 removed outlier: 4.024A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.629A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE9, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF1, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'Z' and resid 139 through 140 removed outlier: 3.515A pdb=" N VAL Z 408 " --> pdb=" O ASP Z 496 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 192 through 196 removed outlier: 6.148A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF5, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.464A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id=AF7, 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: 7.437A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 52 through 55 removed outlier: 7.325A pdb=" N ASP a 42 " --> pdb=" O ASP g 521 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N VAL g 523 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET a 44 " --> pdb=" O VAL g 523 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG1, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG2, first strand: chain 'a' and resid 196 through 199 removed outlier: 6.354A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.423A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.423A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.086A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG7, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.349A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.777A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH1, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.556A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 218 through 220 removed outlier: 3.622A pdb=" N ASP b 357 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH4, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.400A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.626A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.626A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH9, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.256A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.855A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.404A pdb=" N CYS e 377 " --> pdb=" O ALA e 356 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA e 356 " --> pdb=" O CYS e 377 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 248 through 250 removed outlier: 6.142A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.169A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI7, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI8, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.853A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AJ1, first strand: chain 'g' and resid 310 through 312 removed outlier: 6.242A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ3, first strand: chain 'h' and resid 14 through 17 Processing sheet with id=AJ4, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.494A pdb=" N GLY h 196 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU h 374 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS h 198 " --> pdb=" O LEU h 374 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY h 376 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL h 200 " --> pdb=" O GLY h 376 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ6, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ7, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ8, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ9, first strand: chain 'q' and resid 20 through 22 removed outlier: 5.056A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.804A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.760A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 220 through 223 removed outlier: 3.505A pdb=" N VAL q 350 " --> pdb=" O VAL q 234 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK6, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK7, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.467A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK9, first strand: chain 'z' and resid 310 through 313 removed outlier: 8.978A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AL2, first strand: chain 'P' and resid 162 through 164 removed outlier: 5.952A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 4072 hydrogen bonds defined for protein. 11616 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: 35.27 Time building geometry restraints manager: 15.73 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: 22561 1.34 - 1.46: 8787 1.46 - 1.58: 35784 1.58 - 1.69: 48 1.69 - 1.81: 735 Bond restraints: 67915 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.46e+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 6.40e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 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 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.795 -0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 67910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 90252 1.91 - 3.82: 1111 3.82 - 5.73: 252 5.73 - 7.63: 69 7.63 - 9.54: 6 Bond angle restraints: 91690 Sorted by residual: angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.99 -8.81 2.37e+00 1.78e-01 1.38e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.42 -8.24 2.37e+00 1.78e-01 1.21e+01 angle pdb=" CB MET E 60 " pdb=" CG MET E 60 " pdb=" SD MET E 60 " ideal model delta sigma weight residual 112.70 103.16 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C GLN q 472 " pdb=" N GLU q 473 " pdb=" CA GLU q 473 " ideal model delta sigma weight residual 121.18 115.08 6.10 1.98e+00 2.55e-01 9.50e+00 angle pdb=" CB MET b 488 " pdb=" CG MET b 488 " pdb=" SD MET b 488 " ideal model delta sigma weight residual 112.70 103.55 9.15 3.00e+00 1.11e-01 9.30e+00 ... (remaining 91685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 41168 35.15 - 70.30: 742 70.30 - 105.45: 64 105.45 - 140.60: 10 140.60 - 175.75: 7 Dihedral angle restraints: 41991 sinusoidal: 16914 harmonic: 25077 Sorted by residual: 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 300.00 124.25 175.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 114.15 -174.15 1 2.00e+01 2.50e-03 4.79e+01 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 -60.00 111.72 -171.72 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7989 0.043 - 0.085: 2131 0.085 - 0.128: 749 0.128 - 0.171: 49 0.171 - 0.214: 2 Chirality restraints: 10920 Sorted by residual: chirality pdb=" CB THR h 57 " pdb=" CA THR h 57 " pdb=" OG1 THR h 57 " pdb=" CG2 THR h 57 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 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 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB VAL g 183 " pdb=" CA VAL g 183 " pdb=" CG1 VAL g 183 " pdb=" CG2 VAL g 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 10917 not shown) Planarity restraints: 11702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO a 478 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS a 69 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO a 70 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO a 70 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO a 70 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 438 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C ARG G 438 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG G 438 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA G 439 " 0.011 2.00e-02 2.50e+03 ... (remaining 11699 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 487 2.50 - 3.10: 49322 3.10 - 3.70: 102333 3.70 - 4.30: 150221 4.30 - 4.90: 257089 Nonbonded interactions: 559452 Sorted by model distance: nonbonded pdb="MG MG B 602 " pdb=" F1 AF3 B 603 " model vdw 1.897 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.906 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.908 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.923 2.120 nonbonded pdb=" OD2 ASP b 97 " pdb="MG MG b 602 " model vdw 1.931 2.170 ... (remaining 559447 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 8 or resid 10 through 536 or resid 601 through 603)) selection = (chain 'e' and (resid 8 or resid 10 through 536 or resid 601 through 603)) } 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: 1.240 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: 0.070 Extract box with map and model: 1.910 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 135.530 Find NCS groups from input model: 5.920 Set up NCS constraints: 0.450 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.006 0.161 67915 Z= 0.412 Angle : 0.599 9.543 91690 Z= 0.296 Chirality : 0.043 0.214 10920 Planarity : 0.003 0.119 11702 Dihedral : 14.840 175.754 25745 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.34 (0.09), residues: 8670 helix: 2.16 (0.08), residues: 4447 sheet: -0.10 (0.16), residues: 1155 loop : -0.61 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.009 0.001 HIS Z 161 PHE 0.027 0.001 PHE B 12 TYR 0.017 0.001 TYR G 437 ARG 0.015 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 6.277 Fit side-chains revert: symmetry clash REVERT: N 226 SER cc_start: 0.9049 (t) cc_final: 0.8754 (t) REVERT: N 228 GLN cc_start: 0.8653 (mm110) cc_final: 0.8278 (mp10) REVERT: A 171 MET cc_start: 0.8973 (ttm) cc_final: 0.8743 (ttm) REVERT: B 384 ASP cc_start: 0.8262 (m-30) cc_final: 0.8047 (m-30) REVERT: D 24 TYR cc_start: 0.8867 (t80) cc_final: 0.8614 (t80) REVERT: D 467 GLU cc_start: 0.8382 (tp30) cc_final: 0.8126 (tp30) REVERT: G 255 ASP cc_start: 0.8044 (m-30) cc_final: 0.7086 (m-30) REVERT: H 194 MET cc_start: 0.8827 (mmp) cc_final: 0.8411 (mmp) REVERT: H 403 ASP cc_start: 0.7885 (p0) cc_final: 0.7529 (p0) REVERT: H 524 ARG cc_start: 0.7537 (tmm-80) cc_final: 0.7302 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8302 (t70) cc_final: 0.8024 (t0) REVERT: Z 522 MET cc_start: 0.8417 (mtm) cc_final: 0.7925 (mtm) REVERT: b 384 ASP cc_start: 0.8452 (m-30) cc_final: 0.8099 (m-30) REVERT: b 445 MET cc_start: 0.8826 (tpp) cc_final: 0.8540 (mmm) REVERT: d 446 MET cc_start: 0.8214 (mtt) cc_final: 0.7951 (mtt) REVERT: e 125 ASP cc_start: 0.8097 (m-30) cc_final: 0.7790 (m-30) REVERT: g 358 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8258 (mt-10) REVERT: g 395 MET cc_start: 0.9310 (mtm) cc_final: 0.9063 (mtm) REVERT: h 524 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7193 (tpt90) REVERT: z 272 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8483 (mppt) REVERT: z 364 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7691 (mm-30) REVERT: P 173 MET cc_start: 0.7891 (ttt) cc_final: 0.7353 (tpp) outliers start: 0 outliers final: 1 residues processed: 563 average time/residue: 1.4790 time to fit residues: 1093.8652 Evaluate side-chains 471 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 6.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 728 optimal weight: 10.0000 chunk 654 optimal weight: 7.9990 chunk 362 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 441 optimal weight: 0.0770 chunk 349 optimal weight: 6.9990 chunk 676 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 411 optimal weight: 6.9990 chunk 503 optimal weight: 7.9990 chunk 783 optimal weight: 10.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN A 534 HIS ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 502 ASN G 12 GLN G 28 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 283 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 470 HIS a 217 ASN ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 537 ASN g 526 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 67915 Z= 0.310 Angle : 0.599 9.787 91690 Z= 0.299 Chirality : 0.043 0.176 10920 Planarity : 0.004 0.070 11702 Dihedral : 7.944 172.966 9425 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 0.78 % Allowed : 6.16 % Favored : 93.06 % 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: 1.33 (0.09), residues: 8670 helix: 2.16 (0.08), residues: 4500 sheet: -0.18 (0.16), residues: 1118 loop : -0.65 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.010 0.001 HIS Z 161 PHE 0.023 0.001 PHE P 170 TYR 0.018 0.001 TYR G 437 ARG 0.009 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 518 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 226 SER cc_start: 0.9091 (t) cc_final: 0.8795 (t) REVERT: N 228 GLN cc_start: 0.8556 (mm110) cc_final: 0.8181 (mp10) REVERT: A 171 MET cc_start: 0.8972 (ttm) cc_final: 0.8710 (ttm) REVERT: D 24 TYR cc_start: 0.8904 (t80) cc_final: 0.8646 (t80) REVERT: D 467 GLU cc_start: 0.8330 (tp30) cc_final: 0.8069 (tp30) REVERT: G 521 ASP cc_start: 0.7745 (t0) cc_final: 0.7296 (t0) REVERT: H 403 ASP cc_start: 0.8001 (p0) cc_final: 0.7607 (p0) REVERT: H 524 ARG cc_start: 0.7584 (tmm-80) cc_final: 0.7262 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8291 (t70) cc_final: 0.8042 (t0) REVERT: Z 32 ASP cc_start: 0.7894 (m-30) cc_final: 0.7520 (m-30) REVERT: Z 46 MET cc_start: 0.8698 (ttm) cc_final: 0.8361 (ttt) REVERT: b 384 ASP cc_start: 0.8413 (m-30) cc_final: 0.8175 (m-30) REVERT: b 445 MET cc_start: 0.8758 (tpp) cc_final: 0.8486 (mmm) REVERT: e 21 ASP cc_start: 0.7678 (t70) cc_final: 0.7335 (t0) REVERT: e 474 MET cc_start: 0.8409 (tmm) cc_final: 0.7909 (tmm) REVERT: g 358 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8124 (mt-10) REVERT: g 395 MET cc_start: 0.9268 (mtm) cc_final: 0.9041 (mtm) REVERT: h 440 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8593 (tppp) REVERT: h 524 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7309 (mmm-85) REVERT: z 244 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (t) REVERT: z 272 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8479 (mppt) REVERT: z 364 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7662 (mm-30) REVERT: P 144 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6570 (mmm160) REVERT: P 173 MET cc_start: 0.7938 (ttt) cc_final: 0.7417 (OUTLIER) REVERT: P 236 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8072 (tm) outliers start: 57 outliers final: 21 residues processed: 539 average time/residue: 1.5186 time to fit residues: 1077.8314 Evaluate side-chains 501 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 477 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Z residue 337 ASP Chi-restraints excluded: chain a residue 534 HIS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 435 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 652 optimal weight: 4.9990 chunk 533 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 785 optimal weight: 4.9990 chunk 848 optimal weight: 0.9990 chunk 699 optimal weight: 0.9980 chunk 778 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 629 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN G 12 GLN G 28 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 380 GLN ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 139 GLN h 30 GLN P 287 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 67915 Z= 0.304 Angle : 0.580 9.437 91690 Z= 0.288 Chirality : 0.043 0.176 10920 Planarity : 0.003 0.053 11702 Dihedral : 7.560 167.713 9422 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Rotamer: Outliers : 0.93 % Allowed : 8.29 % Favored : 90.78 % 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: 1.32 (0.09), residues: 8670 helix: 2.19 (0.08), residues: 4510 sheet: -0.31 (0.15), residues: 1132 loop : -0.64 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.011 0.001 HIS Z 161 PHE 0.021 0.001 PHE P 170 TYR 0.017 0.001 TYR G 437 ARG 0.005 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 510 time to evaluate : 6.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 226 SER cc_start: 0.9084 (t) cc_final: 0.8704 (t) REVERT: N 228 GLN cc_start: 0.8572 (mm110) cc_final: 0.8127 (mp10) REVERT: A 171 MET cc_start: 0.8977 (ttm) cc_final: 0.8720 (ttm) REVERT: B 387 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: D 24 TYR cc_start: 0.8926 (t80) cc_final: 0.8679 (t80) REVERT: D 467 GLU cc_start: 0.8340 (tp30) cc_final: 0.8041 (tp30) REVERT: G 47 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: H 403 ASP cc_start: 0.7974 (p0) cc_final: 0.7583 (p0) REVERT: H 524 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.7182 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8219 (t70) cc_final: 0.7989 (t0) REVERT: Z 15 ARG cc_start: 0.8779 (mtm-85) cc_final: 0.8522 (mtm110) REVERT: b 384 ASP cc_start: 0.8389 (m-30) cc_final: 0.8093 (m-30) REVERT: b 445 MET cc_start: 0.8791 (tpp) cc_final: 0.8473 (mmm) REVERT: e 21 ASP cc_start: 0.7670 (t70) cc_final: 0.7278 (t0) REVERT: e 121 GLU cc_start: 0.7960 (tp30) cc_final: 0.7578 (tm-30) REVERT: g 8 LEU cc_start: 0.8653 (mt) cc_final: 0.8418 (tp) REVERT: g 358 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8182 (mt-10) REVERT: h 440 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8577 (tppp) REVERT: h 524 ARG cc_start: 0.7659 (mmm160) cc_final: 0.7189 (tpt90) REVERT: z 272 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8477 (mppt) REVERT: z 430 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8570 (tmtm) REVERT: P 80 GLN cc_start: 0.7637 (tp-100) cc_final: 0.6828 (tp40) REVERT: P 84 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6903 (mmt) REVERT: P 144 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6366 (mmm160) REVERT: P 173 MET cc_start: 0.7945 (ttt) cc_final: 0.7662 (OUTLIER) outliers start: 68 outliers final: 35 residues processed: 542 average time/residue: 1.4591 time to fit residues: 1047.4186 Evaluate side-chains 509 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 470 time to evaluate : 5.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 775 optimal weight: 1.9990 chunk 590 optimal weight: 0.9990 chunk 407 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 527 optimal weight: 6.9990 chunk 787 optimal weight: 10.0000 chunk 834 optimal weight: 10.0000 chunk 411 optimal weight: 5.9990 chunk 746 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN G 12 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 283 HIS P 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 67915 Z= 0.316 Angle : 0.584 11.155 91690 Z= 0.288 Chirality : 0.043 0.173 10920 Planarity : 0.003 0.046 11702 Dihedral : 7.460 172.077 9422 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Rotamer: Outliers : 1.20 % Allowed : 9.62 % Favored : 89.18 % 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: 1.31 (0.09), residues: 8670 helix: 2.20 (0.08), residues: 4510 sheet: -0.35 (0.15), residues: 1121 loop : -0.68 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.015 0.001 HIS Z 161 PHE 0.036 0.001 PHE P 136 TYR 0.018 0.001 TYR z 498 ARG 0.004 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 507 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8559 (mm110) cc_final: 0.8176 (mm-40) REVERT: A 171 MET cc_start: 0.8975 (ttm) cc_final: 0.8728 (ttm) REVERT: B 387 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: D 24 TYR cc_start: 0.8948 (t80) cc_final: 0.8709 (t80) REVERT: D 467 GLU cc_start: 0.8355 (tp30) cc_final: 0.8057 (tp30) REVERT: G 422 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9147 (tp) REVERT: H 403 ASP cc_start: 0.7972 (p0) cc_final: 0.7589 (p0) REVERT: H 524 ARG cc_start: 0.7658 (tmm-80) cc_final: 0.7163 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8218 (t70) cc_final: 0.7973 (t0) REVERT: Z 15 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8523 (mtm110) REVERT: Z 32 ASP cc_start: 0.7881 (m-30) cc_final: 0.7516 (m-30) REVERT: b 87 MET cc_start: 0.9069 (ttp) cc_final: 0.8814 (ttp) REVERT: b 384 ASP cc_start: 0.8392 (m-30) cc_final: 0.8101 (m-30) REVERT: b 445 MET cc_start: 0.8854 (tpp) cc_final: 0.8506 (mmm) REVERT: e 21 ASP cc_start: 0.7685 (t70) cc_final: 0.7262 (t0) REVERT: e 121 GLU cc_start: 0.7996 (tp30) cc_final: 0.7595 (tm-30) REVERT: e 426 GLU cc_start: 0.8513 (mp0) cc_final: 0.8196 (mp0) REVERT: g 8 LEU cc_start: 0.8568 (mt) cc_final: 0.8366 (tp) REVERT: g 358 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8159 (mt-10) REVERT: h 70 ASP cc_start: 0.7362 (t0) cc_final: 0.7137 (t0) REVERT: h 440 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8604 (tppp) REVERT: h 524 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7223 (tpt90) REVERT: z 207 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8863 (mm) REVERT: z 244 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8656 (t) REVERT: z 272 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8487 (mppt) REVERT: P 144 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6417 (mmm160) REVERT: P 173 MET cc_start: 0.8014 (ttt) cc_final: 0.7661 (tpp) outliers start: 87 outliers final: 45 residues processed: 555 average time/residue: 1.4394 time to fit residues: 1059.4575 Evaluate side-chains 525 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 474 time to evaluate : 5.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 202 SER Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 694 optimal weight: 9.9990 chunk 473 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 621 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 711 optimal weight: 0.3980 chunk 576 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 425 optimal weight: 0.9980 chunk 748 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN E 515 GLN G 12 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 394 ASN e 504 GLN g 390 ASN h 283 HIS h 431 GLN P 287 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 67915 Z= 0.307 Angle : 0.580 10.500 91690 Z= 0.286 Chirality : 0.043 0.170 10920 Planarity : 0.003 0.047 11702 Dihedral : 7.388 177.755 9422 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.66 % Favored : 96.33 % Rotamer: Outliers : 1.24 % Allowed : 10.78 % Favored : 87.98 % 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: 1.33 (0.09), residues: 8670 helix: 2.22 (0.08), residues: 4504 sheet: -0.37 (0.15), residues: 1106 loop : -0.67 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.014 0.001 HIS Z 161 PHE 0.031 0.001 PHE P 136 TYR 0.018 0.001 TYR z 498 ARG 0.005 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 499 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8472 (mm110) cc_final: 0.8195 (mm-40) REVERT: A 47 ASP cc_start: 0.7653 (t0) cc_final: 0.7106 (t0) REVERT: A 171 MET cc_start: 0.8979 (ttm) cc_final: 0.8743 (ttm) REVERT: B 387 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: D 24 TYR cc_start: 0.8948 (t80) cc_final: 0.8715 (t80) REVERT: D 467 GLU cc_start: 0.8365 (tp30) cc_final: 0.8064 (tp30) REVERT: G 144 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8588 (m) REVERT: H 227 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: H 403 ASP cc_start: 0.7989 (p0) cc_final: 0.7609 (p0) REVERT: H 524 ARG cc_start: 0.7654 (tmm-80) cc_final: 0.7440 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8222 (t70) cc_final: 0.7972 (t0) REVERT: Z 15 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8511 (mtm110) REVERT: b 87 MET cc_start: 0.9118 (ttp) cc_final: 0.8902 (ttp) REVERT: b 384 ASP cc_start: 0.8393 (m-30) cc_final: 0.8109 (m-30) REVERT: b 445 MET cc_start: 0.8850 (tpp) cc_final: 0.8488 (mmm) REVERT: e 21 ASP cc_start: 0.7681 (t70) cc_final: 0.7245 (t0) REVERT: e 121 GLU cc_start: 0.8007 (tp30) cc_final: 0.7603 (tm-30) REVERT: e 426 GLU cc_start: 0.8520 (mp0) cc_final: 0.8186 (mp0) REVERT: g 358 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8167 (mt-10) REVERT: h 440 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8613 (tppp) REVERT: h 524 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7276 (tpt90) REVERT: z 207 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8851 (mm) REVERT: z 244 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8554 (t) REVERT: z 272 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8486 (mppt) REVERT: P 144 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6404 (mmm160) REVERT: P 173 MET cc_start: 0.8016 (ttt) cc_final: 0.7657 (tpp) outliers start: 90 outliers final: 48 residues processed: 550 average time/residue: 1.5003 time to fit residues: 1099.0598 Evaluate side-chains 529 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 474 time to evaluate : 6.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 202 SER Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 233 HIS 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 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 280 optimal weight: 9.9990 chunk 751 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 489 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 834 optimal weight: 9.9990 chunk 693 optimal weight: 2.9990 chunk 386 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 438 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN B 124 GLN G 12 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 283 HIS h 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 67915 Z= 0.360 Angle : 0.600 11.377 91690 Z= 0.296 Chirality : 0.043 0.175 10920 Planarity : 0.003 0.046 11702 Dihedral : 7.354 177.037 9422 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 11.27 % Favored : 87.27 % 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: 1.25 (0.09), residues: 8670 helix: 2.18 (0.08), residues: 4503 sheet: -0.41 (0.15), residues: 1115 loop : -0.73 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 136 TYR 0.017 0.001 TYR z 498 ARG 0.005 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 493 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 211 LEU cc_start: 0.6321 (mp) cc_final: 0.5962 (mp) REVERT: N 228 GLN cc_start: 0.8481 (mm110) cc_final: 0.8201 (mm-40) REVERT: A 47 ASP cc_start: 0.7680 (t0) cc_final: 0.7428 (t0) REVERT: A 171 MET cc_start: 0.8981 (ttm) cc_final: 0.8751 (ttm) REVERT: B 387 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: D 24 TYR cc_start: 0.8958 (t80) cc_final: 0.8740 (t80) REVERT: D 467 GLU cc_start: 0.8377 (tp30) cc_final: 0.8075 (tp30) REVERT: H 227 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8524 (mtp) REVERT: H 403 ASP cc_start: 0.7996 (p0) cc_final: 0.7662 (p0) REVERT: H 524 ARG cc_start: 0.7713 (tmm-80) cc_final: 0.7469 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8230 (t70) cc_final: 0.7981 (t0) REVERT: Z 15 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8511 (mtm110) REVERT: Z 32 ASP cc_start: 0.7881 (m-30) cc_final: 0.7542 (m-30) REVERT: b 10 ASN cc_start: 0.8898 (p0) cc_final: 0.8672 (p0) REVERT: b 87 MET cc_start: 0.9138 (ttp) cc_final: 0.8929 (ttp) REVERT: b 384 ASP cc_start: 0.8399 (m-30) cc_final: 0.8118 (m-30) REVERT: b 445 MET cc_start: 0.8888 (tpp) cc_final: 0.8524 (mmm) REVERT: e 21 ASP cc_start: 0.7705 (t70) cc_final: 0.7253 (t0) REVERT: e 121 GLU cc_start: 0.8048 (tp30) cc_final: 0.7643 (tm-30) REVERT: e 426 GLU cc_start: 0.8510 (mp0) cc_final: 0.8169 (mp0) REVERT: g 291 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9054 (mt) REVERT: g 358 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8138 (mt-10) REVERT: h 440 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8606 (tppp) REVERT: h 524 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7287 (tpt90) REVERT: z 207 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8870 (mm) REVERT: z 244 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8577 (t) REVERT: z 272 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8450 (mppt) REVERT: P 144 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6410 (mmm160) REVERT: P 173 MET cc_start: 0.8014 (ttt) cc_final: 0.7630 (tpp) outliers start: 106 outliers final: 55 residues processed: 555 average time/residue: 1.4662 time to fit residues: 1076.1393 Evaluate side-chains 537 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 475 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 233 HIS 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 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 291 ILE Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 805 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 475 optimal weight: 6.9990 chunk 609 optimal weight: 8.9990 chunk 472 optimal weight: 10.0000 chunk 702 optimal weight: 3.9990 chunk 466 optimal weight: 7.9990 chunk 831 optimal weight: 7.9990 chunk 520 optimal weight: 0.9990 chunk 507 optimal weight: 4.9990 chunk 384 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN G 12 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 283 HIS z 161 HIS P 287 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 67915 Z= 0.346 Angle : 0.601 10.642 91690 Z= 0.296 Chirality : 0.043 0.173 10920 Planarity : 0.003 0.047 11702 Dihedral : 7.312 173.361 9422 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.72 % Favored : 96.27 % Rotamer: Outliers : 1.31 % Allowed : 12.11 % Favored : 86.58 % 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: 1.25 (0.09), residues: 8670 helix: 2.17 (0.08), residues: 4503 sheet: -0.42 (0.16), residues: 1097 loop : -0.73 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 266 HIS 0.014 0.001 HIS Z 161 PHE 0.021 0.001 PHE a 167 TYR 0.016 0.001 TYR G 437 ARG 0.005 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 486 time to evaluate : 6.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8531 (mm110) cc_final: 0.8198 (mp10) REVERT: A 171 MET cc_start: 0.8980 (ttm) cc_final: 0.8755 (ttm) REVERT: B 387 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: D 24 TYR cc_start: 0.8961 (t80) cc_final: 0.8746 (t80) REVERT: D 467 GLU cc_start: 0.8378 (tp30) cc_final: 0.8080 (tp30) REVERT: H 227 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: H 403 ASP cc_start: 0.8002 (p0) cc_final: 0.7668 (p0) REVERT: H 524 ARG cc_start: 0.7712 (tmm-80) cc_final: 0.7452 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8235 (t70) cc_final: 0.7987 (t0) REVERT: Z 15 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8505 (mtm110) REVERT: Z 32 ASP cc_start: 0.7883 (m-30) cc_final: 0.7527 (m-30) REVERT: b 10 ASN cc_start: 0.8905 (p0) cc_final: 0.8696 (p0) REVERT: b 87 MET cc_start: 0.9125 (ttp) cc_final: 0.8917 (ttp) REVERT: b 384 ASP cc_start: 0.8400 (m-30) cc_final: 0.8106 (m-30) REVERT: b 445 MET cc_start: 0.8884 (tpp) cc_final: 0.8609 (mmm) REVERT: e 21 ASP cc_start: 0.7722 (t70) cc_final: 0.7262 (t0) REVERT: e 121 GLU cc_start: 0.8063 (tp30) cc_final: 0.7644 (tm-30) REVERT: e 426 GLU cc_start: 0.8523 (mp0) cc_final: 0.8185 (mp0) REVERT: g 291 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9049 (mt) REVERT: g 358 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8129 (mt-10) REVERT: h 440 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8611 (tppp) REVERT: h 482 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: h 524 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7310 (tpt90) REVERT: z 207 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8866 (mm) REVERT: z 244 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8616 (t) REVERT: z 272 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8448 (mppt) REVERT: P 144 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6563 (mmm160) REVERT: P 173 MET cc_start: 0.7973 (ttt) cc_final: 0.7594 (tpp) outliers start: 95 outliers final: 61 residues processed: 541 average time/residue: 1.4846 time to fit residues: 1066.4043 Evaluate side-chains 544 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 475 time to evaluate : 6.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 266 TRP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 233 HIS 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 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 291 ILE Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 514 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 496 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 528 optimal weight: 10.0000 chunk 566 optimal weight: 2.9990 chunk 411 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 653 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN E 46 ASN G 12 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN g 390 ASN h 283 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 67915 Z= 0.288 Angle : 0.586 11.512 91690 Z= 0.288 Chirality : 0.042 0.164 10920 Planarity : 0.003 0.047 11702 Dihedral : 7.230 170.734 9422 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.61 % Favored : 96.38 % Rotamer: Outliers : 1.29 % Allowed : 12.41 % Favored : 86.29 % 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: 1.28 (0.09), residues: 8670 helix: 2.21 (0.08), residues: 4502 sheet: -0.41 (0.16), residues: 1093 loop : -0.72 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.014 0.001 HIS a 534 PHE 0.021 0.001 PHE a 167 TYR 0.015 0.001 TYR Z 351 ARG 0.005 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 507 time to evaluate : 6.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8534 (mm110) cc_final: 0.8216 (mp10) REVERT: A 171 MET cc_start: 0.8976 (ttm) cc_final: 0.8754 (ttm) REVERT: B 323 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9310 (mm) REVERT: B 387 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: D 24 TYR cc_start: 0.8932 (t80) cc_final: 0.8718 (t80) REVERT: D 60 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8654 (tpp) REVERT: D 467 GLU cc_start: 0.8367 (tp30) cc_final: 0.8053 (tp30) REVERT: H 524 ARG cc_start: 0.7695 (tmm-80) cc_final: 0.7421 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8218 (t70) cc_final: 0.7955 (t0) REVERT: Z 15 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8501 (mtm110) REVERT: Z 32 ASP cc_start: 0.7874 (m-30) cc_final: 0.7509 (m-30) REVERT: Z 195 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7504 (mm-30) REVERT: b 10 ASN cc_start: 0.8913 (p0) cc_final: 0.8688 (p0) REVERT: b 87 MET cc_start: 0.9125 (ttp) cc_final: 0.8923 (ttp) REVERT: b 384 ASP cc_start: 0.8392 (m-30) cc_final: 0.8102 (m-30) REVERT: b 445 MET cc_start: 0.8865 (tpp) cc_final: 0.8595 (mmm) REVERT: e 21 ASP cc_start: 0.7733 (t70) cc_final: 0.7261 (t0) REVERT: e 121 GLU cc_start: 0.8053 (tp30) cc_final: 0.7655 (tm-30) REVERT: e 426 GLU cc_start: 0.8548 (mp0) cc_final: 0.8229 (mp0) REVERT: g 15 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8382 (mmtm) REVERT: g 291 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9040 (mt) REVERT: g 358 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8132 (mt-10) REVERT: h 440 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8603 (tppp) REVERT: h 482 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: h 524 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7337 (tpt90) REVERT: z 196 MET cc_start: 0.8070 (mmm) cc_final: 0.7688 (mtt) REVERT: z 207 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8861 (mm) REVERT: z 244 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8597 (t) REVERT: z 272 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8438 (mppt) REVERT: P 144 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6544 (mmm160) REVERT: P 173 MET cc_start: 0.7968 (ttt) cc_final: 0.7590 (tpp) outliers start: 94 outliers final: 60 residues processed: 563 average time/residue: 1.5300 time to fit residues: 1140.3731 Evaluate side-chains 550 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 481 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 266 TRP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 480 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 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 291 ILE Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 756 optimal weight: 8.9990 chunk 796 optimal weight: 7.9990 chunk 727 optimal weight: 6.9990 chunk 775 optimal weight: 2.9990 chunk 466 optimal weight: 1.9990 chunk 337 optimal weight: 0.0370 chunk 608 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 700 optimal weight: 0.4980 chunk 733 optimal weight: 0.5980 chunk 772 optimal weight: 10.0000 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN D 172 ASN G 12 GLN G 28 ASN H 283 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN g 390 ASN h 283 HIS h 501 ASN q 53 ASN q 346 HIS ** z 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 67915 Z= 0.160 Angle : 0.555 12.937 91690 Z= 0.271 Chirality : 0.041 0.169 10920 Planarity : 0.003 0.049 11702 Dihedral : 6.993 167.465 9422 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.35 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 12.99 % Favored : 86.05 % 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: 1.50 (0.09), residues: 8670 helix: 2.39 (0.08), residues: 4485 sheet: -0.29 (0.16), residues: 1103 loop : -0.62 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 266 HIS 0.016 0.001 HIS Z 161 PHE 0.021 0.001 PHE P 170 TYR 0.020 0.001 TYR z 498 ARG 0.004 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 541 time to evaluate : 6.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8510 (mm110) cc_final: 0.8260 (mm-40) REVERT: A 171 MET cc_start: 0.8955 (ttm) cc_final: 0.8726 (ttm) REVERT: B 387 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: D 467 GLU cc_start: 0.8333 (tp30) cc_final: 0.8026 (tp30) REVERT: H 403 ASP cc_start: 0.7824 (p0) cc_final: 0.7514 (p0) REVERT: H 524 ARG cc_start: 0.7613 (tmm-80) cc_final: 0.7334 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8150 (t70) cc_final: 0.7906 (t0) REVERT: Z 32 ASP cc_start: 0.7849 (m-30) cc_final: 0.7478 (m-30) REVERT: b 10 ASN cc_start: 0.8883 (p0) cc_final: 0.8631 (p0) REVERT: b 87 MET cc_start: 0.9076 (ttp) cc_final: 0.8865 (ttp) REVERT: b 384 ASP cc_start: 0.8377 (m-30) cc_final: 0.8085 (m-30) REVERT: b 445 MET cc_start: 0.8723 (tpp) cc_final: 0.8372 (mmm) REVERT: e 21 ASP cc_start: 0.7735 (t70) cc_final: 0.7251 (t0) REVERT: e 121 GLU cc_start: 0.7983 (tp30) cc_final: 0.7563 (tm-30) REVERT: e 426 GLU cc_start: 0.8532 (mp0) cc_final: 0.8224 (mp0) REVERT: e 526 MET cc_start: 0.9117 (ttt) cc_final: 0.8852 (ttt) REVERT: g 358 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8094 (mt-10) REVERT: h 440 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8535 (tppp) REVERT: h 524 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7213 (tpt90) REVERT: q 38 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8025 (mt-10) REVERT: z 244 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8450 (t) REVERT: z 272 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8415 (mppt) REVERT: P 84 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: P 144 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6779 (mmm160) REVERT: P 173 MET cc_start: 0.8002 (ttt) cc_final: 0.7604 (tpp) outliers start: 70 outliers final: 29 residues processed: 582 average time/residue: 1.4565 time to fit residues: 1134.1848 Evaluate side-chains 538 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 504 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 266 TRP Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 534 HIS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 508 optimal weight: 6.9990 chunk 819 optimal weight: 7.9990 chunk 500 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 569 optimal weight: 2.9990 chunk 859 optimal weight: 2.9990 chunk 791 optimal weight: 6.9990 chunk 684 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 528 optimal weight: 0.0570 chunk 419 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN D 172 ASN G 12 GLN G 28 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 283 HIS h 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 67915 Z= 0.237 Angle : 0.578 13.073 91690 Z= 0.281 Chirality : 0.042 0.238 10920 Planarity : 0.003 0.047 11702 Dihedral : 6.960 166.363 9422 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.53 % Favored : 96.46 % Rotamer: Outliers : 0.65 % Allowed : 13.76 % Favored : 85.59 % 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: 1.50 (0.09), residues: 8670 helix: 2.40 (0.08), residues: 4484 sheet: -0.30 (0.16), residues: 1125 loop : -0.64 (0.11), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 266 HIS 0.027 0.001 HIS a 534 PHE 0.021 0.001 PHE a 167 TYR 0.026 0.001 TYR D 24 ARG 0.007 0.000 ARG Z 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 504 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 212 THR cc_start: 0.6707 (m) cc_final: 0.6456 (p) REVERT: N 228 GLN cc_start: 0.8504 (mm110) cc_final: 0.8216 (mp10) REVERT: A 171 MET cc_start: 0.8973 (ttm) cc_final: 0.8758 (ttm) REVERT: B 323 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9297 (mm) REVERT: B 387 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: D 100 ILE cc_start: 0.9237 (mm) cc_final: 0.9004 (mp) REVERT: D 467 GLU cc_start: 0.8340 (tp30) cc_final: 0.8022 (tp30) REVERT: H 403 ASP cc_start: 0.7863 (p0) cc_final: 0.7556 (p0) REVERT: H 524 ARG cc_start: 0.7646 (tmm-80) cc_final: 0.7361 (tmm-80) REVERT: Q 322 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7838 (ptp-170) REVERT: Q 393 ASP cc_start: 0.8169 (t70) cc_final: 0.7925 (t0) REVERT: Z 32 ASP cc_start: 0.7858 (m-30) cc_final: 0.7484 (m-30) REVERT: b 10 ASN cc_start: 0.8887 (p0) cc_final: 0.8641 (p0) REVERT: b 87 MET cc_start: 0.9106 (ttp) cc_final: 0.8903 (ttp) REVERT: b 384 ASP cc_start: 0.8390 (m-30) cc_final: 0.8089 (m-30) REVERT: b 445 MET cc_start: 0.8759 (tpp) cc_final: 0.8508 (mmm) REVERT: e 21 ASP cc_start: 0.7752 (t70) cc_final: 0.7264 (t0) REVERT: e 121 GLU cc_start: 0.8013 (tp30) cc_final: 0.7601 (tm-30) REVERT: e 426 GLU cc_start: 0.8542 (mp0) cc_final: 0.8237 (mp0) REVERT: g 358 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8118 (mt-10) REVERT: h 440 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8541 (tppp) REVERT: h 524 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7273 (tpt90) REVERT: z 244 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8511 (t) REVERT: z 272 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8434 (mppt) REVERT: P 84 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6039 (mmm) REVERT: P 144 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6806 (mmm160) REVERT: P 173 MET cc_start: 0.8001 (ttt) cc_final: 0.7612 (tpp) outliers start: 47 outliers final: 28 residues processed: 532 average time/residue: 1.5314 time to fit residues: 1080.5675 Evaluate side-chains 531 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 497 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 266 TRP Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 144 ARG Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 543 optimal weight: 2.9990 chunk 729 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 631 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 685 optimal weight: 3.9990 chunk 286 optimal weight: 0.0980 chunk 704 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN A 56 ASN D 172 ASN G 12 GLN G 28 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 283 HIS ** z 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.064434 restraints weight = 201190.868| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.05 r_work: 0.2664 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 67915 Z= 0.164 Angle : 0.558 14.613 91690 Z= 0.272 Chirality : 0.041 0.205 10920 Planarity : 0.003 0.048 11702 Dihedral : 6.835 161.257 9422 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.28 % Favored : 96.71 % Rotamer: Outliers : 0.65 % Allowed : 13.73 % Favored : 85.62 % 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: 1.56 (0.09), residues: 8670 helix: 2.45 (0.08), residues: 4489 sheet: -0.24 (0.16), residues: 1129 loop : -0.62 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 266 HIS 0.017 0.001 HIS Z 161 PHE 0.022 0.001 PHE a 167 TYR 0.031 0.001 TYR D 24 ARG 0.007 0.000 ARG H 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18001.63 seconds wall clock time: 312 minutes 2.02 seconds (18722.02 seconds total)