Starting phenix.real_space_refine on Sun Oct 13 22:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/10_2024/8shl_40488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/10_2024/8shl_40488.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/8shl_40488/10_2024/8shl_40488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/10_2024/8shl_40488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/10_2024/8shl_40488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/10_2024/8shl_40488.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= 0.047 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 419 5.16 5 C 42201 2.51 5 N 11748 2.21 5 O 13066 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 32 residue(s): 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 67546 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 767 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 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: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1683 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 1 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: 35.35, per 1000 atoms: 0.52 Number of scatterers: 67546 At special positions: 0 Unit cell: (181.976, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 419 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13066 8.00 N 11748 7.00 C 42201 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 "HETATM67325 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67133 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67197 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.57 Conformation dependent library (CDL) restraints added in 7.3 seconds 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16338 Finding SS restraints... Secondary structure from input PDB file: 366 helices and 99 sheets defined 56.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.645A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.634A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.594A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.434A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.609A 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: 4.551A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 432 through 445 removed outlier: 4.254A pdb=" N LEU A 436 " --> pdb=" O SER A 432 " (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: 3.817A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.509A 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 118 removed outlier: 3.546A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.392A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.610A 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 removed outlier: 3.562A pdb=" N SER B 212 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.558A 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 430 through 454 removed outlier: 4.174A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.711A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.330A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 127 removed outlier: 3.702A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.553A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.734A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 292 removed outlier: 3.868A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.650A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.938A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.006A 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: 3.512A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.557A 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: 3.613A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.588A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.939A 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: 3.778A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.732A 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: 3.642A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) 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 114 removed outlier: 3.675A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.693A 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: 3.649A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 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 307 removed outlier: 3.670A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.600A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.736A 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 36 through 40 removed outlier: 3.615A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.769A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 3.873A 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: 3.701A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.623A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 removed outlier: 3.500A pdb=" N MET H 227 " --> pdb=" O GLY H 224 " (cutoff:3.500A) 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: 3.630A 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: 3.551A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.277A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.334A 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: 4.303A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.489A 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 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.842A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.733A 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 340 through 344 removed outlier: 3.793A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.631A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.347A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 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: 3.676A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.742A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.149A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.610A 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: 3.709A 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: 3.602A 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 329 removed outlier: 3.605A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.220A 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 removed outlier: 3.516A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.156A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.625A 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 'a' and resid 14 through 33 removed outlier: 3.502A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.932A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.875A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.245A 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: 4.878A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.773A 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 428 removed outlier: 4.453A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 445 removed outlier: 3.817A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 removed outlier: 3.564A pdb=" N LEU a 483 " --> pdb=" O ARG a 480 " (cutoff:3.500A) 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 168 Processing helix chain 'b' and resid 169 through 174 removed outlier: 6.428A pdb=" N LEU b 172 " --> pdb=" O SER b 169 " (cutoff:3.500A) removed outlier: 3.720A 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 removed outlier: 3.588A pdb=" N SER b 212 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.779A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.629A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.725A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.674A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.741A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.331A 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: 3.654A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.722A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.755A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.885A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 25 removed outlier: 3.651A pdb=" N LYS e 25 " --> pdb=" O GLN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.539A 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 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: 6.550A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.902A 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 391 through 415 Processing helix chain 'e' and resid 423 through 438 removed outlier: 3.523A pdb=" N ASP e 438 " --> pdb=" O SER e 434 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.555A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 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: 3.946A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.888A 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 removed outlier: 3.590A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.655A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.593A 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: 3.640A 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: 3.545A 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 471 removed outlier: 3.525A 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: 3.526A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.521A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.643A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.095A 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: 3.686A 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: 3.702A 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 342 removed outlier: 3.884A 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: 3.608A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.200A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 75 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 121 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 166 removed outlier: 3.728A pdb=" N VAL q 160 " --> pdb=" O ASP q 156 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (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: 4.762A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.690A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS q 430 " --> pdb=" O TYR q 426 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.150A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.695A 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 92 through 111 removed outlier: 3.531A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.862A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.295A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.583A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.804A 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: 3.743A 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: 3.723A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.305A 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: 4.108A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.704A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 56 through 61 removed outlier: 4.185A pdb=" N LYS P 60 " --> pdb=" O ASN P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.737A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU P 83 " --> pdb=" O GLU P 79 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU P 85 " --> pdb=" O CYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 136 through 139 Processing helix chain 'P' and resid 140 through 151 removed outlier: 4.382A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 194 through 209 removed outlier: 3.511A pdb=" N MET P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) 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 256 removed outlier: 3.708A pdb=" N GLN P 254 " --> pdb=" O ARG P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 270 Processing sheet with id=AA1, first strand: chain 'N' and resid 209 through 213 removed outlier: 6.853A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 240 through 245 removed outlier: 7.227A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.217A pdb=" N ASP D 58 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A 529 " --> pdb=" O ASP D 58 " (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: 6.254A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.638A 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: 6.598A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.344A 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: 9.134A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.071A 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: 6.564A 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: 4.161A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.478A 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: 6.821A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.656A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.483A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.504A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.919A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.919A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.385A 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 removed outlier: 3.654A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.586A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (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: 3.908A 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: 6.551A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.377A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 185 through 187 removed outlier: 3.565A pdb=" N GLU G 187 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.898A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD5, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.579A pdb=" N VAL G 290 " --> pdb=" O ILE G 312 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 407 through 409 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 removed outlier: 6.225A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.643A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE2, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE3, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 removed outlier: 3.706A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.066A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.468A 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: 4.091A 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: 6.500A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.402A 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 Processing sheet with id=AF3, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.330A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.592A 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: 9.272A pdb=" N VAL Z 311 " --> pdb=" O LYS Z 287 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE Z 289 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU Z 313 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL Z 291 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.302A 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 removed outlier: 3.670A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.789A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.680A 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: 6.523A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (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 201 removed outlier: 6.286A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.615A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.680A 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: 6.615A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.624A 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: 8.959A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU h 254 " --> pdb=" O ILE q 259 " (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: 4.532A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.506A 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: 6.980A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.951A 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: 3.678A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.359A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (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: 4.165A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.602A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH8, first strand: chain 'e' and resid 28 through 29 removed outlier: 4.745A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI1, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.842A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.376A pdb=" N CYS e 377 " --> pdb=" O ALA e 356 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA e 356 " --> pdb=" O CYS e 377 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.088A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI5, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.840A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI7, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.433A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AI9, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ1, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.393A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ3, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.492A pdb=" N GLY h 196 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU h 374 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS h 198 " --> pdb=" O LEU h 374 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLY h 376 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL h 200 " --> pdb=" O GLY h 376 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ5, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ6, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ7, first strand: chain 'q' and resid 20 through 23 removed outlier: 4.647A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.702A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.509A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK2, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK3, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK4, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK5, first strand: chain 'z' and resid 192 through 196 removed outlier: 6.502A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK7, first strand: chain 'z' and resid 311 through 313 removed outlier: 9.261A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK9, first strand: chain 'P' and resid 162 through 164 removed outlier: 6.036A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU P 236 " --> pdb=" O ASN P 247 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN P 247 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE P 238 " --> pdb=" O ILE P 245 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE P 245 " --> pdb=" O ILE P 238 " (cutoff:3.500A) 4034 hydrogen bonds defined for protein. 11541 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: 29.05 Time building geometry restraints manager: 15.05 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: 22735 1.34 - 1.46: 11880 1.46 - 1.58: 32916 1.58 - 1.70: 48 1.70 - 1.81: 740 Bond restraints: 68319 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 6.50e+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 6.37e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" F2 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 Q 603 " pdb="AL AF3 Q 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 68314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 91166 2.07 - 4.13: 827 4.13 - 6.20: 229 6.20 - 8.26: 16 8.26 - 10.33: 4 Bond angle restraints: 92242 Sorted by residual: angle pdb=" CA ARG P 77 " pdb=" CB ARG P 77 " pdb=" CG ARG P 77 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " pdb=" CD ARG P 149 " ideal model delta sigma weight residual 111.30 119.94 -8.64 2.30e+00 1.89e-01 1.41e+01 angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 122.38 115.68 6.70 1.81e+00 3.05e-01 1.37e+01 angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C GLN P 76 " pdb=" N ARG P 77 " pdb=" CA ARG P 77 " ideal model delta sigma weight residual 121.14 115.06 6.08 1.75e+00 3.27e-01 1.21e+01 ... (remaining 92237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 41568 35.54 - 71.09: 590 71.09 - 106.63: 59 106.63 - 142.17: 9 142.17 - 177.71: 6 Dihedral angle restraints: 42232 sinusoidal: 17002 harmonic: 25230 Sorted by residual: dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.72 -177.71 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 122.97 177.03 1 2.00e+01 2.50e-03 4.80e+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 -60.00 116.80 -176.80 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 42229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 7978 0.039 - 0.078: 2107 0.078 - 0.117: 784 0.117 - 0.155: 102 0.155 - 0.194: 4 Chirality restraints: 10975 Sorted by residual: chirality pdb=" CA ARG P 77 " pdb=" N ARG P 77 " pdb=" C ARG P 77 " pdb=" CB ARG P 77 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL Z 160 " pdb=" CA VAL Z 160 " pdb=" CG1 VAL Z 160 " pdb=" CG2 VAL Z 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 10972 not shown) Planarity restraints: 11780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 14 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO E 15 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO e 441 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ILE b 11 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.012 2.00e-02 2.50e+03 ... (remaining 11777 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 567 2.53 - 3.12: 51301 3.12 - 3.71: 106605 3.71 - 4.31: 148250 4.31 - 4.90: 255384 Nonbonded interactions: 562107 Sorted by model distance: nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.935 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.943 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.952 2.170 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.961 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.975 2.120 ... (remaining 562102 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.090 Check model and map are aligned: 0.500 Set scattering table: 0.630 Process input model: 125.190 Find NCS groups from input model: 5.630 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 68319 Z= 0.256 Angle : 0.534 10.330 92242 Z= 0.263 Chirality : 0.041 0.194 10975 Planarity : 0.003 0.074 11780 Dihedral : 14.108 177.714 25894 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.71 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4471 sheet: 0.18 (0.16), residues: 1173 loop : -0.48 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 168 HIS 0.013 0.001 HIS Z 161 PHE 0.024 0.001 PHE b 12 TYR 0.016 0.001 TYR h 475 ARG 0.015 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 6.018 Fit side-chains revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8102 (mp10) cc_final: 0.7606 (mp10) REVERT: N 250 THR cc_start: 0.6852 (t) cc_final: 0.6632 (p) REVERT: A 416 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7752 (mp0) REVERT: A 430 MET cc_start: 0.8180 (mmm) cc_final: 0.7947 (mmm) REVERT: B 30 ILE cc_start: 0.9241 (mm) cc_final: 0.8964 (tt) REVERT: D 63 ASP cc_start: 0.8599 (t70) cc_final: 0.8396 (t70) REVERT: E 21 ASP cc_start: 0.8300 (t70) cc_final: 0.8020 (t0) REVERT: E 532 ASP cc_start: 0.7716 (m-30) cc_final: 0.7410 (m-30) REVERT: H 14 ASP cc_start: 0.8169 (t0) cc_final: 0.7812 (t0) REVERT: H 524 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6896 (tmm160) REVERT: Q 41 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8489 (tm-30) REVERT: Q 318 LYS cc_start: 0.8911 (pptt) cc_final: 0.8585 (pptt) REVERT: e 82 ASP cc_start: 0.8286 (t0) cc_final: 0.7688 (t0) REVERT: g 59 MET cc_start: 0.9062 (ttp) cc_final: 0.8809 (ttp) REVERT: h 70 ASP cc_start: 0.7551 (t0) cc_final: 0.7249 (t0) REVERT: h 130 GLN cc_start: 0.8379 (tp40) cc_final: 0.8036 (tp-100) REVERT: h 324 MET cc_start: 0.9107 (mmm) cc_final: 0.8798 (mmm) REVERT: q 130 GLU cc_start: 0.8307 (tp30) cc_final: 0.7949 (tp30) REVERT: q 249 MET cc_start: 0.8059 (pmm) cc_final: 0.7838 (pmt) REVERT: z 53 ASP cc_start: 0.8578 (m-30) cc_final: 0.8304 (p0) REVERT: z 381 LYS cc_start: 0.8544 (tptm) cc_final: 0.8328 (tppt) REVERT: P 68 ARG cc_start: 0.7855 (tpm170) cc_final: 0.7213 (tpm170) REVERT: P 80 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7761 (tp40) REVERT: P 163 GLU cc_start: 0.8701 (tt0) cc_final: 0.8426 (pp20) outliers start: 0 outliers final: 3 residues processed: 626 average time/residue: 1.6038 time to fit residues: 1292.8021 Evaluate side-chains 473 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain a residue 479 GLU Chi-restraints excluded: chain e residue 292 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 733 optimal weight: 5.9990 chunk 658 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 681 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 414 optimal weight: 10.0000 chunk 506 optimal weight: 9.9990 chunk 789 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 GLN Z 84 GLN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 ASN d 250 GLN g 390 ASN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN z 84 GLN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 68319 Z= 0.465 Angle : 0.669 9.894 92242 Z= 0.333 Chirality : 0.045 0.177 10975 Planarity : 0.004 0.065 11780 Dihedral : 7.668 179.695 9492 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.85 % Allowed : 7.14 % Favored : 92.02 % 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: 1.44 (0.09), residues: 8734 helix: 2.22 (0.08), residues: 4524 sheet: -0.08 (0.16), residues: 1170 loop : -0.55 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.013 0.001 HIS Z 161 PHE 0.018 0.002 PHE E 306 TYR 0.025 0.002 TYR A 181 ARG 0.008 0.001 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 477 time to evaluate : 6.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8105 (t70) cc_final: 0.7641 (t0) REVERT: A 306 MET cc_start: 0.8793 (mtp) cc_final: 0.8405 (mtm) REVERT: A 416 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8024 (mp0) REVERT: A 430 MET cc_start: 0.8216 (mmm) cc_final: 0.8003 (mmm) REVERT: D 63 ASP cc_start: 0.8652 (t70) cc_final: 0.8429 (t70) REVERT: D 320 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8514 (mtt) REVERT: E 21 ASP cc_start: 0.8335 (t70) cc_final: 0.8088 (t0) REVERT: E 259 LYS cc_start: 0.9231 (mtpp) cc_final: 0.9013 (mtmm) REVERT: E 474 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: G 21 LYS cc_start: 0.8595 (tptt) cc_final: 0.8379 (tptt) REVERT: G 113 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9016 (mp) REVERT: H 7 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8271 (pp) REVERT: Q 41 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8537 (tm-30) REVERT: Q 318 LYS cc_start: 0.8840 (pptt) cc_final: 0.8552 (pptt) REVERT: g 59 MET cc_start: 0.9120 (ttp) cc_final: 0.8805 (ttp) REVERT: h 7 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8415 (pp) REVERT: h 70 ASP cc_start: 0.7670 (t0) cc_final: 0.7332 (t0) REVERT: h 130 GLN cc_start: 0.8473 (tp40) cc_final: 0.8104 (tp-100) REVERT: h 324 MET cc_start: 0.9205 (mmm) cc_final: 0.8834 (mmm) REVERT: q 130 GLU cc_start: 0.8399 (tp30) cc_final: 0.8041 (tp30) REVERT: z 53 ASP cc_start: 0.8507 (m-30) cc_final: 0.8188 (p0) REVERT: z 381 LYS cc_start: 0.8500 (tptm) cc_final: 0.8200 (tppt) REVERT: P 80 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7777 (tp40) outliers start: 62 outliers final: 19 residues processed: 503 average time/residue: 1.5049 time to fit residues: 989.6958 Evaluate side-chains 475 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 451 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 111 HIS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain P residue 93 MET Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 438 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 656 optimal weight: 4.9990 chunk 537 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 790 optimal weight: 10.0000 chunk 854 optimal weight: 7.9990 chunk 704 optimal weight: 0.9980 chunk 783 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 634 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN g 390 ASN ** g 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 431 GLN h 448 GLN q 53 ASN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68319 Z= 0.194 Angle : 0.559 9.317 92242 Z= 0.276 Chirality : 0.041 0.164 10975 Planarity : 0.003 0.060 11780 Dihedral : 7.187 177.928 9485 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 1.00 % Allowed : 8.65 % Favored : 90.35 % 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: 1.58 (0.09), residues: 8734 helix: 2.37 (0.08), residues: 4524 sheet: -0.10 (0.16), residues: 1136 loop : -0.51 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.047 0.001 PHE P 69 TYR 0.021 0.001 TYR A 181 ARG 0.008 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 492 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8555 (tp30) cc_final: 0.8148 (tp30) REVERT: A 47 ASP cc_start: 0.7988 (t70) cc_final: 0.7529 (t0) REVERT: A 430 MET cc_start: 0.8159 (mmm) cc_final: 0.7929 (mmm) REVERT: D 63 ASP cc_start: 0.8617 (t70) cc_final: 0.8406 (t70) REVERT: D 320 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8432 (mtt) REVERT: D 524 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: E 21 ASP cc_start: 0.8288 (t70) cc_final: 0.8002 (t0) REVERT: E 259 LYS cc_start: 0.9193 (mtpp) cc_final: 0.8993 (mtmm) REVERT: E 474 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7797 (tmm) REVERT: G 21 LYS cc_start: 0.8535 (tptt) cc_final: 0.8294 (tptt) REVERT: H 7 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8254 (pp) REVERT: Q 41 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8491 (tm-30) REVERT: Q 116 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: Q 318 LYS cc_start: 0.8841 (pptt) cc_final: 0.8553 (pptt) REVERT: d 48 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8647 (pp) REVERT: e 287 GLU cc_start: 0.8781 (tt0) cc_final: 0.8530 (tt0) REVERT: g 59 MET cc_start: 0.9132 (ttp) cc_final: 0.8855 (ttp) REVERT: h 7 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8350 (pp) REVERT: h 70 ASP cc_start: 0.7674 (t0) cc_final: 0.7327 (t0) REVERT: h 130 GLN cc_start: 0.8391 (tp40) cc_final: 0.8064 (tp-100) REVERT: h 324 MET cc_start: 0.9200 (mmm) cc_final: 0.8825 (mmm) REVERT: q 130 GLU cc_start: 0.8358 (tp30) cc_final: 0.7975 (tp30) REVERT: z 53 ASP cc_start: 0.8497 (m-30) cc_final: 0.8220 (p0) REVERT: z 381 LYS cc_start: 0.8394 (tptm) cc_final: 0.8102 (tppt) REVERT: P 66 TRP cc_start: 0.7915 (t-100) cc_final: 0.6760 (t-100) REVERT: P 80 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7724 (tp40) REVERT: P 82 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7442 (tpp80) outliers start: 73 outliers final: 22 residues processed: 527 average time/residue: 1.5244 time to fit residues: 1053.7939 Evaluate side-chains 491 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 462 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 781 optimal weight: 10.0000 chunk 594 optimal weight: 9.9990 chunk 410 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 377 optimal weight: 9.9990 chunk 530 optimal weight: 9.9990 chunk 793 optimal weight: 5.9990 chunk 839 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 751 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 469 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 514 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN q 53 ASN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 68319 Z= 0.501 Angle : 0.663 10.032 92242 Z= 0.328 Chirality : 0.045 0.179 10975 Planarity : 0.004 0.064 11780 Dihedral : 7.240 178.295 9485 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.16 % Favored : 95.83 % Rotamer: Outliers : 1.33 % Allowed : 10.32 % Favored : 88.35 % 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: 1.35 (0.09), residues: 8734 helix: 2.21 (0.08), residues: 4519 sheet: -0.28 (0.15), residues: 1158 loop : -0.61 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.024 0.002 PHE P 69 TYR 0.019 0.002 TYR A 181 ARG 0.007 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 461 time to evaluate : 6.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 272 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8804 (mt0) REVERT: A 47 ASP cc_start: 0.8102 (t70) cc_final: 0.7618 (t0) REVERT: A 306 MET cc_start: 0.8753 (mtp) cc_final: 0.8350 (mtm) REVERT: A 344 MET cc_start: 0.8720 (mmm) cc_final: 0.8261 (mmm) REVERT: A 430 MET cc_start: 0.8203 (mmm) cc_final: 0.7986 (mmm) REVERT: B 415 MET cc_start: 0.9486 (mmm) cc_final: 0.9286 (mmp) REVERT: D 25 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8564 (tp-100) REVERT: D 63 ASP cc_start: 0.8647 (t70) cc_final: 0.8373 (t70) REVERT: D 320 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: D 524 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: E 21 ASP cc_start: 0.8326 (t70) cc_final: 0.8051 (t0) REVERT: E 474 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7770 (tmm) REVERT: G 21 LYS cc_start: 0.8722 (tptt) cc_final: 0.8384 (tptt) REVERT: H 7 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8321 (pp) REVERT: Q 41 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8573 (tm-30) REVERT: Q 116 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: Q 318 LYS cc_start: 0.8847 (pptt) cc_final: 0.8559 (pptt) REVERT: b 316 ASP cc_start: 0.8046 (t70) cc_final: 0.7827 (t0) REVERT: b 452 ASP cc_start: 0.8445 (m-30) cc_final: 0.8104 (m-30) REVERT: d 48 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8785 (pp) REVERT: g 59 MET cc_start: 0.9123 (ttp) cc_final: 0.8853 (ttp) REVERT: h 70 ASP cc_start: 0.7759 (t0) cc_final: 0.7352 (t0) REVERT: h 130 GLN cc_start: 0.8490 (tp40) cc_final: 0.8135 (tp-100) REVERT: h 324 MET cc_start: 0.9207 (mmm) cc_final: 0.8831 (mmm) REVERT: q 37 LYS cc_start: 0.8940 (tttt) cc_final: 0.8706 (ttmm) REVERT: q 130 GLU cc_start: 0.8443 (tp30) cc_final: 0.8063 (tp30) REVERT: z 53 ASP cc_start: 0.8514 (m-30) cc_final: 0.8147 (p0) REVERT: P 66 TRP cc_start: 0.7656 (t-100) cc_final: 0.7445 (t-100) outliers start: 97 outliers final: 46 residues processed: 514 average time/residue: 1.5310 time to fit residues: 1028.0706 Evaluate side-chains 500 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 447 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain h residue 524 ARG Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 699 optimal weight: 0.9980 chunk 476 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 625 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 716 optimal weight: 5.9990 chunk 580 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 428 optimal weight: 9.9990 chunk 753 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS H 25 ASN H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 361 HIS g 526 HIS h 501 ASN q 53 ASN z 218 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 68319 Z= 0.166 Angle : 0.555 11.012 92242 Z= 0.272 Chirality : 0.041 0.165 10975 Planarity : 0.003 0.056 11780 Dihedral : 6.904 173.947 9485 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 1.00 % Allowed : 11.58 % Favored : 87.42 % 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: 8734 helix: 2.39 (0.08), residues: 4532 sheet: -0.24 (0.16), residues: 1112 loop : -0.53 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 66 HIS 0.011 0.001 HIS Z 161 PHE 0.018 0.001 PHE P 69 TYR 0.019 0.001 TYR A 181 ARG 0.009 0.000 ARG e 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 522 time to evaluate : 6.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8358 (tp30) cc_final: 0.8113 (tp30) REVERT: A 47 ASP cc_start: 0.7934 (t70) cc_final: 0.7477 (t0) REVERT: A 430 MET cc_start: 0.8205 (mmm) cc_final: 0.7976 (mmm) REVERT: B 86 ASP cc_start: 0.8896 (t0) cc_final: 0.8650 (t0) REVERT: D 25 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8514 (tp-100) REVERT: D 63 ASP cc_start: 0.8589 (t70) cc_final: 0.8341 (t70) REVERT: D 320 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: D 524 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: E 21 ASP cc_start: 0.8287 (t70) cc_final: 0.7995 (t0) REVERT: E 259 LYS cc_start: 0.9267 (mtpp) cc_final: 0.9039 (mtmm) REVERT: E 474 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7727 (tmm) REVERT: G 21 LYS cc_start: 0.8576 (tptt) cc_final: 0.8244 (tptt) REVERT: H 7 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8275 (pp) REVERT: H 524 ARG cc_start: 0.7247 (ttp80) cc_final: 0.7044 (ttt-90) REVERT: Q 41 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8494 (tm-30) REVERT: Q 116 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: a 344 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7958 (ptt) REVERT: b 316 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7657 (t0) REVERT: b 415 MET cc_start: 0.9118 (mmm) cc_final: 0.8900 (mmp) REVERT: b 452 ASP cc_start: 0.8400 (m-30) cc_final: 0.8025 (m-30) REVERT: d 48 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8583 (pp) REVERT: e 29 MET cc_start: 0.7866 (mtm) cc_final: 0.7604 (ttm) REVERT: e 287 GLU cc_start: 0.8811 (tt0) cc_final: 0.8584 (tt0) REVERT: g 59 MET cc_start: 0.9064 (ttp) cc_final: 0.8845 (ttp) REVERT: h 70 ASP cc_start: 0.7699 (t0) cc_final: 0.7329 (t0) REVERT: h 130 GLN cc_start: 0.8383 (tp40) cc_final: 0.8084 (tp-100) REVERT: h 324 MET cc_start: 0.9171 (mmm) cc_final: 0.8833 (mmm) REVERT: q 130 GLU cc_start: 0.8374 (tp30) cc_final: 0.7969 (tp30) REVERT: z 53 ASP cc_start: 0.8540 (m-30) cc_final: 0.8242 (p0) REVERT: z 520 GLU cc_start: 0.8302 (tt0) cc_final: 0.7965 (tt0) REVERT: P 68 ARG cc_start: 0.7898 (tpm170) cc_final: 0.7265 (tpm170) REVERT: P 69 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7815 (p90) REVERT: P 250 ARG cc_start: 0.6536 (mmp-170) cc_final: 0.6275 (mmp-170) outliers start: 73 outliers final: 29 residues processed: 564 average time/residue: 1.4786 time to fit residues: 1095.4599 Evaluate side-chains 512 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 474 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 282 optimal weight: 6.9990 chunk 756 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 493 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 840 optimal weight: 0.9990 chunk 697 optimal weight: 0.9980 chunk 389 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 441 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS D 502 ASN Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS g 28 ASN z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 68319 Z= 0.244 Angle : 0.573 14.723 92242 Z= 0.279 Chirality : 0.042 0.172 10975 Planarity : 0.003 0.054 11780 Dihedral : 6.818 172.806 9485 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.76 % Favored : 96.23 % Rotamer: Outliers : 1.15 % Allowed : 12.26 % Favored : 86.59 % 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: 1.56 (0.09), residues: 8734 helix: 2.41 (0.08), residues: 4523 sheet: -0.28 (0.15), residues: 1145 loop : -0.54 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.013 0.001 HIS Z 161 PHE 0.027 0.001 PHE P 69 TYR 0.017 0.001 TYR A 181 ARG 0.006 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 488 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8380 (tp30) cc_final: 0.8136 (tp30) REVERT: N 272 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8855 (mt0) REVERT: A 47 ASP cc_start: 0.7883 (t70) cc_final: 0.7379 (t0) REVERT: A 416 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 430 MET cc_start: 0.8232 (mmm) cc_final: 0.8014 (mmm) REVERT: D 25 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8523 (tp-100) REVERT: D 63 ASP cc_start: 0.8583 (t70) cc_final: 0.8333 (t70) REVERT: D 320 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8514 (mtt) REVERT: D 524 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 21 ASP cc_start: 0.8302 (t70) cc_final: 0.8005 (t0) REVERT: E 259 LYS cc_start: 0.9259 (mtpp) cc_final: 0.9051 (mtmm) REVERT: E 468 MET cc_start: 0.8794 (mtm) cc_final: 0.8531 (ptm) REVERT: G 21 LYS cc_start: 0.8601 (tptt) cc_final: 0.8230 (tptt) REVERT: H 7 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8278 (pp) REVERT: Q 41 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8505 (tm-30) REVERT: Q 116 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: b 316 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7740 (t0) REVERT: b 415 MET cc_start: 0.9203 (mmm) cc_final: 0.8904 (mmp) REVERT: b 452 ASP cc_start: 0.8388 (m-30) cc_final: 0.8000 (m-30) REVERT: d 48 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (pp) REVERT: e 29 MET cc_start: 0.7926 (mtm) cc_final: 0.7638 (ttm) REVERT: e 287 GLU cc_start: 0.8802 (tt0) cc_final: 0.8580 (tt0) REVERT: g 15 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8453 (mttt) REVERT: g 59 MET cc_start: 0.9060 (ttp) cc_final: 0.8834 (ttp) REVERT: h 70 ASP cc_start: 0.7725 (t0) cc_final: 0.7362 (t0) REVERT: h 130 GLN cc_start: 0.8411 (tp40) cc_final: 0.8057 (tp-100) REVERT: h 324 MET cc_start: 0.9182 (mmm) cc_final: 0.8884 (mmm) REVERT: q 37 LYS cc_start: 0.8877 (tttt) cc_final: 0.8634 (ttmm) REVERT: q 130 GLU cc_start: 0.8366 (tp30) cc_final: 0.7959 (tp30) REVERT: z 53 ASP cc_start: 0.8533 (m-30) cc_final: 0.8209 (p0) REVERT: z 112 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: z 520 GLU cc_start: 0.8323 (tt0) cc_final: 0.7965 (tt0) REVERT: P 80 GLN cc_start: 0.8378 (mm110) cc_final: 0.8021 (tp-100) REVERT: P 82 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7629 (tpp80) REVERT: P 250 ARG cc_start: 0.6490 (mmp-170) cc_final: 0.6221 (mmp-170) outliers start: 84 outliers final: 38 residues processed: 537 average time/residue: 1.5186 time to fit residues: 1072.9609 Evaluate side-chains 513 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 465 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 212 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 112 GLU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 77 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 810 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 479 optimal weight: 7.9990 chunk 614 optimal weight: 0.7980 chunk 475 optimal weight: 20.0000 chunk 707 optimal weight: 5.9990 chunk 469 optimal weight: 0.9980 chunk 837 optimal weight: 6.9990 chunk 524 optimal weight: 0.9980 chunk 510 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 68319 Z= 0.253 Angle : 0.580 13.017 92242 Z= 0.282 Chirality : 0.042 0.164 10975 Planarity : 0.003 0.053 11780 Dihedral : 6.777 170.595 9485 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.62 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 12.52 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.09), residues: 8734 helix: 2.40 (0.08), residues: 4528 sheet: -0.23 (0.16), residues: 1131 loop : -0.55 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 66 HIS 0.015 0.001 HIS Z 161 PHE 0.058 0.001 PHE P 69 TYR 0.017 0.001 TYR a 426 ARG 0.006 0.000 ARG h 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 481 time to evaluate : 5.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 272 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8787 (mt0) REVERT: A 47 ASP cc_start: 0.7882 (t70) cc_final: 0.7370 (t0) REVERT: A 416 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 430 MET cc_start: 0.8233 (mmm) cc_final: 0.8018 (mmm) REVERT: A 505 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7908 (mt-10) REVERT: D 25 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8527 (tp-100) REVERT: D 63 ASP cc_start: 0.8575 (t70) cc_final: 0.8319 (t70) REVERT: D 320 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8530 (mtt) REVERT: D 524 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 21 ASP cc_start: 0.8289 (t70) cc_final: 0.7989 (t0) REVERT: E 468 MET cc_start: 0.8812 (mtm) cc_final: 0.8561 (ptm) REVERT: G 21 LYS cc_start: 0.8598 (tptt) cc_final: 0.8248 (tptt) REVERT: H 7 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8285 (pp) REVERT: Q 41 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8509 (tm-30) REVERT: Q 116 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: Z 46 MET cc_start: 0.8520 (ttm) cc_final: 0.8189 (ttt) REVERT: a 344 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7992 (ptt) REVERT: b 316 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7729 (t0) REVERT: b 415 MET cc_start: 0.9258 (mmm) cc_final: 0.8927 (mmp) REVERT: b 452 ASP cc_start: 0.8394 (m-30) cc_final: 0.8017 (m-30) REVERT: d 48 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8667 (pp) REVERT: e 29 MET cc_start: 0.7937 (mtm) cc_final: 0.7652 (ttm) REVERT: e 287 GLU cc_start: 0.8809 (tt0) cc_final: 0.8589 (tt0) REVERT: g 15 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8441 (mttt) REVERT: g 59 MET cc_start: 0.9052 (ttp) cc_final: 0.8839 (ttp) REVERT: h 70 ASP cc_start: 0.7726 (t0) cc_final: 0.7356 (t0) REVERT: h 130 GLN cc_start: 0.8412 (tp40) cc_final: 0.8061 (tp-100) REVERT: h 324 MET cc_start: 0.9176 (mmm) cc_final: 0.8874 (mmm) REVERT: q 37 LYS cc_start: 0.8881 (tttt) cc_final: 0.8633 (ttmm) REVERT: q 130 GLU cc_start: 0.8372 (tp30) cc_final: 0.7980 (tp30) REVERT: z 10 LYS cc_start: 0.8536 (ptpt) cc_final: 0.7959 (pmtt) REVERT: z 53 ASP cc_start: 0.8548 (m-30) cc_final: 0.8220 (p0) REVERT: z 112 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: z 520 GLU cc_start: 0.8331 (tt0) cc_final: 0.7915 (tt0) REVERT: z 522 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7431 (mtm) REVERT: P 173 MET cc_start: 0.8711 (ppp) cc_final: 0.8440 (ppp) REVERT: P 250 ARG cc_start: 0.6477 (mmp-170) cc_final: 0.6217 (mmp-170) outliers start: 86 outliers final: 43 residues processed: 533 average time/residue: 1.5169 time to fit residues: 1058.5566 Evaluate side-chains 520 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 465 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 212 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 112 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 228 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 518 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 500 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 532 optimal weight: 5.9990 chunk 570 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 658 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS h 501 ASN z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68319 Z= 0.267 Angle : 0.585 12.821 92242 Z= 0.285 Chirality : 0.042 0.162 10975 Planarity : 0.003 0.053 11780 Dihedral : 6.740 169.277 9485 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer: Outliers : 1.09 % Allowed : 13.02 % Favored : 85.89 % 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: 1.54 (0.09), residues: 8734 helix: 2.40 (0.08), residues: 4529 sheet: -0.26 (0.16), residues: 1133 loop : -0.56 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 66 HIS 0.015 0.001 HIS Z 161 PHE 0.018 0.001 PHE P 69 TYR 0.016 0.001 TYR A 181 ARG 0.005 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 483 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 272 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8783 (mt0) REVERT: A 47 ASP cc_start: 0.7896 (t70) cc_final: 0.7373 (t0) REVERT: A 344 MET cc_start: 0.8500 (mmm) cc_final: 0.8208 (mmm) REVERT: A 416 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 430 MET cc_start: 0.8238 (mmm) cc_final: 0.8022 (mmm) REVERT: A 505 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7905 (mt-10) REVERT: D 25 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8528 (tp-100) REVERT: D 63 ASP cc_start: 0.8569 (t70) cc_final: 0.8309 (t70) REVERT: D 320 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8557 (mtt) REVERT: D 524 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: E 21 ASP cc_start: 0.8289 (t70) cc_final: 0.8003 (t0) REVERT: E 259 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8938 (mtpp) REVERT: E 468 MET cc_start: 0.8821 (mtm) cc_final: 0.8578 (ptm) REVERT: G 21 LYS cc_start: 0.8640 (tptt) cc_final: 0.8276 (tptt) REVERT: H 7 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8285 (pp) REVERT: Q 41 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8514 (tm-30) REVERT: Q 116 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: Z 46 MET cc_start: 0.8534 (ttm) cc_final: 0.8251 (ttt) REVERT: a 44 MET cc_start: 0.8888 (ptp) cc_final: 0.8663 (ptp) REVERT: b 316 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (t0) REVERT: b 415 MET cc_start: 0.9268 (mmm) cc_final: 0.8926 (mmp) REVERT: b 452 ASP cc_start: 0.8364 (m-30) cc_final: 0.7976 (m-30) REVERT: d 48 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8646 (pp) REVERT: e 287 GLU cc_start: 0.8814 (tt0) cc_final: 0.8587 (tt0) REVERT: g 15 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: g 59 MET cc_start: 0.9033 (ttp) cc_final: 0.8818 (ttp) REVERT: h 130 GLN cc_start: 0.8419 (tp40) cc_final: 0.8068 (tp-100) REVERT: h 324 MET cc_start: 0.9174 (mmm) cc_final: 0.8870 (mmm) REVERT: q 37 LYS cc_start: 0.8884 (tttt) cc_final: 0.8631 (ttmm) REVERT: q 75 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8096 (mm-30) REVERT: q 130 GLU cc_start: 0.8381 (tp30) cc_final: 0.7983 (tp30) REVERT: z 53 ASP cc_start: 0.8555 (m-30) cc_final: 0.8222 (p0) REVERT: z 112 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: z 520 GLU cc_start: 0.8359 (tt0) cc_final: 0.7940 (tt0) REVERT: z 522 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: P 68 ARG cc_start: 0.7536 (tpm170) cc_final: 0.6734 (tpm170) REVERT: P 82 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7634 (tpp80) REVERT: P 214 PHE cc_start: 0.9154 (m-80) cc_final: 0.8835 (m-80) REVERT: P 250 ARG cc_start: 0.6446 (mmp-170) cc_final: 0.6186 (mmp-170) REVERT: P 260 PHE cc_start: 0.9117 (m-80) cc_final: 0.8900 (m-80) REVERT: P 271 PHE cc_start: 0.8463 (m-80) cc_final: 0.7977 (m-80) outliers start: 80 outliers final: 42 residues processed: 532 average time/residue: 1.5207 time to fit residues: 1062.3904 Evaluate side-chains 517 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 464 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 212 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 112 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 228 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 761 optimal weight: 6.9990 chunk 802 optimal weight: 4.9990 chunk 732 optimal weight: 8.9990 chunk 780 optimal weight: 9.9990 chunk 469 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 612 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 705 optimal weight: 1.9990 chunk 738 optimal weight: 2.9990 chunk 777 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS h 501 ASN z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 68319 Z= 0.326 Angle : 0.611 13.675 92242 Z= 0.298 Chirality : 0.043 0.169 10975 Planarity : 0.003 0.053 11780 Dihedral : 6.749 169.310 9485 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.86 % Favored : 96.13 % Rotamer: Outliers : 1.00 % Allowed : 13.26 % Favored : 85.74 % 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: 1.48 (0.09), residues: 8734 helix: 2.35 (0.08), residues: 4526 sheet: -0.31 (0.15), residues: 1135 loop : -0.58 (0.11), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 66 HIS 0.015 0.001 HIS Z 161 PHE 0.036 0.001 PHE P 162 TYR 0.017 0.001 TYR z 353 ARG 0.005 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 467 time to evaluate : 6.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 272 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8770 (mt0) REVERT: A 47 ASP cc_start: 0.7969 (t70) cc_final: 0.7404 (t0) REVERT: A 344 MET cc_start: 0.8469 (mmm) cc_final: 0.8240 (mmm) REVERT: A 416 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 430 MET cc_start: 0.8252 (mmm) cc_final: 0.8028 (mmm) REVERT: A 505 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 25 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8539 (tp-100) REVERT: D 63 ASP cc_start: 0.8588 (t70) cc_final: 0.8315 (t70) REVERT: D 320 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: D 524 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: E 21 ASP cc_start: 0.8292 (t70) cc_final: 0.8008 (t0) REVERT: E 259 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8942 (mtpp) REVERT: E 468 MET cc_start: 0.8859 (mtm) cc_final: 0.8518 (ptm) REVERT: G 21 LYS cc_start: 0.8673 (tptt) cc_final: 0.8301 (tptt) REVERT: H 7 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (pp) REVERT: Q 41 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8522 (tm-30) REVERT: Q 116 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: Z 46 MET cc_start: 0.8623 (ttm) cc_final: 0.8348 (ttt) REVERT: a 44 MET cc_start: 0.8880 (ptp) cc_final: 0.8666 (ptp) REVERT: b 316 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7732 (t0) REVERT: b 415 MET cc_start: 0.9287 (mmm) cc_final: 0.8847 (mmp) REVERT: b 452 ASP cc_start: 0.8415 (m-30) cc_final: 0.8047 (m-30) REVERT: d 48 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8723 (pp) REVERT: e 287 GLU cc_start: 0.8817 (tt0) cc_final: 0.8588 (tt0) REVERT: g 15 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8446 (mttt) REVERT: h 70 ASP cc_start: 0.7738 (t0) cc_final: 0.7357 (t0) REVERT: h 130 GLN cc_start: 0.8439 (tp40) cc_final: 0.8088 (tp-100) REVERT: h 324 MET cc_start: 0.9171 (mmm) cc_final: 0.8865 (mmm) REVERT: q 75 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8137 (mm-30) REVERT: q 130 GLU cc_start: 0.8400 (tp30) cc_final: 0.7999 (tp30) REVERT: z 53 ASP cc_start: 0.8561 (m-30) cc_final: 0.8215 (p0) REVERT: z 112 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: z 520 GLU cc_start: 0.8381 (tt0) cc_final: 0.7952 (tt0) REVERT: z 522 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7412 (mtm) REVERT: P 80 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7699 (tp-100) REVERT: P 84 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8115 (mpm) REVERT: P 86 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7762 (tpt170) REVERT: P 250 ARG cc_start: 0.6411 (mmp-170) cc_final: 0.6178 (mmp-170) outliers start: 73 outliers final: 43 residues processed: 512 average time/residue: 1.5448 time to fit residues: 1041.4981 Evaluate side-chains 514 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 458 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 212 SER Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 276 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 112 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 86 ARG Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 228 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 512 optimal weight: 1.9990 chunk 825 optimal weight: 3.9990 chunk 503 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 573 optimal weight: 10.0000 chunk 865 optimal weight: 7.9990 chunk 796 optimal weight: 4.9990 chunk 689 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 532 optimal weight: 5.9990 chunk 422 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68319 Z= 0.253 Angle : 0.597 14.123 92242 Z= 0.290 Chirality : 0.042 0.163 10975 Planarity : 0.003 0.066 11780 Dihedral : 6.653 167.544 9485 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.61 % Favored : 96.38 % Rotamer: Outliers : 0.89 % Allowed : 13.52 % 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: 8734 helix: 2.36 (0.08), residues: 4533 sheet: -0.30 (0.16), residues: 1127 loop : -0.57 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 66 HIS 0.016 0.001 HIS Z 161 PHE 0.025 0.001 PHE P 162 TYR 0.016 0.001 TYR A 181 ARG 0.012 0.000 ARG P 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 478 time to evaluate : 6.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8290 (tp30) cc_final: 0.7969 (tp30) REVERT: N 272 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: A 47 ASP cc_start: 0.7926 (t70) cc_final: 0.7383 (t0) REVERT: A 344 MET cc_start: 0.8434 (mmm) cc_final: 0.8182 (mmm) REVERT: A 416 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 430 MET cc_start: 0.8237 (mmm) cc_final: 0.8013 (mmm) REVERT: A 505 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 25 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8519 (tp-100) REVERT: D 63 ASP cc_start: 0.8572 (t70) cc_final: 0.8307 (t70) REVERT: D 320 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8587 (mtt) REVERT: D 524 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: E 21 ASP cc_start: 0.8285 (t70) cc_final: 0.7995 (t0) REVERT: E 259 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8954 (mtpp) REVERT: E 468 MET cc_start: 0.8820 (mtm) cc_final: 0.8573 (ptm) REVERT: G 21 LYS cc_start: 0.8664 (tptt) cc_final: 0.8291 (tptt) REVERT: H 7 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (pp) REVERT: H 524 ARG cc_start: 0.6599 (ttt-90) cc_final: 0.6196 (tmm160) REVERT: Q 41 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8508 (tm-30) REVERT: Q 116 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: Z 46 MET cc_start: 0.8578 (ttm) cc_final: 0.8325 (ttt) REVERT: a 44 MET cc_start: 0.8869 (ptp) cc_final: 0.8658 (ptp) REVERT: a 344 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8011 (ptt) REVERT: b 316 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7735 (t0) REVERT: b 415 MET cc_start: 0.9274 (mmm) cc_final: 0.8831 (mmp) REVERT: b 452 ASP cc_start: 0.8467 (m-30) cc_final: 0.8040 (m-30) REVERT: d 48 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8640 (pp) REVERT: e 29 MET cc_start: 0.7919 (mtm) cc_final: 0.7650 (ttm) REVERT: e 287 GLU cc_start: 0.8815 (tt0) cc_final: 0.8588 (tt0) REVERT: g 15 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: h 130 GLN cc_start: 0.8414 (tp40) cc_final: 0.8065 (tp-100) REVERT: h 324 MET cc_start: 0.9164 (mmm) cc_final: 0.8862 (mmm) REVERT: q 75 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8128 (mm-30) REVERT: q 130 GLU cc_start: 0.8387 (tp30) cc_final: 0.7989 (tp30) REVERT: z 10 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7957 (pmtt) REVERT: z 53 ASP cc_start: 0.8557 (m-30) cc_final: 0.8220 (p0) REVERT: z 112 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: z 520 GLU cc_start: 0.8395 (tt0) cc_final: 0.7979 (tt0) REVERT: z 522 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7547 (mtm) REVERT: P 80 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7624 (tp-100) REVERT: P 86 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7780 (tpt170) REVERT: P 173 MET cc_start: 0.8654 (ppp) cc_final: 0.8162 (ppp) REVERT: P 184 MET cc_start: 0.8146 (mpt) cc_final: 0.7924 (mpt) REVERT: P 250 ARG cc_start: 0.6342 (mmp-170) cc_final: 0.5800 (mmp-170) outliers start: 65 outliers final: 46 residues processed: 519 average time/residue: 1.5365 time to fit residues: 1045.9735 Evaluate side-chains 525 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 466 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 316 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 212 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 276 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 112 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 522 MET Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 86 ARG Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 228 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 547 optimal weight: 7.9990 chunk 734 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 635 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 690 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 709 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 65 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 269 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 = 0.2949 r_free = 0.2949 target = 0.067391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.054884 restraints weight = 197957.720| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.11 r_work: 0.2528 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 68319 Z= 0.271 Angle : 0.600 13.584 92242 Z= 0.291 Chirality : 0.042 0.154 10975 Planarity : 0.003 0.052 11780 Dihedral : 6.605 167.107 9485 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.82 % Favored : 96.17 % Rotamer: Outliers : 0.92 % Allowed : 13.45 % Favored : 85.63 % 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: 8734 helix: 2.36 (0.08), residues: 4532 sheet: -0.28 (0.16), residues: 1123 loop : -0.58 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 66 HIS 0.016 0.001 HIS Z 161 PHE 0.023 0.001 PHE P 162 TYR 0.017 0.001 TYR z 353 ARG 0.010 0.000 ARG g 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16684.48 seconds wall clock time: 293 minutes 11.59 seconds (17591.59 seconds total)