Starting phenix.real_space_refine on Fri Sep 27 17:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/09_2024/8sg8_40452.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 412 5.16 5 C 41760 2.51 5 N 11628 2.21 5 O 12927 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 48 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 66839 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 89 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} 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: "P" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 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: 33.01, per 1000 atoms: 0.49 Number of scatterers: 66839 At special positions: 0 Unit cell: (179.86, 177.744, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 412 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12927 8.00 N 11628 7.00 C 41760 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 "HETATM66490 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66362 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66746 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 7.2 seconds 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16166 Finding SS restraints... Secondary structure from input PDB file: 363 helices and 97 sheets defined 56.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.523A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.908A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.568A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.240A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 258 through 280 removed outlier: 4.551A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.613A pdb=" N MET A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 345 " --> pdb=" O ALA A 342 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.516A pdb=" N ALA A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.847A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.496A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.578A 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: 3.536A 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: 3.823A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 455 Proline residue: B 447 - end of helix removed outlier: 3.645A 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: 4.336A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 4.245A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.762A 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: 4.584A 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: 3.837A 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: 3.979A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.960A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.877A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.588A pdb=" N GLY D 487 " --> pdb=" O ARG D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.909A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.601A 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 125 removed outlier: 3.597A 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 176 through 180 removed outlier: 3.939A 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: 3.942A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 439 removed outlier: 3.824A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.604A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.911A 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: 3.773A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) 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: 3.972A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.623A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.645A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.603A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.506A pdb=" N ARG G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.559A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.521A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 40 removed outlier: 4.049A 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: 3.672A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.018A 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: 3.738A 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: 3.770A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.911A 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: 4.147A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 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 28 Processing helix chain 'Q' and resid 28 through 45 removed outlier: 4.339A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 4.120A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.832A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.056A 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 429 removed outlier: 3.664A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 444 removed outlier: 4.346A 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 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.769A 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: 3.555A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.871A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.158A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.634A 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: 3.794A 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: 3.572A 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: 3.717A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.767A pdb=" N LEU Z 344 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.171A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.747A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 removed outlier: 3.531A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) 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: 3.674A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.879A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 135 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.807A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.344A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.905A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 removed outlier: 3.545A 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 removed outlier: 4.035A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.913A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.119A 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: 4.320A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.548A 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 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 removed outlier: 3.580A pdb=" N VAL b 341 " --> pdb=" O PRO b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.132A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.776A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 removed outlier: 3.558A pdb=" N GLN d 32 " --> pdb=" O ASP d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.661A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 103 Processing helix chain 'd' and resid 107 through 126 removed outlier: 3.827A 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: 3.507A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.594A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix removed outlier: 3.606A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE d 195 " --> pdb=" O VAL d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 4.123A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.897A 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 441 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.888A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.925A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.982A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.728A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 126 removed outlier: 3.585A 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 176 through 180 removed outlier: 3.910A 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: 3.901A 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: 3.929A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.691A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 37 removed outlier: 3.630A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 68 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.632A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.593A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 4.225A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.577A 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 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 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 36 removed outlier: 3.900A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.670A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 114 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.684A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.686A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 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: 3.517A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.082A 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: 4.607A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 75 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 168 removed outlier: 4.331A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.543A 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: 4.825A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.984A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS q 430 " --> pdb=" O TYR q 426 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.332A 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 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.616A 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: 3.554A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.820A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.982A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.764A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 431 No H-bonds generated for 'chain 'z' and resid 430 through 431' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.266A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.568A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 62 through 88 removed outlier: 3.725A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU P 85 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE P 88 " --> pdb=" O MET P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 139 Processing helix chain 'P' and resid 140 through 152 removed outlier: 4.191A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU P 152 " --> pdb=" O MET P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 195 through 209 Processing helix chain 'P' and resid 219 through 223 Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 251 through 256 Processing helix chain 'P' and resid 260 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.166A pdb=" N ASP D 58 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 529 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.149A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.587A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.567A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.567A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.152A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.269A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.899A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.815A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.418A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.406A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.309A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.626A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.589A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.969A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.451A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.451A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.405A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.619A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD3, first strand: chain 'G' and resid 310 through 312 removed outlier: 9.052A pdb=" N VAL G 332 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU G 240 " --> pdb=" O VAL G 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD5, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.188A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.651A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD9, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'Q' and resid 20 through 23 removed outlier: 4.990A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.907A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.533A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE6, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE7, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AE9, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.396A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF2, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.316A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.534A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.348A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.296A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF7, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AF8, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.595A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.520A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 234 through 237 Processing sheet with id=AG2, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.132A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.532A pdb=" N ARG a 496 " --> pdb=" O GLY a 487 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.343A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.035A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG7, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.779A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.226A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS b 346 " --> pdb=" O ALA b 235 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH2, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.466A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.977A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.977A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH6, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.643A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH8, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.879A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.526A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU e 299 " --> pdb=" O LYS e 247 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.244A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI3, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI4, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.838A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI6, first strand: chain 'g' and resid 238 through 241 Processing sheet with id=AI7, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AI8, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.485A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ1, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.871A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ3, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ4, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ5, first strand: chain 'q' and resid 20 through 23 removed outlier: 4.624A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.846A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.671A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AJ9, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK1, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK2, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK3, first strand: chain 'z' and resid 192 through 196 Processing sheet with id=AK4, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK5, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.035A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK7, first strand: chain 'P' and resid 162 through 164 removed outlier: 5.773A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 4089 hydrogen bonds defined for protein. 11697 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: 34.44 Time building geometry restraints manager: 14.92 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: 22496 1.34 - 1.46: 11757 1.46 - 1.58: 32563 1.58 - 1.70: 49 1.70 - 1.81: 731 Bond restraints: 67596 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.46e+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 6.44e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" F2 AF3 q 603 " pdb="AL AF3 q 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 67591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 90424 2.37 - 4.73: 650 4.73 - 7.10: 183 7.10 - 9.47: 4 9.47 - 11.83: 2 Bond angle restraints: 91263 Sorted by residual: angle pdb=" CA PRO G 6 " pdb=" N PRO G 6 " pdb=" CD PRO G 6 " ideal model delta sigma weight residual 112.00 100.17 11.83 1.40e+00 5.10e-01 7.14e+01 angle pdb=" N PRO G 6 " pdb=" CD PRO G 6 " pdb=" CG PRO G 6 " ideal model delta sigma weight residual 103.20 97.18 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C ILE A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.13 -7.95 2.37e+00 1.78e-01 1.12e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 91258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 41068 35.52 - 71.04: 665 71.04 - 106.56: 60 106.56 - 142.08: 12 142.08 - 177.60: 6 Dihedral angle restraints: 41811 sinusoidal: 16850 harmonic: 24961 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.60 -177.60 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.53 -170.52 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual 300.00 135.09 164.91 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 41808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 8582 0.046 - 0.093: 1661 0.093 - 0.139: 617 0.139 - 0.186: 6 0.186 - 0.232: 1 Chirality restraints: 10867 Sorted by residual: chirality pdb=" CA PRO G 6 " pdb=" N PRO G 6 " pdb=" C PRO G 6 " pdb=" CB PRO G 6 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE g 83 " pdb=" CA ILE g 83 " pdb=" CG1 ILE g 83 " pdb=" CG2 ILE g 83 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-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 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 10864 not shown) Planarity restraints: 11652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO a 478 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 5 " 0.057 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO G 6 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 6 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 6 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG e 14 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO e 15 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO e 15 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 15 " -0.029 5.00e-02 4.00e+02 ... (remaining 11649 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 574 2.53 - 3.13: 50821 3.13 - 3.72: 105196 3.72 - 4.31: 146371 4.31 - 4.90: 252719 Nonbonded interactions: 555681 Sorted by model distance: nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.943 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.949 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.950 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.957 2.120 nonbonded pdb=" O2A ADP Z 601 " pdb="MG MG Z 602 " model vdw 1.966 2.170 ... (remaining 555676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.040 Extract box with map and model: 1.870 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 130.290 Find NCS groups from input model: 5.700 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 67596 Z= 0.269 Angle : 0.537 11.832 91263 Z= 0.264 Chirality : 0.041 0.232 10867 Planarity : 0.003 0.098 11652 Dihedral : 14.663 177.595 25645 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 1.72 (0.09), residues: 8639 helix: 2.43 (0.08), residues: 4433 sheet: 0.26 (0.16), residues: 1116 loop : -0.44 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 319 HIS 0.006 0.001 HIS a 201 PHE 0.029 0.001 PHE e 386 TYR 0.015 0.001 TYR G 437 ARG 0.014 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 5.776 Fit side-chains REVERT: B 37 ASP cc_start: 0.8123 (m-30) cc_final: 0.7852 (m-30) REVERT: E 58 ASP cc_start: 0.8173 (m-30) cc_final: 0.7743 (m-30) REVERT: H 46 ASP cc_start: 0.8474 (m-30) cc_final: 0.8237 (m-30) REVERT: Q 249 MET cc_start: 0.8310 (pmm) cc_final: 0.8087 (pmm) REVERT: Z 44 MET cc_start: 0.8406 (ttm) cc_final: 0.8185 (mtt) REVERT: e 4 MET cc_start: 0.4941 (ttp) cc_final: 0.3639 (mpt) REVERT: e 118 GLU cc_start: 0.8167 (tt0) cc_final: 0.7890 (tt0) REVERT: h 423 TYR cc_start: 0.9070 (t80) cc_final: 0.8772 (t80) REVERT: q 322 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7815 (mtm180) REVERT: q 443 GLU cc_start: 0.8400 (tt0) cc_final: 0.8060 (tt0) REVERT: z 66 GLU cc_start: 0.7922 (mp0) cc_final: 0.7615 (mp0) REVERT: z 241 LYS cc_start: 0.8700 (tttp) cc_final: 0.8315 (tppp) REVERT: z 364 GLU cc_start: 0.7929 (mp0) cc_final: 0.7500 (mp0) REVERT: P 93 MET cc_start: 0.5711 (mmm) cc_final: 0.4706 (ppp) REVERT: P 199 ASN cc_start: 0.8199 (m110) cc_final: 0.7970 (m110) outliers start: 0 outliers final: 1 residues processed: 612 average time/residue: 1.4563 time to fit residues: 1171.5451 Evaluate side-chains 494 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 493 time to evaluate : 5.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 726 optimal weight: 9.9990 chunk 651 optimal weight: 0.9980 chunk 361 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 674 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 501 optimal weight: 8.9990 chunk 780 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 288 ASN B 380 GLN D 502 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN a 164 ASN ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 361 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 461 ASN z 23 ASN z 84 GLN z 182 GLN ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 67596 Z= 0.282 Angle : 0.581 9.162 91263 Z= 0.289 Chirality : 0.043 0.165 10867 Planarity : 0.004 0.071 11652 Dihedral : 7.888 177.570 9389 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.72 % 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: 1.61 (0.09), residues: 8639 helix: 2.38 (0.08), residues: 4487 sheet: 0.05 (0.16), residues: 1119 loop : -0.54 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 435 HIS 0.007 0.001 HIS a 201 PHE 0.024 0.001 PHE e 386 TYR 0.018 0.001 TYR z 351 ARG 0.005 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 522 time to evaluate : 5.865 Fit side-chains REVERT: B 37 ASP cc_start: 0.8155 (m-30) cc_final: 0.7875 (m-30) REVERT: E 58 ASP cc_start: 0.8198 (m-30) cc_final: 0.7789 (m-30) REVERT: H 46 ASP cc_start: 0.8493 (m-30) cc_final: 0.8250 (m-30) REVERT: H 227 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: Q 61 GLU cc_start: 0.7935 (mp0) cc_final: 0.7728 (mp0) REVERT: Q 249 MET cc_start: 0.8337 (pmm) cc_final: 0.8034 (pmm) REVERT: Q 250 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8282 (tp) REVERT: Z 44 MET cc_start: 0.8382 (ttm) cc_final: 0.8164 (mtt) REVERT: Z 53 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: a 416 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: e 4 MET cc_start: 0.5176 (ttp) cc_final: 0.3800 (mmt) REVERT: e 24 ARG cc_start: 0.8328 (mtp85) cc_final: 0.7984 (ttm-80) REVERT: g 54 MET cc_start: 0.8982 (mpp) cc_final: 0.8582 (mpp) REVERT: h 2 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.6580 (tmm) REVERT: h 423 TYR cc_start: 0.9081 (t80) cc_final: 0.8770 (t80) REVERT: q 322 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7801 (mtm180) REVERT: q 443 GLU cc_start: 0.8433 (tt0) cc_final: 0.8089 (tt0) REVERT: z 66 GLU cc_start: 0.7853 (mp0) cc_final: 0.7485 (mp0) REVERT: z 241 LYS cc_start: 0.8696 (tttp) cc_final: 0.8290 (tppp) REVERT: z 364 GLU cc_start: 0.7885 (mp0) cc_final: 0.7454 (mp0) REVERT: P 93 MET cc_start: 0.5700 (mmm) cc_final: 0.4716 (ppp) outliers start: 56 outliers final: 19 residues processed: 541 average time/residue: 1.4994 time to fit residues: 1064.9605 Evaluate side-chains 513 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 489 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 14 ASP Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 434 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 649 optimal weight: 10.0000 chunk 531 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 782 optimal weight: 8.9990 chunk 845 optimal weight: 20.0000 chunk 696 optimal weight: 0.9980 chunk 775 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 627 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 352 GLN a 164 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 67596 Z= 0.263 Angle : 0.561 8.152 91263 Z= 0.278 Chirality : 0.042 0.160 10867 Planarity : 0.003 0.055 11652 Dihedral : 7.603 175.005 9386 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.97 % Allowed : 8.59 % Favored : 90.44 % 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: 1.57 (0.09), residues: 8639 helix: 2.38 (0.08), residues: 4484 sheet: -0.03 (0.16), residues: 1111 loop : -0.58 (0.11), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS a 201 PHE 0.020 0.001 PHE e 386 TYR 0.020 0.001 TYR z 351 ARG 0.007 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 520 time to evaluate : 5.846 Fit side-chains REVERT: N 267 ASP cc_start: 0.8526 (t70) cc_final: 0.8293 (t70) REVERT: B 37 ASP cc_start: 0.8146 (m-30) cc_final: 0.7811 (m-30) REVERT: E 58 ASP cc_start: 0.8163 (m-30) cc_final: 0.7777 (m-30) REVERT: H 46 ASP cc_start: 0.8503 (m-30) cc_final: 0.8255 (m-30) REVERT: H 194 MET cc_start: 0.9225 (mmp) cc_final: 0.8983 (mmp) REVERT: H 227 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8026 (mpp) REVERT: H 316 GLU cc_start: 0.8091 (tp30) cc_final: 0.7830 (tp30) REVERT: Q 249 MET cc_start: 0.8314 (pmm) cc_final: 0.7989 (pmm) REVERT: Q 250 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8287 (tp) REVERT: Z 44 MET cc_start: 0.8358 (ttm) cc_final: 0.8121 (mtt) REVERT: a 358 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: a 416 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: d 48 ILE cc_start: 0.8721 (pt) cc_final: 0.8493 (pp) REVERT: e 24 ARG cc_start: 0.8301 (mtp85) cc_final: 0.8049 (ttm-80) REVERT: g 47 MET cc_start: 0.8531 (mtm) cc_final: 0.8136 (ttm) REVERT: g 529 LYS cc_start: 0.8187 (ptmt) cc_final: 0.7931 (ptpp) REVERT: h 2 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6618 (tmm) REVERT: h 37 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7995 (ttp-110) REVERT: h 423 TYR cc_start: 0.9081 (t80) cc_final: 0.8810 (t80) REVERT: h 455 PHE cc_start: 0.8194 (m-10) cc_final: 0.7765 (m-10) REVERT: h 482 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7891 (mm-30) REVERT: q 322 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7783 (mtt180) REVERT: q 443 GLU cc_start: 0.8444 (tt0) cc_final: 0.8103 (tt0) REVERT: z 66 GLU cc_start: 0.7891 (mp0) cc_final: 0.7494 (mp0) REVERT: z 241 LYS cc_start: 0.8689 (tttp) cc_final: 0.8303 (tppp) REVERT: z 244 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8352 (t) REVERT: z 364 GLU cc_start: 0.7934 (mp0) cc_final: 0.7460 (mp0) REVERT: z 415 GLU cc_start: 0.8572 (mp0) cc_final: 0.8359 (mp0) REVERT: P 93 MET cc_start: 0.5758 (mmm) cc_final: 0.4772 (ppp) outliers start: 70 outliers final: 25 residues processed: 548 average time/residue: 1.4897 time to fit residues: 1075.7955 Evaluate side-chains 515 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 483 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 487 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 773 optimal weight: 4.9990 chunk 588 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 785 optimal weight: 6.9990 chunk 831 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 744 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN q 309 ASN ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 67596 Z= 0.494 Angle : 0.662 9.536 91263 Z= 0.329 Chirality : 0.046 0.188 10867 Planarity : 0.004 0.056 11652 Dihedral : 7.728 177.882 9386 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.58 % Allowed : 10.21 % Favored : 88.21 % 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: 1.27 (0.09), residues: 8639 helix: 2.14 (0.08), residues: 4495 sheet: -0.22 (0.16), residues: 1122 loop : -0.72 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 304 HIS 0.011 0.001 HIS a 201 PHE 0.023 0.002 PHE e 16 TYR 0.023 0.002 TYR z 351 ARG 0.008 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 490 time to evaluate : 5.914 Fit side-chains REVERT: N 267 ASP cc_start: 0.8546 (t70) cc_final: 0.8330 (t70) REVERT: A 47 ASP cc_start: 0.8145 (t0) cc_final: 0.7743 (t0) REVERT: B 37 ASP cc_start: 0.8225 (m-30) cc_final: 0.7859 (m-30) REVERT: B 248 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (ptpp) REVERT: E 58 ASP cc_start: 0.8157 (m-30) cc_final: 0.7796 (m-30) REVERT: E 523 MET cc_start: 0.8924 (tpp) cc_final: 0.8694 (mmt) REVERT: G 111 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7802 (t-90) REVERT: H 46 ASP cc_start: 0.8481 (m-30) cc_final: 0.8239 (m-30) REVERT: H 227 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8032 (mpp) REVERT: H 316 GLU cc_start: 0.8170 (tp30) cc_final: 0.7951 (tp30) REVERT: H 470 GLN cc_start: 0.8542 (pp30) cc_final: 0.8212 (pp30) REVERT: Q 249 MET cc_start: 0.8337 (pmm) cc_final: 0.7973 (pmm) REVERT: Q 250 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8391 (tp) REVERT: Z 10 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8908 (ptpt) REVERT: Z 44 MET cc_start: 0.8496 (ttm) cc_final: 0.8202 (mtt) REVERT: Z 53 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: a 416 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: b 445 MET cc_start: 0.8287 (tpp) cc_final: 0.8021 (tpp) REVERT: d 48 ILE cc_start: 0.8929 (pt) cc_final: 0.8606 (pp) REVERT: e 4 MET cc_start: 0.5303 (ttp) cc_final: 0.3841 (mmt) REVERT: g 47 MET cc_start: 0.8671 (mtm) cc_final: 0.8463 (mtm) REVERT: h 2 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: h 22 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8834 (tt) REVERT: h 37 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8027 (ttp-110) REVERT: h 423 TYR cc_start: 0.9096 (t80) cc_final: 0.8806 (t80) REVERT: h 482 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7770 (mm-30) REVERT: q 322 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7769 (mtm180) REVERT: q 443 GLU cc_start: 0.8486 (tt0) cc_final: 0.8145 (tt0) REVERT: z 66 GLU cc_start: 0.8035 (mp0) cc_final: 0.7585 (mp0) REVERT: z 241 LYS cc_start: 0.8674 (tttp) cc_final: 0.8288 (tppp) REVERT: z 244 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8411 (t) REVERT: z 364 GLU cc_start: 0.7984 (mp0) cc_final: 0.7462 (mp0) REVERT: P 93 MET cc_start: 0.5778 (mmm) cc_final: 0.4705 (pp-130) outliers start: 114 outliers final: 46 residues processed: 553 average time/residue: 1.4838 time to fit residues: 1074.8422 Evaluate side-chains 525 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 468 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 10 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 14 ASP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 692 optimal weight: 0.8980 chunk 471 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 618 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 709 optimal weight: 0.9980 chunk 574 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 chunk 746 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 67596 Z= 0.155 Angle : 0.539 9.285 91263 Z= 0.266 Chirality : 0.041 0.170 10867 Planarity : 0.003 0.056 11652 Dihedral : 7.319 165.908 9386 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.84 % Allowed : 11.85 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.09), residues: 8639 helix: 2.39 (0.08), residues: 4486 sheet: -0.08 (0.16), residues: 1075 loop : -0.61 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.005 0.001 HIS Z 161 PHE 0.016 0.001 PHE P 267 TYR 0.024 0.001 TYR z 351 ARG 0.008 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 548 time to evaluate : 5.823 Fit side-chains REVERT: N 267 ASP cc_start: 0.8507 (t70) cc_final: 0.8195 (t70) REVERT: A 47 ASP cc_start: 0.8038 (t0) cc_final: 0.7715 (t0) REVERT: A 425 ASN cc_start: 0.8207 (m-40) cc_final: 0.7902 (m-40) REVERT: B 37 ASP cc_start: 0.8056 (m-30) cc_final: 0.7705 (m-30) REVERT: D 93 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8069 (mp0) REVERT: E 58 ASP cc_start: 0.8112 (m-30) cc_final: 0.7768 (m-30) REVERT: E 185 MET cc_start: 0.9000 (mmp) cc_final: 0.8789 (mmp) REVERT: G 365 ASP cc_start: 0.8449 (t0) cc_final: 0.8136 (t0) REVERT: H 46 ASP cc_start: 0.8479 (m-30) cc_final: 0.8238 (m-30) REVERT: H 316 GLU cc_start: 0.8028 (tp30) cc_final: 0.7771 (tp30) REVERT: H 470 GLN cc_start: 0.8444 (pp30) cc_final: 0.8077 (pp30) REVERT: Q 249 MET cc_start: 0.8372 (pmm) cc_final: 0.7995 (pmm) REVERT: Q 250 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8523 (tp) REVERT: Q 311 MET cc_start: 0.8912 (ttt) cc_final: 0.8609 (ttt) REVERT: Z 10 LYS cc_start: 0.9355 (ptmt) cc_final: 0.8966 (ptpt) REVERT: a 416 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: b 17 ASP cc_start: 0.7099 (t0) cc_final: 0.6790 (t0) REVERT: b 445 MET cc_start: 0.7960 (tpp) cc_final: 0.7729 (tpp) REVERT: e 4 MET cc_start: 0.5174 (ttp) cc_final: 0.3711 (mmt) REVERT: e 24 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7933 (ttm-80) REVERT: g 47 MET cc_start: 0.8556 (mtm) cc_final: 0.8269 (ttm) REVERT: h 2 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.6598 (tmm) REVERT: h 22 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8637 (tt) REVERT: h 423 TYR cc_start: 0.9068 (t80) cc_final: 0.8801 (t80) REVERT: h 482 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8043 (mm-30) REVERT: q 322 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7730 (mtm180) REVERT: q 443 GLU cc_start: 0.8443 (tt0) cc_final: 0.8110 (tt0) REVERT: z 66 GLU cc_start: 0.8000 (mp0) cc_final: 0.7472 (mp0) REVERT: z 241 LYS cc_start: 0.8692 (tttp) cc_final: 0.8307 (tppp) REVERT: z 244 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8248 (t) REVERT: P 93 MET cc_start: 0.5751 (mmm) cc_final: 0.4734 (ppp) outliers start: 61 outliers final: 16 residues processed: 580 average time/residue: 1.4219 time to fit residues: 1093.1784 Evaluate side-chains 520 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 499 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 390 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 14 ASP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 279 optimal weight: 6.9990 chunk 748 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 488 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 832 optimal weight: 0.9980 chunk 690 optimal weight: 0.5980 chunk 385 optimal weight: 0.0870 chunk 69 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 436 optimal weight: 6.9990 overall best weight: 2.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN G 115 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 67596 Z= 0.277 Angle : 0.573 9.266 91263 Z= 0.281 Chirality : 0.042 0.183 10867 Planarity : 0.003 0.052 11652 Dihedral : 7.304 174.898 9386 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.09 % Allowed : 12.50 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.09), residues: 8639 helix: 2.38 (0.08), residues: 4498 sheet: -0.09 (0.16), residues: 1109 loop : -0.61 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.016 0.001 HIS Z 161 PHE 0.025 0.001 PHE P 267 TYR 0.021 0.001 TYR z 498 ARG 0.010 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 507 time to evaluate : 6.055 Fit side-chains REVERT: N 267 ASP cc_start: 0.8567 (t70) cc_final: 0.8292 (t70) REVERT: A 47 ASP cc_start: 0.8028 (t0) cc_final: 0.7684 (t0) REVERT: A 425 ASN cc_start: 0.8228 (m-40) cc_final: 0.7917 (m-40) REVERT: B 37 ASP cc_start: 0.8123 (m-30) cc_final: 0.7766 (m-30) REVERT: E 58 ASP cc_start: 0.8130 (m-30) cc_final: 0.7790 (m-30) REVERT: G 365 ASP cc_start: 0.8491 (t0) cc_final: 0.8191 (t0) REVERT: H 46 ASP cc_start: 0.8483 (m-30) cc_final: 0.8244 (m-30) REVERT: H 194 MET cc_start: 0.9199 (mmp) cc_final: 0.8869 (mmp) REVERT: H 227 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: H 316 GLU cc_start: 0.8053 (tp30) cc_final: 0.7812 (tp30) REVERT: H 470 GLN cc_start: 0.8488 (pp30) cc_final: 0.8097 (pp30) REVERT: Q 249 MET cc_start: 0.8363 (pmm) cc_final: 0.7989 (pmm) REVERT: Q 250 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8309 (tp) REVERT: Q 311 MET cc_start: 0.8975 (ttt) cc_final: 0.8659 (ttt) REVERT: Z 10 LYS cc_start: 0.9311 (ptmt) cc_final: 0.8918 (ptpt) REVERT: Z 44 MET cc_start: 0.8416 (ttm) cc_final: 0.8145 (mtt) REVERT: Z 53 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: a 416 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: b 17 ASP cc_start: 0.7207 (t0) cc_final: 0.6943 (t0) REVERT: b 445 MET cc_start: 0.8122 (tpp) cc_final: 0.7817 (tpp) REVERT: e 24 ARG cc_start: 0.8267 (mtp85) cc_final: 0.8062 (ttm-80) REVERT: g 47 MET cc_start: 0.8622 (mtm) cc_final: 0.8276 (ttm) REVERT: h 2 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.6655 (tmm) REVERT: h 22 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (tt) REVERT: h 423 TYR cc_start: 0.9082 (t80) cc_final: 0.8806 (t80) REVERT: h 482 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7817 (mm-30) REVERT: q 322 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7733 (mtm180) REVERT: q 443 GLU cc_start: 0.8475 (tt0) cc_final: 0.8140 (tt0) REVERT: z 66 GLU cc_start: 0.8004 (mp0) cc_final: 0.7510 (mp0) REVERT: z 241 LYS cc_start: 0.8698 (tttp) cc_final: 0.8293 (tppp) REVERT: z 244 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8349 (t) REVERT: z 364 GLU cc_start: 0.7868 (mp0) cc_final: 0.7419 (mp0) REVERT: P 93 MET cc_start: 0.5792 (mmm) cc_final: 0.4672 (pp-130) REVERT: P 158 PHE cc_start: 0.5802 (m-80) cc_final: 0.5578 (m-10) REVERT: P 240 LYS cc_start: 0.4966 (tptp) cc_final: 0.4707 (tptp) outliers start: 79 outliers final: 32 residues processed: 551 average time/residue: 1.4822 time to fit residues: 1076.6400 Evaluate side-chains 530 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 491 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 14 ASP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 347 CYS Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 802 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 474 optimal weight: 10.0000 chunk 607 optimal weight: 0.9980 chunk 470 optimal weight: 4.9990 chunk 700 optimal weight: 6.9990 chunk 464 optimal weight: 0.9990 chunk 828 optimal weight: 6.9990 chunk 518 optimal weight: 10.0000 chunk 505 optimal weight: 0.6980 chunk 382 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 GLN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 448 GLN h 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 67596 Z= 0.168 Angle : 0.546 10.424 91263 Z= 0.267 Chirality : 0.041 0.197 10867 Planarity : 0.003 0.051 11652 Dihedral : 7.187 179.544 9386 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.91 % Allowed : 13.19 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 8639 helix: 2.44 (0.08), residues: 4499 sheet: -0.08 (0.16), residues: 1086 loop : -0.56 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS Z 161 PHE 0.023 0.001 PHE P 267 TYR 0.023 0.001 TYR z 351 ARG 0.008 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 524 time to evaluate : 6.421 Fit side-chains REVERT: N 267 ASP cc_start: 0.8531 (t70) cc_final: 0.8227 (t70) REVERT: A 47 ASP cc_start: 0.8009 (t0) cc_final: 0.7671 (t0) REVERT: A 425 ASN cc_start: 0.8192 (m-40) cc_final: 0.7883 (m-40) REVERT: B 37 ASP cc_start: 0.8061 (m-30) cc_final: 0.7722 (m-30) REVERT: D 93 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8053 (mp0) REVERT: E 58 ASP cc_start: 0.8133 (m-30) cc_final: 0.7796 (m-30) REVERT: E 468 MET cc_start: 0.8631 (mtp) cc_final: 0.8430 (mtm) REVERT: G 144 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8675 (m) REVERT: G 365 ASP cc_start: 0.8469 (t0) cc_final: 0.8167 (t0) REVERT: H 46 ASP cc_start: 0.8484 (m-30) cc_final: 0.8252 (m-30) REVERT: H 227 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: H 316 GLU cc_start: 0.7999 (tp30) cc_final: 0.7769 (tp30) REVERT: H 470 GLN cc_start: 0.8461 (pp30) cc_final: 0.8057 (pp30) REVERT: Q 249 MET cc_start: 0.8368 (pmm) cc_final: 0.7939 (pmm) REVERT: Q 250 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8494 (tp) REVERT: Z 44 MET cc_start: 0.8347 (ttm) cc_final: 0.8081 (mtt) REVERT: Z 53 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: a 225 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8883 (mtm) REVERT: a 416 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: b 17 ASP cc_start: 0.7170 (t0) cc_final: 0.6878 (t0) REVERT: b 445 MET cc_start: 0.7994 (tpp) cc_final: 0.7700 (tpp) REVERT: e 4 MET cc_start: 0.5248 (ttp) cc_final: 0.3911 (mmt) REVERT: e 24 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8071 (ttm-80) REVERT: h 22 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8698 (tt) REVERT: h 423 TYR cc_start: 0.9073 (t80) cc_final: 0.8805 (t80) REVERT: h 455 PHE cc_start: 0.8134 (m-10) cc_final: 0.7840 (m-10) REVERT: h 482 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7746 (mm-30) REVERT: q 178 PHE cc_start: 0.8222 (t80) cc_final: 0.7993 (t80) REVERT: q 322 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7744 (mtm180) REVERT: q 443 GLU cc_start: 0.8446 (tt0) cc_final: 0.8110 (tt0) REVERT: z 66 GLU cc_start: 0.8027 (mp0) cc_final: 0.7520 (mp0) REVERT: z 86 ASP cc_start: 0.7986 (m-30) cc_final: 0.7672 (m-30) REVERT: z 241 LYS cc_start: 0.8703 (tttp) cc_final: 0.8310 (tppp) REVERT: z 244 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8267 (t) REVERT: z 364 GLU cc_start: 0.7882 (mp0) cc_final: 0.7366 (mp0) REVERT: P 93 MET cc_start: 0.5886 (mmm) cc_final: 0.4675 (pp-130) REVERT: P 158 PHE cc_start: 0.5785 (m-80) cc_final: 0.5570 (m-10) REVERT: P 240 LYS cc_start: 0.4887 (tptp) cc_final: 0.4624 (tptp) outliers start: 66 outliers final: 30 residues processed: 563 average time/residue: 1.4162 time to fit residues: 1057.0287 Evaluate side-chains 541 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 503 time to evaluate : 5.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 390 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 14 ASP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 512 optimal weight: 3.9990 chunk 331 optimal weight: 0.4980 chunk 495 optimal weight: 0.0060 chunk 249 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 526 optimal weight: 5.9990 chunk 564 optimal weight: 2.9990 chunk 409 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 651 optimal weight: 0.8980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN H 25 ASN Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 67596 Z= 0.158 Angle : 0.543 10.910 91263 Z= 0.264 Chirality : 0.041 0.188 10867 Planarity : 0.003 0.050 11652 Dihedral : 6.911 168.165 9386 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.77 % Allowed : 13.73 % Favored : 85.49 % 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: 8639 helix: 2.51 (0.08), residues: 4506 sheet: -0.05 (0.16), residues: 1084 loop : -0.53 (0.11), residues: 3049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 267 TYR 0.026 0.001 TYR D 24 ARG 0.011 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 549 time to evaluate : 5.827 Fit side-chains REVERT: N 267 ASP cc_start: 0.8548 (t70) cc_final: 0.8244 (t70) REVERT: A 47 ASP cc_start: 0.7999 (t0) cc_final: 0.7692 (OUTLIER) REVERT: A 425 ASN cc_start: 0.8109 (m-40) cc_final: 0.7799 (m-40) REVERT: B 37 ASP cc_start: 0.8035 (m-30) cc_final: 0.7753 (m-30) REVERT: B 384 ASP cc_start: 0.8281 (m-30) cc_final: 0.8019 (m-30) REVERT: D 93 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8056 (mp0) REVERT: D 524 GLU cc_start: 0.8205 (tt0) cc_final: 0.7962 (mt-10) REVERT: E 58 ASP cc_start: 0.8115 (m-30) cc_final: 0.7807 (m-30) REVERT: G 144 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8744 (m) REVERT: G 365 ASP cc_start: 0.8474 (t0) cc_final: 0.8163 (t0) REVERT: H 46 ASP cc_start: 0.8478 (m-30) cc_final: 0.8259 (m-30) REVERT: H 227 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: H 470 GLN cc_start: 0.8409 (pp30) cc_final: 0.8030 (pp30) REVERT: Q 249 MET cc_start: 0.8483 (pmm) cc_final: 0.8022 (pmm) REVERT: Q 250 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8378 (tp) REVERT: Q 296 LYS cc_start: 0.8813 (pttm) cc_final: 0.8566 (ptmt) REVERT: Q 311 MET cc_start: 0.8934 (ttt) cc_final: 0.8705 (ttt) REVERT: Z 44 MET cc_start: 0.8329 (ttm) cc_final: 0.8103 (mtt) REVERT: Z 53 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: a 225 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8902 (mtm) REVERT: a 416 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: b 17 ASP cc_start: 0.7231 (t0) cc_final: 0.6925 (t0) REVERT: b 445 MET cc_start: 0.7950 (tpp) cc_final: 0.7603 (tpp) REVERT: e 24 ARG cc_start: 0.8241 (mtp85) cc_final: 0.8039 (ttm-80) REVERT: g 47 MET cc_start: 0.8615 (mtm) cc_final: 0.8379 (ttm) REVERT: g 437 TYR cc_start: 0.8865 (t80) cc_final: 0.8500 (t80) REVERT: h 22 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8592 (tt) REVERT: h 423 TYR cc_start: 0.9062 (t80) cc_final: 0.8800 (t80) REVERT: h 455 PHE cc_start: 0.8115 (m-10) cc_final: 0.7686 (m-10) REVERT: h 482 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7829 (mm-30) REVERT: q 178 PHE cc_start: 0.8164 (t80) cc_final: 0.7940 (t80) REVERT: q 322 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7755 (mtm180) REVERT: q 443 GLU cc_start: 0.8444 (tt0) cc_final: 0.8109 (tt0) REVERT: z 86 ASP cc_start: 0.7993 (m-30) cc_final: 0.7704 (m-30) REVERT: z 241 LYS cc_start: 0.8719 (tttp) cc_final: 0.8317 (tppp) REVERT: z 244 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8203 (t) REVERT: P 93 MET cc_start: 0.5900 (mmm) cc_final: 0.4725 (pp-130) REVERT: P 158 PHE cc_start: 0.5772 (m-80) cc_final: 0.5572 (m-10) REVERT: P 198 MET cc_start: 0.7982 (ptt) cc_final: 0.7772 (ppp) REVERT: P 240 LYS cc_start: 0.4858 (tptp) cc_final: 0.4597 (tptp) outliers start: 56 outliers final: 28 residues processed: 576 average time/residue: 1.4302 time to fit residues: 1100.9296 Evaluate side-chains 551 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 516 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 390 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 444 ILE Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 754 optimal weight: 7.9990 chunk 794 optimal weight: 1.9990 chunk 724 optimal weight: 0.9980 chunk 772 optimal weight: 8.9990 chunk 793 optimal weight: 4.9990 chunk 464 optimal weight: 0.7980 chunk 336 optimal weight: 7.9990 chunk 606 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 698 optimal weight: 10.0000 chunk 730 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN a 534 HIS e 46 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 67596 Z= 0.278 Angle : 0.588 10.628 91263 Z= 0.287 Chirality : 0.042 0.262 10867 Planarity : 0.003 0.057 11652 Dihedral : 6.891 170.928 9386 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.82 % Allowed : 13.98 % Favored : 85.20 % 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: 8639 helix: 2.46 (0.08), residues: 4498 sheet: -0.09 (0.16), residues: 1126 loop : -0.56 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.017 0.001 HIS Z 161 PHE 0.031 0.001 PHE P 267 TYR 0.023 0.001 TYR z 351 ARG 0.013 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 510 time to evaluate : 5.892 Fit side-chains REVERT: N 267 ASP cc_start: 0.8561 (t70) cc_final: 0.8273 (t70) REVERT: A 47 ASP cc_start: 0.8056 (t0) cc_final: 0.7694 (t0) REVERT: A 425 ASN cc_start: 0.8165 (m-40) cc_final: 0.7862 (m-40) REVERT: B 37 ASP cc_start: 0.8081 (m-30) cc_final: 0.7763 (m-30) REVERT: D 93 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8049 (mp0) REVERT: E 58 ASP cc_start: 0.8122 (m-30) cc_final: 0.7807 (m-30) REVERT: G 144 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8691 (m) REVERT: G 229 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8573 (mtm) REVERT: G 365 ASP cc_start: 0.8487 (t0) cc_final: 0.8177 (t0) REVERT: H 46 ASP cc_start: 0.8482 (m-30) cc_final: 0.8255 (m-30) REVERT: H 227 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8359 (mtp) REVERT: H 470 GLN cc_start: 0.8409 (pp30) cc_final: 0.8004 (pp30) REVERT: Q 249 MET cc_start: 0.8448 (pmm) cc_final: 0.8067 (pmm) REVERT: Q 250 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8360 (tp) REVERT: Q 296 LYS cc_start: 0.8858 (pttm) cc_final: 0.8599 (ptmt) REVERT: Q 311 MET cc_start: 0.8950 (ttt) cc_final: 0.8665 (ttt) REVERT: Z 44 MET cc_start: 0.8407 (ttm) cc_final: 0.8142 (mtt) REVERT: Z 46 MET cc_start: 0.9249 (ttm) cc_final: 0.8933 (ttm) REVERT: Z 53 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: Z 161 HIS cc_start: 0.6394 (t-170) cc_final: 0.6127 (t70) REVERT: a 225 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8945 (mtm) REVERT: a 416 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: b 17 ASP cc_start: 0.7291 (t0) cc_final: 0.6988 (t0) REVERT: b 445 MET cc_start: 0.8144 (tpp) cc_final: 0.7843 (tpp) REVERT: e 24 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8058 (ttm-80) REVERT: g 416 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8669 (mmm) REVERT: h 2 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7368 (tmm) REVERT: h 22 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (tt) REVERT: h 423 TYR cc_start: 0.9082 (t80) cc_final: 0.8808 (t80) REVERT: q 55 MET cc_start: 0.8627 (mtm) cc_final: 0.8103 (mtm) REVERT: q 322 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7754 (mtm180) REVERT: q 443 GLU cc_start: 0.8479 (tt0) cc_final: 0.8145 (tt0) REVERT: z 86 ASP cc_start: 0.8072 (m-30) cc_final: 0.7774 (m-30) REVERT: z 241 LYS cc_start: 0.8715 (tttp) cc_final: 0.8317 (tppp) REVERT: z 244 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8314 (t) REVERT: P 93 MET cc_start: 0.5901 (mmm) cc_final: 0.4735 (pp-130) REVERT: P 158 PHE cc_start: 0.5881 (m-80) cc_final: 0.5645 (m-10) REVERT: P 198 MET cc_start: 0.7980 (ptt) cc_final: 0.7775 (ppp) REVERT: P 240 LYS cc_start: 0.4879 (tptp) cc_final: 0.4615 (tptp) outliers start: 59 outliers final: 30 residues processed: 544 average time/residue: 1.4730 time to fit residues: 1062.7164 Evaluate side-chains 539 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 498 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 10 ASP Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 416 MET Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 769 optimal weight: 0.6980 chunk 507 optimal weight: 0.0980 chunk 816 optimal weight: 10.0000 chunk 498 optimal weight: 5.9990 chunk 387 optimal weight: 0.7980 chunk 567 optimal weight: 6.9990 chunk 856 optimal weight: 0.0010 chunk 788 optimal weight: 7.9990 chunk 682 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 526 optimal weight: 0.2980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN z 65 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 67596 Z= 0.139 Angle : 0.555 12.336 91263 Z= 0.270 Chirality : 0.041 0.226 10867 Planarity : 0.003 0.053 11652 Dihedral : 6.549 163.704 9386 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.46 % Allowed : 14.48 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.09), residues: 8639 helix: 2.53 (0.08), residues: 4505 sheet: -0.01 (0.16), residues: 1080 loop : -0.50 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 496 HIS 0.017 0.001 HIS Z 161 PHE 0.023 0.001 PHE P 69 TYR 0.031 0.001 TYR Z 498 ARG 0.014 0.000 ARG h 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 561 time to evaluate : 5.850 Fit side-chains REVERT: N 267 ASP cc_start: 0.8592 (t70) cc_final: 0.8309 (t70) REVERT: A 425 ASN cc_start: 0.8091 (m-40) cc_final: 0.7776 (m-40) REVERT: B 37 ASP cc_start: 0.8023 (m-30) cc_final: 0.7739 (m-30) REVERT: D 93 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8084 (mp0) REVERT: D 524 GLU cc_start: 0.8224 (tt0) cc_final: 0.7943 (mt-10) REVERT: E 58 ASP cc_start: 0.8108 (m-30) cc_final: 0.7811 (m-30) REVERT: E 457 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8932 (p) REVERT: E 468 MET cc_start: 0.8900 (mtm) cc_final: 0.8681 (mpp) REVERT: G 365 ASP cc_start: 0.8433 (t0) cc_final: 0.8122 (t0) REVERT: H 46 ASP cc_start: 0.8491 (m-30) cc_final: 0.8287 (m-30) REVERT: H 470 GLN cc_start: 0.8329 (pp30) cc_final: 0.7927 (pp30) REVERT: Q 249 MET cc_start: 0.8437 (pmm) cc_final: 0.7982 (pmm) REVERT: Q 250 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8403 (tp) REVERT: Q 296 LYS cc_start: 0.8833 (pttm) cc_final: 0.8566 (ptmt) REVERT: Q 311 MET cc_start: 0.8927 (ttt) cc_final: 0.8689 (ttt) REVERT: Z 44 MET cc_start: 0.8304 (ttm) cc_final: 0.8097 (mtt) REVERT: Z 53 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: Z 351 TYR cc_start: 0.9200 (p90) cc_final: 0.8965 (p90) REVERT: Z 498 TYR cc_start: 0.8135 (t80) cc_final: 0.7910 (t80) REVERT: a 225 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: a 416 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: b 17 ASP cc_start: 0.7214 (t0) cc_final: 0.6920 (t0) REVERT: b 445 MET cc_start: 0.7914 (tpp) cc_final: 0.7593 (tpp) REVERT: g 437 TYR cc_start: 0.8800 (t80) cc_final: 0.8524 (t80) REVERT: h 22 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8545 (tt) REVERT: h 423 TYR cc_start: 0.9038 (t80) cc_final: 0.8735 (t80) REVERT: q 178 PHE cc_start: 0.8160 (t80) cc_final: 0.7909 (t80) REVERT: q 322 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7752 (mtm180) REVERT: q 443 GLU cc_start: 0.8391 (tt0) cc_final: 0.8058 (tt0) REVERT: z 86 ASP cc_start: 0.7979 (m-30) cc_final: 0.7682 (m-30) REVERT: z 241 LYS cc_start: 0.8694 (tttp) cc_final: 0.8282 (tppp) REVERT: z 244 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8167 (t) REVERT: P 93 MET cc_start: 0.5898 (mmm) cc_final: 0.4645 (pp-130) REVERT: P 158 PHE cc_start: 0.5794 (m-80) cc_final: 0.5528 (m-10) outliers start: 33 outliers final: 18 residues processed: 580 average time/residue: 1.4419 time to fit residues: 1115.0724 Evaluate side-chains 546 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 521 time to evaluate : 5.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 416 GLU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 275 VAL Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 63 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 418 optimal weight: 9.9990 chunk 541 optimal weight: 9.9990 chunk 726 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 629 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 683 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 701 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 25 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.066008 restraints weight = 144653.626| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.68 r_work: 0.2711 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 67596 Z= 0.310 Angle : 0.610 12.190 91263 Z= 0.298 Chirality : 0.043 0.212 10867 Planarity : 0.003 0.057 11652 Dihedral : 6.639 170.380 9386 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.62 % Allowed : 14.66 % Favored : 84.72 % 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: 1.65 (0.09), residues: 8639 helix: 2.46 (0.08), residues: 4498 sheet: -0.08 (0.16), residues: 1132 loop : -0.56 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP h 474 HIS 0.008 0.001 HIS P 186 PHE 0.019 0.002 PHE a 167 TYR 0.031 0.001 TYR Z 498 ARG 0.013 0.000 ARG h 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18088.11 seconds wall clock time: 313 minutes 1.01 seconds (18781.01 seconds total)