Starting phenix.real_space_refine on Sun Oct 13 12:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8she_40485/10_2024/8she_40485.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 409 5.16 5 C 41332 2.51 5 N 11515 2.21 5 O 12811 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 42 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 66179 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1056 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} 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: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} 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: "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: 1 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: 31.59, per 1000 atoms: 0.48 Number of scatterers: 66179 At special positions: 0 Unit cell: (179.86, 177.744, 181.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 409 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12811 8.00 N 11515 7.00 C 41332 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 "HETATM66086 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65958 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65766 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.52 Conformation dependent library (CDL) restraints added in 6.7 seconds 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16024 Finding SS restraints... Secondary structure from input PDB file: 355 helices and 100 sheets defined 56.2% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'N' and resid 174 through 178 removed outlier: 3.799A pdb=" N THR N 177 " --> pdb=" O TYR N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 253 removed outlier: 3.595A pdb=" N THR N 253 " --> pdb=" O THR N 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.521A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.593A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.097A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.161A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (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 281 removed outlier: 3.927A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.146A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 removed outlier: 4.188A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.542A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.561A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.503A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.713A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.071A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.716A 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: 4.527A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.884A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.630A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.616A 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: 3.655A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.849A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.000A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.977A 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: 3.542A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.634A 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 80 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.626A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.596A 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: 6.634A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.859A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.917A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.799A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.547A 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 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.642A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.895A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.647A 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: 4.239A 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 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.522A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 40 removed outlier: 3.844A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 37 through 40' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.696A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.074A 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: 3.662A 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 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: 3.538A pdb=" N MET H 227 " --> pdb=" O GLY H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.551A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.551A 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: 3.634A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.023A 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: 4.427A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.351A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.834A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 430 removed outlier: 3.599A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.383A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.702A 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 removed outlier: 3.792A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.699A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.594A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.723A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.093A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.670A 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: 3.546A 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: 3.601A 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: 4.210A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.707A pdb=" N LEU Z 344 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.518A 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: 4.151A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.708A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.608A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) 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: 3.694A 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: 3.742A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.286A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.867A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 removed outlier: 3.517A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 4.063A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.381A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.601A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 427 removed outlier: 3.870A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.154A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.766A 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 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.685A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.842A 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: 3.723A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.764A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 Proline residue: d 185 - end of helix removed outlier: 3.597A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.870A 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: 3.705A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.522A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.886A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.576A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 126 removed outlier: 4.009A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.522A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.855A 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: 3.832A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.572A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.613A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.775A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.574A 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: 3.967A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.523A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) 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: 3.641A 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: 3.647A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.537A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.545A 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: 3.685A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.181A 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: 3.690A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 171 through 185 removed outlier: 3.645A 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 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 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: 3.625A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 3.977A 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: 4.347A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.406A 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 removed outlier: 3.568A pdb=" N VAL q 147 " --> pdb=" O PRO q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 144 through 147' Processing helix chain 'q' and resid 156 through 166 removed outlier: 4.421A 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: 4.729A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.789A 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: 3.794A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.341A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 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: 3.630A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.568A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.682A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.501A pdb=" N LEU z 148 " --> pdb=" O ASP z 144 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.721A 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: 3.542A 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: 3.649A 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: 3.772A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.228A 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: 3.505A 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 432 through 445 removed outlier: 4.122A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.601A 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 sheet with id=AA1, first strand: chain 'N' and resid 209 through 213 removed outlier: 3.519A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 242 through 243 removed outlier: 3.647A pdb=" N MET N 264 " --> pdb=" O SER N 256 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 286 through 289 removed outlier: 3.662A pdb=" N GLY N 299 " --> pdb=" O SER N 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR N 308 " --> pdb=" O PHE N 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.466A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.447A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.542A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.542A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.128A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.592A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.299A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.958A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.902A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.526A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 289 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.261A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.763A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.763A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.577A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.122A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC8, first strand: chain 'E' and resid 209 through 213 removed outlier: 6.656A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.731A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.731A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.343A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD5, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.729A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD7, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.290A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.734A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE4, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE5, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE6, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.104A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.942A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.571A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AF1, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF2, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF3, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF4, first strand: chain 'Z' and resid 191 through 196 removed outlier: 3.626A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF6, first strand: chain 'Z' and resid 311 through 313 removed outlier: 6.603A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id=AF8, first strand: chain 'a' and resid 9 through 13 removed outlier: 6.240A pdb=" N ASP d 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP a 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.273A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG2, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG3, first strand: chain 'a' and resid 196 through 199 removed outlier: 6.360A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.589A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.589A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.203A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS e 263 " --> pdb=" O ILE h 255 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL h 257 " --> pdb=" O LYS e 263 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS e 265 " --> pdb=" O VAL h 257 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG8, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.468A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.994A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH2, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.821A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.408A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH5, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH6, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.134A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.701A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH9, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.590A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.432A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.421A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 300 through 301 removed outlier: 6.599A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.301A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI7, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.940A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI9, first strand: chain 'g' and resid 238 through 241 Processing sheet with id=AJ1, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AJ2, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ3, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.323A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ5, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.834A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ7, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ8, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ9, first strand: chain 'q' and resid 20 through 23 removed outlier: 7.069A pdb=" N MET z 46 " --> pdb=" O ASP q 522 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE q 524 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL z 48 " --> pdb=" O ILE q 524 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET q 526 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.832A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.585A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK4, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK6, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK7, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.751A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK9, first strand: chain 'z' and resid 310 through 313 removed outlier: 8.910A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'z' and resid 477 through 479 4043 hydrogen bonds defined for protein. 11544 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: 28.53 Time building geometry restraints manager: 14.94 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: 22277 1.34 - 1.46: 10957 1.46 - 1.58: 32926 1.58 - 1.69: 48 1.69 - 1.81: 724 Bond restraints: 66932 Sorted by residual: bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.53e+01 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 6.51e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.795 -0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 66927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 89339 2.15 - 4.29: 816 4.29 - 6.44: 213 6.44 - 8.58: 17 8.58 - 10.73: 1 Bond angle restraints: 90386 Sorted by residual: angle pdb=" C THR N 195 " pdb=" CA THR N 195 " pdb=" CB THR N 195 " ideal model delta sigma weight residual 116.54 110.55 5.99 1.15e+00 7.56e-01 2.71e+01 angle pdb=" CA THR N 195 " pdb=" C THR N 195 " pdb=" N ASN N 196 " ideal model delta sigma weight residual 119.52 116.88 2.64 7.90e-01 1.60e+00 1.11e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.74 -7.56 2.37e+00 1.78e-01 1.02e+01 angle pdb=" C THR Z 158 " pdb=" N LYS Z 159 " pdb=" CA LYS Z 159 " ideal model delta sigma weight residual 122.09 116.39 5.70 1.79e+00 3.12e-01 1.01e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.60 -7.42 2.37e+00 1.78e-01 9.80e+00 ... (remaining 90381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 40729 35.78 - 71.57: 587 71.57 - 107.35: 50 107.35 - 143.14: 10 143.14 - 178.92: 6 Dihedral angle restraints: 41382 sinusoidal: 16637 harmonic: 24745 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 121.08 178.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 114.33 -174.33 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.67 172.33 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 41379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6744 0.031 - 0.062: 2603 0.062 - 0.093: 821 0.093 - 0.124: 559 0.124 - 0.155: 45 Chirality restraints: 10772 Sorted by residual: chirality pdb=" CA GLU b 139 " pdb=" N GLU b 139 " pdb=" C GLU b 139 " pdb=" CB GLU b 139 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA PRO H 428 " pdb=" N PRO H 428 " pdb=" C PRO H 428 " pdb=" CB PRO H 428 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 10769 not shown) Planarity restraints: 11537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO e 441 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ASP a 47 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP g 52 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO g 53 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO g 53 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO g 53 " 0.023 5.00e-02 4.00e+02 ... (remaining 11534 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 471 2.48 - 3.09: 47110 3.09 - 3.69: 99927 3.69 - 4.30: 150562 4.30 - 4.90: 255539 Nonbonded interactions: 553609 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.875 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.894 2.120 nonbonded pdb="MG MG B 602 " pdb=" F1 AF3 B 603 " model vdw 1.915 2.120 nonbonded pdb="MG MG h 602 " pdb=" F1 AF3 h 603 " model vdw 1.930 2.120 nonbonded pdb=" O2A ADP G 601 " pdb="MG MG G 602 " model vdw 1.935 2.170 ... (remaining 553604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.810 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 119.190 Find NCS groups from input model: 5.570 Set up NCS constraints: 0.330 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 66932 Z= 0.358 Angle : 0.563 10.731 90386 Z= 0.276 Chirality : 0.042 0.155 10772 Planarity : 0.003 0.055 11537 Dihedral : 14.082 178.919 25358 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.64 (0.09), residues: 8566 helix: 2.38 (0.08), residues: 4363 sheet: 0.25 (0.16), residues: 1167 loop : -0.49 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 319 HIS 0.011 0.001 HIS z 161 PHE 0.021 0.001 PHE z 289 TYR 0.022 0.001 TYR q 468 ARG 0.008 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 5.758 Fit side-chains REVERT: D 63 ASP cc_start: 0.8473 (m-30) cc_final: 0.8242 (m-30) REVERT: E 468 MET cc_start: 0.8638 (mtm) cc_final: 0.8171 (mtp) REVERT: H 70 ASP cc_start: 0.7794 (t70) cc_final: 0.7327 (t70) REVERT: Z 415 GLU cc_start: 0.8227 (mp0) cc_final: 0.7974 (mp0) REVERT: a 106 GLU cc_start: 0.8423 (tp30) cc_final: 0.8002 (tp30) REVERT: a 388 MET cc_start: 0.9398 (mtp) cc_final: 0.9094 (ttm) REVERT: a 462 ASP cc_start: 0.8269 (m-30) cc_final: 0.7967 (m-30) REVERT: a 492 ASN cc_start: 0.8815 (m110) cc_final: 0.8615 (m110) REVERT: b 53 LEU cc_start: 0.9408 (tp) cc_final: 0.9182 (tm) REVERT: b 353 MET cc_start: 0.8920 (tpt) cc_final: 0.8674 (tpt) REVERT: g 17 GLU cc_start: 0.7680 (tp30) cc_final: 0.7425 (tp30) REVERT: g 18 SER cc_start: 0.9204 (p) cc_final: 0.8635 (p) REVERT: g 395 MET cc_start: 0.9496 (mtm) cc_final: 0.9244 (mtm) REVERT: q 443 GLU cc_start: 0.8501 (tt0) cc_final: 0.8045 (tt0) outliers start: 0 outliers final: 1 residues processed: 543 average time/residue: 1.6222 time to fit residues: 1123.1033 Evaluate side-chains 432 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 5.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 719 optimal weight: 7.9990 chunk 645 optimal weight: 4.9990 chunk 358 optimal weight: 0.1980 chunk 220 optimal weight: 0.9990 chunk 435 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 667 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 406 optimal weight: 2.9990 chunk 497 optimal weight: 0.0370 chunk 773 optimal weight: 0.7980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN B 227 ASN D 178 GLN Z 161 HIS a 103 ASN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN g 73 GLN g 253 GLN g 390 ASN g 526 HIS q 41 GLN z 84 GLN z 161 HIS z 382 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 66932 Z= 0.163 Angle : 0.551 8.242 90386 Z= 0.275 Chirality : 0.041 0.155 10772 Planarity : 0.003 0.057 11537 Dihedral : 7.517 168.990 9306 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.68 % Allowed : 5.74 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.09), residues: 8566 helix: 2.48 (0.08), residues: 4402 sheet: 0.20 (0.16), residues: 1118 loop : -0.49 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 319 HIS 0.010 0.001 HIS z 161 PHE 0.025 0.001 PHE B 252 TYR 0.021 0.001 TYR N 174 ARG 0.009 0.000 ARG h 524 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 482 time to evaluate : 5.708 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7864 (ttp80) REVERT: A 386 ASP cc_start: 0.8811 (m-30) cc_final: 0.8607 (m-30) REVERT: B 414 GLU cc_start: 0.8734 (mp0) cc_final: 0.8467 (mp0) REVERT: E 24 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8444 (ttm-80) REVERT: E 468 MET cc_start: 0.8591 (mtm) cc_final: 0.8166 (mtp) REVERT: H 70 ASP cc_start: 0.7694 (t70) cc_final: 0.7195 (t70) REVERT: H 324 MET cc_start: 0.8908 (mmm) cc_final: 0.8523 (mmm) REVERT: Z 415 GLU cc_start: 0.8312 (mp0) cc_final: 0.8040 (mp0) REVERT: a 51 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8407 (t70) REVERT: a 106 GLU cc_start: 0.8445 (tp30) cc_final: 0.7969 (tp30) REVERT: a 156 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: a 462 ASP cc_start: 0.8274 (m-30) cc_final: 0.7910 (m-30) REVERT: b 445 MET cc_start: 0.8688 (tpp) cc_final: 0.8473 (mmm) REVERT: g 17 GLU cc_start: 0.7676 (tp30) cc_final: 0.7445 (tp30) REVERT: g 18 SER cc_start: 0.9210 (p) cc_final: 0.8834 (p) REVERT: g 395 MET cc_start: 0.9511 (mtm) cc_final: 0.9264 (mtm) REVERT: q 443 GLU cc_start: 0.8461 (tt0) cc_final: 0.8009 (tt0) REVERT: z 244 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8053 (t) outliers start: 49 outliers final: 11 residues processed: 501 average time/residue: 1.5026 time to fit residues: 977.5990 Evaluate side-chains 450 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 436 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 429 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 643 optimal weight: 0.8980 chunk 526 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 775 optimal weight: 10.0000 chunk 837 optimal weight: 9.9990 chunk 690 optimal weight: 10.0000 chunk 768 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 621 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 205 GLN g 390 ASN q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 66932 Z= 0.319 Angle : 0.578 7.613 90386 Z= 0.286 Chirality : 0.043 0.169 10772 Planarity : 0.003 0.060 11537 Dihedral : 7.406 175.958 9304 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.84 % Allowed : 7.97 % Favored : 91.19 % 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: 8566 helix: 2.48 (0.08), residues: 4410 sheet: 0.07 (0.16), residues: 1141 loop : -0.48 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 319 HIS 0.011 0.001 HIS Z 161 PHE 0.026 0.001 PHE B 252 TYR 0.020 0.001 TYR N 174 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 440 time to evaluate : 5.729 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7860 (ttp80) REVERT: A 230 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8289 (t) REVERT: A 416 GLU cc_start: 0.8626 (mp0) cc_final: 0.8411 (mp0) REVERT: B 414 GLU cc_start: 0.8740 (mp0) cc_final: 0.8376 (mp0) REVERT: E 468 MET cc_start: 0.8651 (mtm) cc_final: 0.8199 (mtp) REVERT: H 70 ASP cc_start: 0.7607 (t70) cc_final: 0.7352 (t70) REVERT: H 324 MET cc_start: 0.8915 (mmm) cc_final: 0.8613 (mmm) REVERT: Z 244 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (t) REVERT: Z 415 GLU cc_start: 0.8416 (mp0) cc_final: 0.8064 (mp0) REVERT: a 106 GLU cc_start: 0.8465 (tp30) cc_final: 0.7967 (tp30) REVERT: a 156 MET cc_start: 0.8817 (mtp) cc_final: 0.8287 (mtm) REVERT: b 445 MET cc_start: 0.8771 (tpp) cc_final: 0.8543 (mmm) REVERT: g 18 SER cc_start: 0.9232 (p) cc_final: 0.8859 (p) REVERT: g 395 MET cc_start: 0.9536 (mtm) cc_final: 0.9299 (mtm) REVERT: h 14 ASP cc_start: 0.8503 (t0) cc_final: 0.8194 (t0) REVERT: q 443 GLU cc_start: 0.8524 (tt0) cc_final: 0.8068 (tt0) outliers start: 60 outliers final: 22 residues processed: 471 average time/residue: 1.4983 time to fit residues: 917.6401 Evaluate side-chains 448 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 424 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 398 ILE Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 4 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 765 optimal weight: 3.9990 chunk 582 optimal weight: 0.8980 chunk 402 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 chunk 520 optimal weight: 8.9990 chunk 777 optimal weight: 9.9990 chunk 823 optimal weight: 8.9990 chunk 406 optimal weight: 2.9990 chunk 737 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN Z 161 HIS q 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 66932 Z= 0.197 Angle : 0.540 9.788 90386 Z= 0.266 Chirality : 0.041 0.157 10772 Planarity : 0.003 0.058 11537 Dihedral : 7.262 179.167 9304 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.88 % Allowed : 9.03 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8566 helix: 2.54 (0.08), residues: 4413 sheet: 0.06 (0.16), residues: 1133 loop : -0.45 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 319 HIS 0.009 0.001 HIS Z 161 PHE 0.025 0.001 PHE B 252 TYR 0.020 0.001 TYR N 174 ARG 0.011 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 457 time to evaluate : 5.932 Fit side-chains revert: symmetry clash REVERT: N 229 LEU cc_start: 0.8976 (tp) cc_final: 0.8640 (tm) REVERT: A 189 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7885 (ttp80) REVERT: A 230 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 416 GLU cc_start: 0.8591 (mp0) cc_final: 0.8292 (mp0) REVERT: B 414 GLU cc_start: 0.8685 (mp0) cc_final: 0.8239 (mp0) REVERT: E 468 MET cc_start: 0.8636 (mtm) cc_final: 0.8336 (mtp) REVERT: H 70 ASP cc_start: 0.7568 (t70) cc_final: 0.7316 (t70) REVERT: H 79 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8801 (mp) REVERT: H 324 MET cc_start: 0.8867 (mmm) cc_final: 0.8544 (mmm) REVERT: Q 55 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8490 (mtt) REVERT: Z 244 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8619 (t) REVERT: Z 415 GLU cc_start: 0.8434 (mp0) cc_final: 0.8083 (mp0) REVERT: a 106 GLU cc_start: 0.8448 (tp30) cc_final: 0.7968 (tp30) REVERT: a 156 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8223 (mtm) REVERT: e 446 TYR cc_start: 0.9089 (m-80) cc_final: 0.8852 (m-80) REVERT: g 18 SER cc_start: 0.9141 (p) cc_final: 0.8865 (m) REVERT: g 395 MET cc_start: 0.9537 (mtm) cc_final: 0.9219 (mtm) REVERT: h 14 ASP cc_start: 0.8542 (t0) cc_final: 0.8176 (t0) REVERT: h 455 PHE cc_start: 0.8015 (m-10) cc_final: 0.7624 (m-10) REVERT: q 249 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8389 (pmt) REVERT: q 443 GLU cc_start: 0.8523 (tt0) cc_final: 0.8057 (tt0) REVERT: z 244 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8048 (t) outliers start: 63 outliers final: 26 residues processed: 491 average time/residue: 1.5022 time to fit residues: 961.9963 Evaluate side-chains 459 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 398 ILE Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 685 optimal weight: 7.9990 chunk 467 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 613 optimal weight: 0.4980 chunk 339 optimal weight: 6.9990 chunk 702 optimal weight: 6.9990 chunk 569 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 420 optimal weight: 5.9990 chunk 739 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 380 GLN E 298 ASN E 445 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 30 ASN h 501 ASN q 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 66932 Z= 0.416 Angle : 0.624 10.431 90386 Z= 0.308 Chirality : 0.044 0.178 10772 Planarity : 0.003 0.061 11537 Dihedral : 7.296 178.697 9304 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.23 % Allowed : 9.99 % Favored : 88.78 % 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: 1.60 (0.09), residues: 8566 helix: 2.41 (0.08), residues: 4409 sheet: -0.07 (0.16), residues: 1143 loop : -0.51 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 435 HIS 0.010 0.001 HIS Z 161 PHE 0.026 0.002 PHE B 252 TYR 0.032 0.002 TYR z 229 ARG 0.007 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 430 time to evaluate : 6.004 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7840 (ttp80) REVERT: A 230 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8279 (t) REVERT: A 416 GLU cc_start: 0.8639 (mp0) cc_final: 0.8338 (mp0) REVERT: B 414 GLU cc_start: 0.8725 (mp0) cc_final: 0.8281 (mp0) REVERT: E 231 ASP cc_start: 0.8890 (t0) cc_final: 0.8671 (t0) REVERT: E 526 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8105 (tmm) REVERT: H 7 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8434 (pp) REVERT: H 70 ASP cc_start: 0.7655 (t70) cc_final: 0.7261 (t70) REVERT: H 324 MET cc_start: 0.8888 (mmm) cc_final: 0.8563 (mmm) REVERT: Q 55 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: Z 415 GLU cc_start: 0.8444 (mp0) cc_final: 0.8039 (mp0) REVERT: a 106 GLU cc_start: 0.8478 (tp30) cc_final: 0.7998 (tp30) REVERT: a 156 MET cc_start: 0.8868 (mtp) cc_final: 0.8257 (mtm) REVERT: a 388 MET cc_start: 0.9408 (mtp) cc_final: 0.9111 (ttm) REVERT: g 18 SER cc_start: 0.9317 (p) cc_final: 0.8871 (m) REVERT: g 52 ASP cc_start: 0.8386 (t0) cc_final: 0.8115 (t70) REVERT: g 54 MET cc_start: 0.8480 (mpp) cc_final: 0.8019 (mpp) REVERT: g 395 MET cc_start: 0.9539 (mtm) cc_final: 0.9282 (mtm) REVERT: h 324 MET cc_start: 0.9276 (mmm) cc_final: 0.9046 (mmm) REVERT: q 249 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (pmt) REVERT: q 443 GLU cc_start: 0.8567 (tt0) cc_final: 0.8095 (tt0) REVERT: z 244 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8232 (t) outliers start: 88 outliers final: 36 residues processed: 483 average time/residue: 1.4529 time to fit residues: 920.3477 Evaluate side-chains 459 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 417 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 393 SER Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 398 ILE Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 277 optimal weight: 0.9980 chunk 741 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 483 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 824 optimal weight: 10.0000 chunk 684 optimal weight: 5.9990 chunk 381 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 432 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 233 HIS q 41 GLN q 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 66932 Z= 0.231 Angle : 0.559 10.999 90386 Z= 0.275 Chirality : 0.042 0.168 10772 Planarity : 0.003 0.060 11537 Dihedral : 7.103 179.504 9304 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.13 % Allowed : 10.54 % Favored : 88.33 % 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: 1.69 (0.09), residues: 8566 helix: 2.50 (0.08), residues: 4410 sheet: -0.09 (0.15), residues: 1143 loop : -0.48 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 319 HIS 0.004 0.001 HIS Z 161 PHE 0.025 0.001 PHE B 252 TYR 0.019 0.001 TYR N 174 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 441 time to evaluate : 5.831 Fit side-chains revert: symmetry clash REVERT: N 229 LEU cc_start: 0.9016 (tp) cc_final: 0.8673 (tm) REVERT: N 294 ASP cc_start: 0.8397 (m-30) cc_final: 0.8081 (m-30) REVERT: A 189 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7845 (ttp80) REVERT: A 230 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8326 (t) REVERT: A 416 GLU cc_start: 0.8603 (mp0) cc_final: 0.8279 (mp0) REVERT: A 482 ASN cc_start: 0.8871 (m-40) cc_final: 0.8507 (p0) REVERT: B 414 GLU cc_start: 0.8645 (mp0) cc_final: 0.8190 (mp0) REVERT: E 231 ASP cc_start: 0.8860 (t0) cc_final: 0.8649 (t0) REVERT: G 47 MET cc_start: 0.8402 (mtm) cc_final: 0.8153 (mtm) REVERT: G 194 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8113 (t0) REVERT: H 7 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8321 (pp) REVERT: H 70 ASP cc_start: 0.7631 (t70) cc_final: 0.7261 (t70) REVERT: H 324 MET cc_start: 0.8878 (mmm) cc_final: 0.8572 (mmm) REVERT: Q 55 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8492 (mtt) REVERT: Z 10 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9062 (mtpp) REVERT: Z 415 GLU cc_start: 0.8448 (mp0) cc_final: 0.8033 (mp0) REVERT: a 106 GLU cc_start: 0.8438 (tp30) cc_final: 0.7948 (tp30) REVERT: a 156 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8188 (mtm) REVERT: d 446 MET cc_start: 0.8073 (mtt) cc_final: 0.7545 (mtp) REVERT: e 446 TYR cc_start: 0.9112 (m-80) cc_final: 0.8871 (m-80) REVERT: e 526 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8470 (ttm) REVERT: g 18 SER cc_start: 0.9301 (p) cc_final: 0.8937 (m) REVERT: g 54 MET cc_start: 0.8486 (mpp) cc_final: 0.8178 (mpm) REVERT: g 395 MET cc_start: 0.9529 (mtm) cc_final: 0.9284 (mtm) REVERT: h 324 MET cc_start: 0.9269 (mmm) cc_final: 0.9035 (mmm) REVERT: q 249 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8405 (pmt) REVERT: q 443 GLU cc_start: 0.8554 (tt0) cc_final: 0.8080 (tt0) REVERT: z 244 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8078 (t) outliers start: 81 outliers final: 38 residues processed: 491 average time/residue: 1.4680 time to fit residues: 946.8408 Evaluate side-chains 468 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 421 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 393 SER Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 398 ILE Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 794 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 469 optimal weight: 7.9990 chunk 601 optimal weight: 0.7980 chunk 466 optimal weight: 6.9990 chunk 693 optimal weight: 8.9990 chunk 460 optimal weight: 4.9990 chunk 821 optimal weight: 0.6980 chunk 513 optimal weight: 0.9980 chunk 500 optimal weight: 4.9990 chunk 379 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 382 HIS g 28 ASN g 64 ASN h 501 ASN q 41 GLN z 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 66932 Z= 0.154 Angle : 0.537 11.299 90386 Z= 0.262 Chirality : 0.041 0.179 10772 Planarity : 0.003 0.055 11537 Dihedral : 6.789 179.964 9304 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.10 % Allowed : 10.89 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.09), residues: 8566 helix: 2.62 (0.08), residues: 4414 sheet: -0.00 (0.16), residues: 1133 loop : -0.44 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 319 HIS 0.009 0.001 HIS e 236 PHE 0.020 0.001 PHE B 252 TYR 0.022 0.001 TYR N 174 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 479 time to evaluate : 5.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 229 LEU cc_start: 0.9010 (tp) cc_final: 0.8659 (tm) REVERT: A 230 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8385 (t) REVERT: A 416 GLU cc_start: 0.8563 (mp0) cc_final: 0.8298 (mp0) REVERT: A 482 ASN cc_start: 0.8829 (m-40) cc_final: 0.8496 (p0) REVERT: B 414 GLU cc_start: 0.8619 (mp0) cc_final: 0.8168 (mp0) REVERT: D 179 TYR cc_start: 0.9196 (m-80) cc_final: 0.8962 (m-80) REVERT: E 20 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8885 (ptmm) REVERT: E 24 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8428 (ttm-80) REVERT: H 7 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8207 (pp) REVERT: H 70 ASP cc_start: 0.7598 (t70) cc_final: 0.6896 (t70) REVERT: H 324 MET cc_start: 0.8820 (mmm) cc_final: 0.8460 (mmm) REVERT: Q 55 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (mtt) REVERT: Z 10 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9094 (mtpp) REVERT: Z 415 GLU cc_start: 0.8428 (mp0) cc_final: 0.7873 (mp0) REVERT: a 106 GLU cc_start: 0.8454 (tp30) cc_final: 0.7945 (tp30) REVERT: a 156 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: d 446 MET cc_start: 0.7980 (mtt) cc_final: 0.7377 (mtp) REVERT: d 513 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9006 (tt) REVERT: e 29 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7345 (tmm) REVERT: e 446 TYR cc_start: 0.9084 (m-80) cc_final: 0.8818 (m-80) REVERT: g 18 SER cc_start: 0.9288 (p) cc_final: 0.8927 (m) REVERT: g 52 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7744 (t0) REVERT: g 395 MET cc_start: 0.9517 (mtm) cc_final: 0.9223 (mtm) REVERT: h 324 MET cc_start: 0.9258 (mmm) cc_final: 0.9035 (mmm) REVERT: q 249 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8252 (pmt) REVERT: q 443 GLU cc_start: 0.8551 (tt0) cc_final: 0.8068 (tt0) REVERT: z 213 ASP cc_start: 0.8757 (p0) cc_final: 0.8454 (p0) REVERT: z 244 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (t) outliers start: 79 outliers final: 27 residues processed: 526 average time/residue: 1.4422 time to fit residues: 1002.2240 Evaluate side-chains 474 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 436 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 508 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 490 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 522 optimal weight: 4.9990 chunk 559 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 645 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 380 ASN g 390 ASN h 233 HIS h 501 ASN q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 66932 Z= 0.258 Angle : 0.572 11.718 90386 Z= 0.278 Chirality : 0.042 0.256 10772 Planarity : 0.003 0.054 11537 Dihedral : 6.704 178.859 9304 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.06 % Allowed : 11.54 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.09), residues: 8566 helix: 2.60 (0.08), residues: 4414 sheet: 0.00 (0.16), residues: 1125 loop : -0.44 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 319 HIS 0.004 0.001 HIS a 471 PHE 0.026 0.001 PHE B 252 TYR 0.023 0.001 TYR N 174 ARG 0.013 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 439 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8365 (t) REVERT: A 416 GLU cc_start: 0.8553 (mp0) cc_final: 0.8315 (mp0) REVERT: A 482 ASN cc_start: 0.8836 (m-40) cc_final: 0.8496 (p0) REVERT: B 414 GLU cc_start: 0.8631 (mp0) cc_final: 0.8145 (mp0) REVERT: E 24 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8427 (ttm-80) REVERT: G 194 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8124 (t0) REVERT: H 7 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (pp) REVERT: H 70 ASP cc_start: 0.7670 (t70) cc_final: 0.7305 (t70) REVERT: H 144 LYS cc_start: 0.8510 (tppt) cc_final: 0.8280 (tppt) REVERT: H 324 MET cc_start: 0.8859 (mmm) cc_final: 0.8487 (mmm) REVERT: Q 55 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8490 (mtt) REVERT: Z 10 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9079 (mtpp) REVERT: Z 415 GLU cc_start: 0.8443 (mp0) cc_final: 0.8018 (mp0) REVERT: a 106 GLU cc_start: 0.8484 (tp30) cc_final: 0.7984 (tp30) REVERT: a 156 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8163 (mtm) REVERT: d 513 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9000 (tt) REVERT: e 29 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7291 (tmm) REVERT: e 446 TYR cc_start: 0.9177 (m-80) cc_final: 0.8891 (m-80) REVERT: e 526 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8273 (ttm) REVERT: g 18 SER cc_start: 0.9294 (p) cc_final: 0.8907 (m) REVERT: g 395 MET cc_start: 0.9519 (mtm) cc_final: 0.9229 (mtm) REVERT: h 324 MET cc_start: 0.9295 (mmm) cc_final: 0.9055 (mmm) REVERT: q 249 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (pmt) REVERT: q 443 GLU cc_start: 0.8555 (tt0) cc_final: 0.8080 (tt0) REVERT: z 213 ASP cc_start: 0.8757 (p0) cc_final: 0.8458 (p0) REVERT: z 244 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8036 (t) outliers start: 76 outliers final: 38 residues processed: 483 average time/residue: 1.4673 time to fit residues: 933.5059 Evaluate side-chains 482 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 433 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 747 optimal weight: 0.2980 chunk 786 optimal weight: 9.9990 chunk 717 optimal weight: 9.9990 chunk 765 optimal weight: 3.9990 chunk 460 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 600 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 691 optimal weight: 9.9990 chunk 723 optimal weight: 3.9990 chunk 762 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 233 HIS q 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 66932 Z= 0.295 Angle : 0.588 12.118 90386 Z= 0.287 Chirality : 0.042 0.170 10772 Planarity : 0.003 0.079 11537 Dihedral : 6.678 178.768 9304 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.02 % Allowed : 11.79 % Favored : 87.19 % 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: 1.76 (0.09), residues: 8566 helix: 2.56 (0.08), residues: 4414 sheet: -0.04 (0.16), residues: 1121 loop : -0.47 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 319 HIS 0.004 0.001 HIS A 113 PHE 0.028 0.001 PHE B 252 TYR 0.026 0.001 TYR N 174 ARG 0.015 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 435 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 229 LEU cc_start: 0.9052 (tp) cc_final: 0.8708 (tm) REVERT: A 230 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 416 GLU cc_start: 0.8586 (mp0) cc_final: 0.8276 (mp0) REVERT: A 482 ASN cc_start: 0.8861 (m-40) cc_final: 0.8626 (p0) REVERT: B 414 GLU cc_start: 0.8601 (mp0) cc_final: 0.8137 (mp0) REVERT: E 20 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8916 (ptmm) REVERT: E 24 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8424 (ttm-80) REVERT: G 194 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8107 (t0) REVERT: H 7 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (pp) REVERT: H 70 ASP cc_start: 0.7705 (t70) cc_final: 0.6974 (t70) REVERT: H 144 LYS cc_start: 0.8548 (tppt) cc_final: 0.8263 (tppt) REVERT: H 324 MET cc_start: 0.8855 (mmm) cc_final: 0.8551 (mmm) REVERT: Q 55 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8478 (mtt) REVERT: Z 10 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9080 (mtpp) REVERT: Z 415 GLU cc_start: 0.8431 (mp0) cc_final: 0.8008 (mp0) REVERT: a 106 GLU cc_start: 0.8454 (tp30) cc_final: 0.7952 (tp30) REVERT: a 156 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: b 19 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: d 446 MET cc_start: 0.8382 (mmm) cc_final: 0.7336 (mtp) REVERT: d 513 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9052 (tt) REVERT: e 29 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: e 446 TYR cc_start: 0.9201 (m-80) cc_final: 0.8899 (m-80) REVERT: e 526 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8297 (ttm) REVERT: g 18 SER cc_start: 0.9290 (p) cc_final: 0.8907 (m) REVERT: g 395 MET cc_start: 0.9518 (mtm) cc_final: 0.9217 (mtm) REVERT: h 324 MET cc_start: 0.9331 (mmm) cc_final: 0.9059 (mmm) REVERT: q 249 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8442 (pmt) REVERT: q 443 GLU cc_start: 0.8564 (tt0) cc_final: 0.8093 (tt0) REVERT: z 244 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8094 (t) outliers start: 73 outliers final: 38 residues processed: 483 average time/residue: 1.5070 time to fit residues: 955.1376 Evaluate side-chains 478 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 427 time to evaluate : 5.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 502 optimal weight: 0.7980 chunk 809 optimal weight: 4.9990 chunk 493 optimal weight: 1.9990 chunk 383 optimal weight: 0.0470 chunk 562 optimal weight: 8.9990 chunk 848 optimal weight: 0.9990 chunk 781 optimal weight: 7.9990 chunk 675 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 522 optimal weight: 9.9990 chunk 414 optimal weight: 9.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN h 233 HIS q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 66932 Z= 0.195 Angle : 0.565 12.302 90386 Z= 0.274 Chirality : 0.041 0.189 10772 Planarity : 0.003 0.063 11537 Dihedral : 6.523 179.145 9304 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.84 % Allowed : 11.99 % Favored : 87.17 % 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: 1.82 (0.09), residues: 8566 helix: 2.61 (0.08), residues: 4414 sheet: -0.00 (0.16), residues: 1125 loop : -0.45 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 319 HIS 0.005 0.001 HIS H 283 PHE 0.015 0.001 PHE N 178 TYR 0.019 0.001 TYR N 174 ARG 0.013 0.000 ARG H 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17132 Ramachandran restraints generated. 8566 Oldfield, 0 Emsley, 8566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 452 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 229 LEU cc_start: 0.9042 (tp) cc_final: 0.8693 (tm) REVERT: A 416 GLU cc_start: 0.8541 (mp0) cc_final: 0.8309 (mp0) REVERT: A 482 ASN cc_start: 0.8850 (m-40) cc_final: 0.8619 (p0) REVERT: B 414 GLU cc_start: 0.8602 (mp0) cc_final: 0.8130 (mp0) REVERT: E 24 ARG cc_start: 0.8731 (mtp85) cc_final: 0.8437 (ttm-80) REVERT: E 58 ASP cc_start: 0.8444 (m-30) cc_final: 0.8211 (m-30) REVERT: E 426 GLU cc_start: 0.8682 (mp0) cc_final: 0.8469 (mp0) REVERT: G 194 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8111 (t0) REVERT: H 7 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8244 (pp) REVERT: H 70 ASP cc_start: 0.7684 (t70) cc_final: 0.6977 (t70) REVERT: H 144 LYS cc_start: 0.8549 (tppt) cc_final: 0.8253 (tppt) REVERT: H 324 MET cc_start: 0.8837 (mmm) cc_final: 0.8474 (mmm) REVERT: Z 10 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9073 (mtpp) REVERT: Z 415 GLU cc_start: 0.8423 (mp0) cc_final: 0.7865 (mp0) REVERT: a 106 GLU cc_start: 0.8459 (tp30) cc_final: 0.7957 (tp30) REVERT: a 156 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: b 19 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: d 446 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: d 513 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8970 (tt) REVERT: e 446 TYR cc_start: 0.9158 (m-80) cc_final: 0.8878 (m-80) REVERT: e 526 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8239 (ttm) REVERT: g 18 SER cc_start: 0.9273 (p) cc_final: 0.8950 (m) REVERT: g 395 MET cc_start: 0.9513 (mtm) cc_final: 0.9222 (mtm) REVERT: h 324 MET cc_start: 0.9339 (mmm) cc_final: 0.9074 (mmm) REVERT: q 249 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8318 (pmt) REVERT: q 443 GLU cc_start: 0.8559 (tt0) cc_final: 0.8085 (tt0) REVERT: z 213 ASP cc_start: 0.8768 (p0) cc_final: 0.8478 (p0) REVERT: z 244 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8026 (t) REVERT: z 337 ASP cc_start: 0.8103 (m-30) cc_final: 0.7896 (m-30) outliers start: 60 outliers final: 39 residues processed: 489 average time/residue: 1.4633 time to fit residues: 943.3479 Evaluate side-chains 483 residues out of total 7165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 434 time to evaluate : 5.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 536 optimal weight: 9.9990 chunk 720 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 623 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 676 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 695 optimal weight: 10.0000 chunk 85 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN g 28 ASN h 233 HIS q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.051373 restraints weight = 198249.063| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.16 r_work: 0.2511 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 66932 Z= 0.322 Angle : 0.600 12.168 90386 Z= 0.292 Chirality : 0.043 0.171 10772 Planarity : 0.003 0.056 11537 Dihedral : 6.519 177.956 9304 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.88 % Allowed : 12.07 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 8566 helix: 2.55 (0.08), residues: 4419 sheet: -0.05 (0.16), residues: 1121 loop : -0.48 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 319 HIS 0.004 0.001 HIS A 113 PHE 0.018 0.001 PHE H 455 TYR 0.026 0.001 TYR N 174 ARG 0.013 0.000 ARG H 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15500.91 seconds wall clock time: 278 minutes 9.05 seconds (16689.05 seconds total)