Starting phenix.real_space_refine on Tue Jan 21 07:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_40452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_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/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_40452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_40452.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_40452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg8_40452/01_2025/8sg8_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): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 33.47, per 1000 atoms: 0.50 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: 13.55 Conformation dependent library (CDL) restraints added in 7.0 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: 7.28 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: 33.78 Time building geometry restraints manager: 15.89 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.930 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 131.100 Find NCS groups from input model: 5.750 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.060 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 6.045 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: 1.4546 time to fit residues: 1169.5402 Evaluate side-chains 494 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 5.965 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.083249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.069985 restraints weight = 149052.588| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.62 r_work: 0.2747 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 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 to be fit. rotamer outliers: 56 poor density : 522 time to evaluate : 5.902 Fit side-chains REVERT: B 37 ASP cc_start: 0.8757 (m-30) cc_final: 0.8486 (m-30) REVERT: E 58 ASP cc_start: 0.8785 (m-30) cc_final: 0.8452 (m-30) REVERT: H 46 ASP cc_start: 0.8935 (m-30) cc_final: 0.8729 (m-30) REVERT: H 227 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8324 (mpp) REVERT: Q 249 MET cc_start: 0.8618 (pmm) cc_final: 0.8165 (pmm) REVERT: Q 250 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8188 (tp) REVERT: Z 53 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: a 416 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: e 4 MET cc_start: 0.5138 (ttp) cc_final: 0.3679 (mmt) REVERT: e 24 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8304 (ttm-80) REVERT: g 54 MET cc_start: 0.9074 (mpp) cc_final: 0.8661 (mpp) REVERT: h 2 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6437 (tmm) REVERT: h 423 TYR cc_start: 0.9249 (t80) cc_final: 0.8929 (t80) REVERT: q 322 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8418 (mtm180) REVERT: q 443 GLU cc_start: 0.9117 (tt0) cc_final: 0.8802 (tt0) REVERT: z 66 GLU cc_start: 0.8416 (mp0) cc_final: 0.8023 (mp0) REVERT: z 241 LYS cc_start: 0.8944 (tttp) cc_final: 0.8388 (tppp) REVERT: z 364 GLU cc_start: 0.8348 (mp0) cc_final: 0.7840 (mp0) REVERT: P 93 MET cc_start: 0.5697 (mmm) cc_final: 0.4672 (ppp) outliers start: 56 outliers final: 19 residues processed: 541 average time/residue: 1.4519 time to fit residues: 1034.8753 Evaluate side-chains 513 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 489 time to evaluate : 5.934 ------------------------------------------------------------------------------- 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 321 optimal weight: 10.0000 chunk 430 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 554 optimal weight: 7.9990 chunk 572 optimal weight: 6.9990 chunk 672 optimal weight: 9.9990 chunk 694 optimal weight: 6.9990 chunk 395 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 272 optimal weight: 0.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- 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 Z 386 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069281 restraints weight = 180632.025| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.89 r_work: 0.2723 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0944 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= 0.261 Angle : 0.560 8.166 91263 Z= 0.277 Chirality : 0.042 0.160 10867 Planarity : 0.003 0.054 11652 Dihedral : 7.600 174.948 9386 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.98 % Allowed : 8.65 % Favored : 90.37 % 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: 4485 sheet: -0.03 (0.16), residues: 1111 loop : -0.58 (0.11), residues: 3043 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 592 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 521 time to evaluate : 6.114 Fit side-chains REVERT: N 267 ASP cc_start: 0.8392 (t70) cc_final: 0.8060 (t70) REVERT: B 37 ASP cc_start: 0.8594 (m-30) cc_final: 0.8267 (m-30) REVERT: E 58 ASP cc_start: 0.8584 (m-30) cc_final: 0.8251 (m-30) REVERT: H 46 ASP cc_start: 0.8798 (m-30) cc_final: 0.8573 (m-30) REVERT: H 227 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8274 (mpp) REVERT: H 316 GLU cc_start: 0.8451 (tp30) cc_final: 0.8140 (tp30) REVERT: Q 249 MET cc_start: 0.8524 (pmm) cc_final: 0.8070 (pmm) REVERT: Q 250 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8221 (tp) REVERT: Q 344 MET cc_start: 0.8754 (ttp) cc_final: 0.8487 (ttp) REVERT: Z 17 GLN cc_start: 0.8852 (mt0) cc_final: 0.8595 (mp10) REVERT: a 358 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: a 416 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: d 48 ILE cc_start: 0.8815 (pt) cc_final: 0.8599 (pp) REVERT: d 331 GLU cc_start: 0.8945 (pm20) cc_final: 0.8699 (pm20) REVERT: e 24 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8315 (ttm-80) REVERT: g 47 MET cc_start: 0.9040 (mtm) cc_final: 0.8707 (ttm) REVERT: g 270 MET cc_start: 0.9009 (mtt) cc_final: 0.8808 (mmm) REVERT: g 529 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7895 (ptpp) REVERT: h 2 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.6471 (tmm) REVERT: h 37 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8307 (ttp-110) REVERT: h 185 MET cc_start: 0.9171 (mtt) cc_final: 0.8970 (mtp) REVERT: h 423 TYR cc_start: 0.9191 (t80) cc_final: 0.8911 (t80) REVERT: h 455 PHE cc_start: 0.8257 (m-10) cc_final: 0.7876 (m-10) REVERT: h 482 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8166 (mm-30) REVERT: q 443 GLU cc_start: 0.8974 (tt0) cc_final: 0.8643 (tt0) REVERT: z 66 GLU cc_start: 0.8280 (mp0) cc_final: 0.7853 (mp0) REVERT: z 221 MET cc_start: 0.8559 (mmt) cc_final: 0.8268 (mmt) REVERT: z 241 LYS cc_start: 0.8861 (tttp) cc_final: 0.8348 (tppp) REVERT: z 244 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8434 (t) REVERT: z 364 GLU cc_start: 0.8213 (mp0) cc_final: 0.7674 (mp0) REVERT: z 415 GLU cc_start: 0.9002 (mp0) cc_final: 0.8761 (mp0) REVERT: P 93 MET cc_start: 0.5752 (mmm) cc_final: 0.4734 (ppp) outliers start: 71 outliers final: 25 residues processed: 550 average time/residue: 1.4772 time to fit residues: 1068.1490 Evaluate side-chains 516 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 484 time to evaluate : 5.967 ------------------------------------------------------------------------------- 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 67 optimal weight: 6.9990 chunk 655 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 629 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 328 optimal weight: 8.9990 chunk 545 optimal weight: 0.8980 chunk 688 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** z 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070775 restraints weight = 142157.400| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.55 r_work: 0.2764 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 67596 Z= 0.197 Angle : 0.538 8.528 91263 Z= 0.265 Chirality : 0.041 0.166 10867 Planarity : 0.003 0.057 11652 Dihedral : 7.404 171.747 9386 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.11 % Allowed : 10.22 % Favored : 88.67 % 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: 1.64 (0.09), residues: 8639 helix: 2.44 (0.08), residues: 4489 sheet: -0.02 (0.16), residues: 1119 loop : -0.56 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP q 319 HIS 0.006 0.001 HIS a 201 PHE 0.015 0.001 PHE e 386 TYR 0.021 0.001 TYR z 351 ARG 0.007 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 615 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 535 time to evaluate : 6.915 Fit side-chains REVERT: N 267 ASP cc_start: 0.8474 (t70) cc_final: 0.8102 (t70) REVERT: A 47 ASP cc_start: 0.8584 (t0) cc_final: 0.8220 (OUTLIER) REVERT: A 425 ASN cc_start: 0.8466 (m-40) cc_final: 0.8161 (m-40) REVERT: B 37 ASP cc_start: 0.8725 (m-30) cc_final: 0.8451 (m-30) REVERT: E 58 ASP cc_start: 0.8730 (m-30) cc_final: 0.8430 (m-30) REVERT: G 365 ASP cc_start: 0.9007 (t0) cc_final: 0.8636 (t0) REVERT: H 46 ASP cc_start: 0.8924 (m-30) cc_final: 0.8702 (m-30) REVERT: H 227 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: H 316 GLU cc_start: 0.8563 (tp30) cc_final: 0.8222 (tp30) REVERT: Q 17 GLU cc_start: 0.8260 (pm20) cc_final: 0.7957 (mp0) REVERT: Q 249 MET cc_start: 0.8627 (pmm) cc_final: 0.8107 (pmm) REVERT: Q 250 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8250 (tp) REVERT: Q 492 MET cc_start: 0.8608 (mmm) cc_final: 0.8282 (mtm) REVERT: Z 10 LYS cc_start: 0.9371 (ptmt) cc_final: 0.8998 (ptpt) REVERT: Z 17 GLN cc_start: 0.8934 (mt0) cc_final: 0.8641 (mp10) REVERT: Z 53 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: a 416 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: d 331 GLU cc_start: 0.9107 (pm20) cc_final: 0.8832 (pm20) REVERT: e 24 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8295 (ttm-80) REVERT: g 47 MET cc_start: 0.9157 (mtm) cc_final: 0.8851 (ttm) REVERT: h 2 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.6508 (tmm) REVERT: h 22 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8896 (tt) REVERT: h 423 TYR cc_start: 0.9242 (t80) cc_final: 0.8964 (t80) REVERT: h 455 PHE cc_start: 0.8306 (m-10) cc_final: 0.7999 (m-10) REVERT: h 482 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8233 (mm-30) REVERT: q 443 GLU cc_start: 0.9105 (tt0) cc_final: 0.8793 (tt0) REVERT: z 66 GLU cc_start: 0.8433 (mp0) cc_final: 0.7924 (mp0) REVERT: z 241 LYS cc_start: 0.8928 (tttp) cc_final: 0.8391 (tppp) REVERT: z 244 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8491 (t) REVERT: z 364 GLU cc_start: 0.8286 (mp0) cc_final: 0.7829 (mp0) REVERT: P 93 MET cc_start: 0.5823 (mmm) cc_final: 0.4778 (ppp) REVERT: P 240 LYS cc_start: 0.5023 (tptp) cc_final: 0.4728 (tptp) outliers start: 80 outliers final: 27 residues processed: 574 average time/residue: 1.4639 time to fit residues: 1106.6616 Evaluate side-chains 532 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 499 time to evaluate : 5.904 ------------------------------------------------------------------------------- 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 G residue 11 SER 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 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 g residue 8 LEU Chi-restraints excluded: chain g residue 194 ASP 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 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 63 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 532 optimal weight: 4.9990 chunk 620 optimal weight: 4.9990 chunk 853 optimal weight: 20.0000 chunk 448 optimal weight: 3.9990 chunk 411 optimal weight: 10.0000 chunk 564 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 447 optimal weight: 7.9990 chunk 458 optimal weight: 5.9990 chunk 770 optimal weight: 8.9990 chunk 614 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 115 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN P 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.068229 restraints weight = 161364.683| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.71 r_work: 0.2713 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 67596 Z= 0.338 Angle : 0.588 8.641 91263 Z= 0.290 Chirality : 0.043 0.158 10867 Planarity : 0.003 0.054 11652 Dihedral : 7.443 174.781 9386 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.26 % Allowed : 11.23 % Favored : 87.51 % 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: 1.51 (0.09), residues: 8639 helix: 2.34 (0.08), residues: 4499 sheet: -0.11 (0.16), residues: 1133 loop : -0.62 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.008 0.001 HIS a 201 PHE 0.018 0.002 PHE a 167 TYR 0.022 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 596 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 505 time to evaluate : 5.973 Fit side-chains REVERT: N 267 ASP cc_start: 0.8438 (t70) cc_final: 0.8120 (t70) REVERT: A 47 ASP cc_start: 0.8474 (t0) cc_final: 0.8099 (OUTLIER) REVERT: A 425 ASN cc_start: 0.8360 (m-40) cc_final: 0.8053 (m-40) REVERT: B 37 ASP cc_start: 0.8579 (m-30) cc_final: 0.8262 (m-30) REVERT: E 58 ASP cc_start: 0.8571 (m-30) cc_final: 0.8267 (m-30) REVERT: E 185 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8709 (mmp) REVERT: G 111 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7994 (t-90) REVERT: G 365 ASP cc_start: 0.8926 (t0) cc_final: 0.8565 (t0) REVERT: H 46 ASP cc_start: 0.8786 (m-30) cc_final: 0.8556 (m-30) REVERT: H 227 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8237 (mpp) REVERT: H 316 GLU cc_start: 0.8432 (tp30) cc_final: 0.8133 (tp30) REVERT: H 470 GLN cc_start: 0.8695 (pp30) cc_final: 0.8315 (pp30) REVERT: Q 159 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: Q 249 MET cc_start: 0.8536 (pmm) cc_final: 0.8022 (pmm) REVERT: Q 250 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8269 (tp) REVERT: Q 344 MET cc_start: 0.8766 (ttp) cc_final: 0.8496 (ttp) REVERT: Z 10 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9096 (ptmt) REVERT: Z 17 GLN cc_start: 0.8865 (mt0) cc_final: 0.8616 (mp10) REVERT: Z 53 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: a 416 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: b 18 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8532 (pp20) REVERT: d 331 GLU cc_start: 0.8933 (pm20) cc_final: 0.8626 (pm20) REVERT: e 4 MET cc_start: 0.5242 (ttp) cc_final: 0.3739 (mmt) REVERT: g 47 MET cc_start: 0.9095 (mtm) cc_final: 0.8797 (ttm) REVERT: h 2 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6652 (tmm) REVERT: h 22 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8902 (tt) REVERT: h 37 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8287 (ttp-110) REVERT: h 423 TYR cc_start: 0.9185 (t80) cc_final: 0.8900 (t80) REVERT: h 455 PHE cc_start: 0.8293 (m-10) cc_final: 0.7958 (m-10) REVERT: h 482 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8070 (mm-30) REVERT: q 443 GLU cc_start: 0.8988 (tt0) cc_final: 0.8652 (tt0) REVERT: z 66 GLU cc_start: 0.8350 (mp0) cc_final: 0.7934 (mp0) REVERT: z 244 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8406 (t) REVERT: z 364 GLU cc_start: 0.8187 (mp0) cc_final: 0.7957 (mp0) REVERT: P 93 MET cc_start: 0.5747 (mmm) cc_final: 0.4733 (ppp) REVERT: P 240 LYS cc_start: 0.5014 (tptp) cc_final: 0.4738 (tptp) outliers start: 91 outliers final: 42 residues processed: 551 average time/residue: 1.4653 time to fit residues: 1062.0894 Evaluate side-chains 534 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 481 time to evaluate : 5.974 ------------------------------------------------------------------------------- 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 371 CYS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain G residue 480 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 227 MET Chi-restraints excluded: chain Q residue 159 GLU 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 Z residue 404 ASP Chi-restraints excluded: chain a residue 10 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 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 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 194 ASP 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 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 53 ILE 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 6 optimal weight: 5.9990 chunk 663 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 424 optimal weight: 10.0000 chunk 841 optimal weight: 8.9990 chunk 779 optimal weight: 0.7980 chunk 836 optimal weight: 6.9990 chunk 636 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 773 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN P 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068300 restraints weight = 181460.132| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.90 r_work: 0.2704 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 67596 Z= 0.288 Angle : 0.573 8.949 91263 Z= 0.282 Chirality : 0.042 0.162 10867 Planarity : 0.003 0.052 11652 Dihedral : 7.388 175.954 9386 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 11.95 % Favored : 86.72 % 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: 1.50 (0.09), residues: 8639 helix: 2.34 (0.08), residues: 4497 sheet: -0.11 (0.15), residues: 1131 loop : -0.64 (0.11), residues: 3011 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 0.018 0.001 PHE P 267 TYR 0.023 0.001 TYR z 351 ARG 0.009 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 603 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 507 time to evaluate : 6.025 Fit side-chains REVERT: N 267 ASP cc_start: 0.8402 (t70) cc_final: 0.8069 (t70) REVERT: A 47 ASP cc_start: 0.8496 (t0) cc_final: 0.8113 (t0) REVERT: A 425 ASN cc_start: 0.8360 (m-40) cc_final: 0.8059 (m-40) REVERT: B 37 ASP cc_start: 0.8586 (m-30) cc_final: 0.8247 (m-30) REVERT: B 495 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: E 58 ASP cc_start: 0.8553 (m-30) cc_final: 0.8236 (m-30) REVERT: E 476 GLU cc_start: 0.8700 (tp30) cc_final: 0.8479 (tp30) REVERT: G 365 ASP cc_start: 0.8895 (t0) cc_final: 0.8541 (t0) REVERT: H 46 ASP cc_start: 0.8763 (m-30) cc_final: 0.8531 (m-30) REVERT: H 227 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8253 (mpp) REVERT: H 316 GLU cc_start: 0.8421 (tp30) cc_final: 0.8126 (tp30) REVERT: H 470 GLN cc_start: 0.8730 (pp30) cc_final: 0.8319 (pp30) REVERT: Q 17 GLU cc_start: 0.8065 (pm20) cc_final: 0.7809 (mp0) REVERT: Q 159 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: Q 249 MET cc_start: 0.8601 (pmm) cc_final: 0.8080 (pmm) REVERT: Q 250 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8238 (tp) REVERT: Q 311 MET cc_start: 0.9311 (ttt) cc_final: 0.9054 (ttt) REVERT: Z 10 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8991 (ptpt) REVERT: Z 17 GLN cc_start: 0.8852 (mt0) cc_final: 0.8590 (mp10) REVERT: Z 53 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: a 416 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: b 17 ASP cc_start: 0.7620 (t0) cc_final: 0.7284 (t0) REVERT: b 18 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8489 (pp20) REVERT: b 485 ILE cc_start: 0.9047 (pp) cc_final: 0.8800 (mp) REVERT: d 331 GLU cc_start: 0.8960 (pm20) cc_final: 0.8727 (pm20) REVERT: e 4 MET cc_start: 0.5090 (ttp) cc_final: 0.3653 (mmt) REVERT: e 24 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8359 (ttm-80) REVERT: g 47 MET cc_start: 0.9122 (mtm) cc_final: 0.8902 (mtm) REVERT: h 2 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.6563 (tmm) REVERT: h 423 TYR cc_start: 0.9185 (t80) cc_final: 0.8900 (t80) REVERT: h 455 PHE cc_start: 0.8293 (m-10) cc_final: 0.7897 (m-10) REVERT: h 482 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8154 (mm-30) REVERT: h 524 ARG cc_start: 0.7871 (tmt170) cc_final: 0.7652 (tmt-80) REVERT: q 117 GLU cc_start: 0.8554 (tp30) cc_final: 0.8323 (tp30) REVERT: q 443 GLU cc_start: 0.9004 (tt0) cc_final: 0.8666 (tt0) REVERT: z 66 GLU cc_start: 0.8422 (mp0) cc_final: 0.7921 (mp0) REVERT: z 241 LYS cc_start: 0.8868 (tttp) cc_final: 0.8350 (tppp) REVERT: z 244 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8442 (t) REVERT: z 364 GLU cc_start: 0.8156 (mp0) cc_final: 0.7901 (mp0) REVERT: P 93 MET cc_start: 0.5816 (mmm) cc_final: 0.4766 (ppp) REVERT: P 158 PHE cc_start: 0.5760 (m-80) cc_final: 0.5490 (m-10) REVERT: P 240 LYS cc_start: 0.5058 (tptp) cc_final: 0.4779 (tptp) outliers start: 96 outliers final: 49 residues processed: 567 average time/residue: 1.4341 time to fit residues: 1078.4152 Evaluate side-chains 547 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 489 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 272 GLN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 MET 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 B residue 495 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 83 ILE 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 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 159 GLU 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 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 d residue 377 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 312 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 685 optimal weight: 0.7980 chunk 447 optimal weight: 8.9990 chunk 812 optimal weight: 1.9990 chunk 844 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 477 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** a 217 ASN a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 448 GLN h 501 ASN P 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068434 restraints weight = 144162.559| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.70 r_work: 0.2768 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 67596 Z= 0.145 Angle : 0.536 10.725 91263 Z= 0.262 Chirality : 0.041 0.179 10867 Planarity : 0.003 0.050 11652 Dihedral : 7.126 175.075 9386 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.91 % Allowed : 12.82 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8639 helix: 2.47 (0.08), residues: 4505 sheet: -0.04 (0.16), residues: 1093 loop : -0.54 (0.11), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 319 HIS 0.005 0.001 HIS a 201 PHE 0.024 0.001 PHE P 267 TYR 0.024 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 618 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 552 time to evaluate : 6.015 Fit side-chains REVERT: N 267 ASP cc_start: 0.8394 (t70) cc_final: 0.7992 (t70) REVERT: A 47 ASP cc_start: 0.8595 (t0) cc_final: 0.8241 (OUTLIER) REVERT: A 425 ASN cc_start: 0.8355 (m-40) cc_final: 0.8038 (m-40) REVERT: B 37 ASP cc_start: 0.8663 (m-30) cc_final: 0.8353 (m-30) REVERT: D 93 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8832 (mp0) REVERT: E 58 ASP cc_start: 0.8673 (m-30) cc_final: 0.8418 (m-30) REVERT: G 365 ASP cc_start: 0.8933 (t0) cc_final: 0.8540 (t0) REVERT: H 316 GLU cc_start: 0.8483 (tp30) cc_final: 0.8215 (tp30) REVERT: H 470 GLN cc_start: 0.8731 (pp30) cc_final: 0.8302 (pp30) REVERT: Q 249 MET cc_start: 0.8646 (pmm) cc_final: 0.8016 (pmm) REVERT: Q 250 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8367 (tp) REVERT: Q 311 MET cc_start: 0.9391 (ttt) cc_final: 0.9158 (ttt) REVERT: Q 344 MET cc_start: 0.8825 (ttp) cc_final: 0.8516 (ttp) REVERT: Z 10 LYS cc_start: 0.9337 (ptmt) cc_final: 0.8954 (ptpt) REVERT: Z 17 GLN cc_start: 0.8965 (mt0) cc_final: 0.8636 (mp10) REVERT: Z 53 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: a 416 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: b 18 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8491 (pp20) REVERT: b 456 TYR cc_start: 0.9087 (m-10) cc_final: 0.8847 (m-80) REVERT: d 120 CYS cc_start: 0.9422 (m) cc_final: 0.9148 (m) REVERT: d 331 GLU cc_start: 0.9072 (pm20) cc_final: 0.8793 (pm20) REVERT: e 4 MET cc_start: 0.5040 (ttp) cc_final: 0.3665 (mmt) REVERT: e 24 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8390 (ttm-80) REVERT: g 47 MET cc_start: 0.9199 (mtm) cc_final: 0.8985 (ttm) REVERT: g 437 TYR cc_start: 0.9111 (t80) cc_final: 0.8701 (t80) REVERT: h 423 TYR cc_start: 0.9255 (t80) cc_final: 0.8976 (t80) REVERT: h 482 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8185 (mm-30) REVERT: q 117 GLU cc_start: 0.8659 (tp30) cc_final: 0.8413 (tp30) REVERT: q 178 PHE cc_start: 0.8266 (t80) cc_final: 0.8040 (t80) REVERT: q 322 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8579 (mtm-85) REVERT: q 443 GLU cc_start: 0.9189 (tt0) cc_final: 0.8873 (tt0) REVERT: z 58 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8736 (ttpp) REVERT: z 241 LYS cc_start: 0.8917 (tttp) cc_final: 0.8343 (tppp) REVERT: z 244 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8367 (t) REVERT: z 351 TYR cc_start: 0.9213 (p90) cc_final: 0.8992 (p90) REVERT: z 364 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: P 93 MET cc_start: 0.5866 (mmm) cc_final: 0.4632 (pp-130) REVERT: P 240 LYS cc_start: 0.5010 (tptp) cc_final: 0.4733 (tptp) outliers start: 66 outliers final: 22 residues processed: 585 average time/residue: 1.4166 time to fit residues: 1102.2013 Evaluate side-chains 532 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 505 time to evaluate : 5.900 ------------------------------------------------------------------------------- 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 G residue 9 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 1 MET 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 Z residue 163 GLU Chi-restraints excluded: chain Z residue 246 SER 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 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 211 VAL Chi-restraints excluded: chain z residue 58 LYS 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 364 GLU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 26 optimal weight: 0.0050 chunk 484 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 598 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 653 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 518 optimal weight: 10.0000 chunk 701 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS P 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.068031 restraints weight = 171037.836| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.97 r_work: 0.2752 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1331 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= 0.158 Angle : 0.543 10.378 91263 Z= 0.263 Chirality : 0.041 0.174 10867 Planarity : 0.003 0.051 11652 Dihedral : 6.917 167.950 9386 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.70 % Allowed : 13.62 % Favored : 85.67 % 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: 1.73 (0.09), residues: 8639 helix: 2.51 (0.08), residues: 4505 sheet: -0.01 (0.16), residues: 1100 loop : -0.51 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 319 HIS 0.005 0.001 HIS a 201 PHE 0.031 0.001 PHE P 267 TYR 0.021 0.001 TYR z 351 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 594 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 543 time to evaluate : 6.128 Fit side-chains REVERT: N 267 ASP cc_start: 0.8427 (t70) cc_final: 0.8067 (t70) REVERT: A 47 ASP cc_start: 0.8442 (t0) cc_final: 0.8108 (OUTLIER) REVERT: A 425 ASN cc_start: 0.8230 (m-40) cc_final: 0.7899 (m-40) REVERT: B 37 ASP cc_start: 0.8500 (m-30) cc_final: 0.8216 (m-30) REVERT: D 93 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8581 (mp0) REVERT: D 524 GLU cc_start: 0.8765 (tt0) cc_final: 0.8462 (mt-10) REVERT: E 58 ASP cc_start: 0.8526 (m-30) cc_final: 0.8250 (m-30) REVERT: G 144 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8835 (m) REVERT: G 365 ASP cc_start: 0.8853 (t0) cc_final: 0.8457 (t0) REVERT: H 17 GLN cc_start: 0.8668 (pt0) cc_final: 0.8450 (pt0) REVERT: H 227 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: H 316 GLU cc_start: 0.8361 (tp30) cc_final: 0.8085 (tp30) REVERT: H 470 GLN cc_start: 0.8642 (pp30) cc_final: 0.8240 (pp30) REVERT: Q 249 MET cc_start: 0.8573 (pmm) cc_final: 0.7984 (pmm) REVERT: Q 250 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8360 (tp) REVERT: Q 311 MET cc_start: 0.9304 (ttt) cc_final: 0.9073 (ttt) REVERT: Q 344 MET cc_start: 0.8619 (ttp) cc_final: 0.8346 (ttp) REVERT: Z 17 GLN cc_start: 0.8852 (mt0) cc_final: 0.8565 (mp10) REVERT: Z 46 MET cc_start: 0.9451 (ttm) cc_final: 0.9194 (ttm) REVERT: Z 53 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: a 416 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: b 445 MET cc_start: 0.8149 (tpp) cc_final: 0.7943 (tpp) REVERT: d 120 CYS cc_start: 0.9255 (m) cc_final: 0.8983 (m) REVERT: d 331 GLU cc_start: 0.8928 (pm20) cc_final: 0.8672 (pm20) REVERT: e 24 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8362 (ttm-80) REVERT: g 47 MET cc_start: 0.9118 (mtm) cc_final: 0.8842 (ttm) REVERT: g 437 TYR cc_start: 0.8956 (t80) cc_final: 0.8547 (t80) REVERT: h 423 TYR cc_start: 0.9181 (t80) cc_final: 0.8901 (t80) REVERT: h 455 PHE cc_start: 0.8214 (m-10) cc_final: 0.7919 (m-10) REVERT: h 482 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8148 (mm-30) REVERT: q 178 PHE cc_start: 0.8179 (t80) cc_final: 0.7936 (t80) REVERT: q 322 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8303 (mtm180) REVERT: q 443 GLU cc_start: 0.9038 (tt0) cc_final: 0.8694 (tt0) REVERT: z 241 LYS cc_start: 0.8870 (tttp) cc_final: 0.8304 (tppp) REVERT: z 244 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8241 (t) REVERT: z 364 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: P 93 MET cc_start: 0.5829 (mmm) cc_final: 0.4608 (pp-130) REVERT: P 158 PHE cc_start: 0.5785 (m-80) cc_final: 0.5479 (m-10) REVERT: P 198 MET cc_start: 0.8058 (ptt) cc_final: 0.7848 (ppp) outliers start: 51 outliers final: 30 residues processed: 570 average time/residue: 1.4509 time to fit residues: 1099.6890 Evaluate side-chains 555 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 519 time to evaluate : 6.038 ------------------------------------------------------------------------------- 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 398 ILE 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 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 137 VAL Chi-restraints excluded: chain Z residue 163 GLU Chi-restraints excluded: chain Z residue 463 LEU 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 b residue 390 LEU 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 h residue 211 VAL Chi-restraints excluded: chain h residue 444 ILE 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 190 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 364 GLU 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 105 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 750 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 802 optimal weight: 6.9990 chunk 207 optimal weight: 0.0970 chunk 259 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 overall best weight: 3.2984 ------------------------------------------------------------------------------- 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** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 501 ASN q 309 ASN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.065873 restraints weight = 143530.888| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.67 r_work: 0.2708 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 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 = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 67596 Z= 0.304 Angle : 0.596 11.226 91263 Z= 0.291 Chirality : 0.043 0.178 10867 Planarity : 0.003 0.052 11652 Dihedral : 6.930 171.013 9386 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.75 % Allowed : 13.91 % Favored : 85.34 % 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: 4502 sheet: -0.08 (0.16), residues: 1124 loop : -0.57 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 319 HIS 0.007 0.001 HIS a 201 PHE 0.026 0.002 PHE P 267 TYR 0.029 0.001 TYR Z 498 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 558 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 504 time to evaluate : 6.206 Fit side-chains REVERT: N 267 ASP cc_start: 0.8438 (t70) cc_final: 0.8097 (t70) REVERT: A 47 ASP cc_start: 0.8674 (t0) cc_final: 0.8268 (t0) REVERT: A 425 ASN cc_start: 0.8394 (m-40) cc_final: 0.8090 (m-40) REVERT: B 37 ASP cc_start: 0.8734 (m-30) cc_final: 0.8439 (m-30) REVERT: D 93 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8780 (mp0) REVERT: E 58 ASP cc_start: 0.8724 (m-30) cc_final: 0.8455 (m-30) REVERT: G 144 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8825 (m) REVERT: G 365 ASP cc_start: 0.9021 (t0) cc_final: 0.8654 (t0) REVERT: H 17 GLN cc_start: 0.8794 (pt0) cc_final: 0.8552 (pt0) REVERT: H 227 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: H 316 GLU cc_start: 0.8600 (tp30) cc_final: 0.8294 (tp30) REVERT: H 470 GLN cc_start: 0.8727 (pp30) cc_final: 0.8306 (pp30) REVERT: Q 249 MET cc_start: 0.8664 (pmm) cc_final: 0.8100 (pmm) REVERT: Q 250 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8141 (tp) REVERT: Q 311 MET cc_start: 0.9396 (ttt) cc_final: 0.9145 (ttt) REVERT: Q 344 MET cc_start: 0.8887 (ttp) cc_final: 0.8531 (ttp) REVERT: Z 17 GLN cc_start: 0.9012 (mt0) cc_final: 0.8667 (mp10) REVERT: Z 46 MET cc_start: 0.9504 (ttm) cc_final: 0.9174 (ttm) REVERT: Z 53 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: a 416 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: b 17 ASP cc_start: 0.7866 (t0) cc_final: 0.7537 (t0) REVERT: b 242 THR cc_start: 0.9241 (p) cc_final: 0.9038 (p) REVERT: b 445 MET cc_start: 0.8568 (tpp) cc_final: 0.8255 (tpp) REVERT: d 331 GLU cc_start: 0.9102 (pm20) cc_final: 0.8828 (pm20) REVERT: e 4 MET cc_start: 0.5043 (ttp) cc_final: 0.3588 (mmt) REVERT: e 24 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8412 (ttm-80) REVERT: h 2 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7187 (tmm) REVERT: h 423 TYR cc_start: 0.9249 (t80) cc_final: 0.8957 (t80) REVERT: h 455 PHE cc_start: 0.8362 (m-10) cc_final: 0.8142 (m-10) REVERT: h 482 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8240 (mm-30) REVERT: q 55 MET cc_start: 0.9061 (mtm) cc_final: 0.8615 (mtm) REVERT: q 117 GLU cc_start: 0.8623 (tp30) cc_final: 0.8168 (tm-30) REVERT: q 322 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8409 (mtm180) REVERT: q 443 GLU cc_start: 0.9219 (tt0) cc_final: 0.8896 (tt0) REVERT: z 241 LYS cc_start: 0.8926 (tttp) cc_final: 0.8335 (tppp) REVERT: z 244 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8419 (t) REVERT: z 364 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: z 522 MET cc_start: 0.9093 (ttm) cc_final: 0.8846 (ttp) REVERT: z 526 MET cc_start: 0.7635 (pmm) cc_final: 0.7283 (pmm) REVERT: P 93 MET cc_start: 0.5836 (mmm) cc_final: 0.4599 (pp-130) REVERT: P 158 PHE cc_start: 0.5968 (m-80) cc_final: 0.5630 (m-10) REVERT: P 198 MET cc_start: 0.8092 (ptt) cc_final: 0.7822 (ppp) outliers start: 54 outliers final: 29 residues processed: 534 average time/residue: 1.5253 time to fit residues: 1077.0487 Evaluate side-chains 535 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 498 time to evaluate : 5.972 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 519 ILE 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 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 10 ASP 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 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 h residue 2 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 65 VAL 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 364 GLU 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 489 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 605 optimal weight: 3.9990 chunk 640 optimal weight: 2.9990 chunk 858 optimal weight: 1.9990 chunk 589 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 774 optimal weight: 2.9990 chunk 485 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 720 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.066533 restraints weight = 145051.726| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.69 r_work: 0.2721 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 67596 Z= 0.236 Angle : 0.579 12.070 91263 Z= 0.281 Chirality : 0.042 0.171 10867 Planarity : 0.003 0.056 11652 Dihedral : 6.813 168.234 9386 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.65 % Allowed : 14.15 % 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: 1.62 (0.09), residues: 8639 helix: 2.43 (0.08), residues: 4497 sheet: -0.08 (0.16), residues: 1116 loop : -0.56 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 319 HIS 0.006 0.001 HIS a 201 PHE 0.017 0.001 PHE P 69 TYR 0.026 0.001 TYR z 351 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 553 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 506 time to evaluate : 6.044 Fit side-chains REVERT: N 267 ASP cc_start: 0.8401 (t70) cc_final: 0.8079 (t70) REVERT: A 47 ASP cc_start: 0.8507 (t0) cc_final: 0.8100 (t0) REVERT: A 425 ASN cc_start: 0.8293 (m-40) cc_final: 0.7970 (m-40) REVERT: B 37 ASP cc_start: 0.8526 (m-30) cc_final: 0.8210 (m-30) REVERT: D 67 ASP cc_start: 0.8016 (m-30) cc_final: 0.7771 (t0) REVERT: D 93 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8530 (mp0) REVERT: E 58 ASP cc_start: 0.8511 (m-30) cc_final: 0.8227 (m-30) REVERT: G 144 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8786 (m) REVERT: G 365 ASP cc_start: 0.8862 (t0) cc_final: 0.8494 (t0) REVERT: H 17 GLN cc_start: 0.8662 (pt0) cc_final: 0.8449 (pt0) REVERT: H 184 MET cc_start: 0.8336 (mtm) cc_final: 0.8044 (mmm) REVERT: H 227 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8648 (mtp) REVERT: H 316 GLU cc_start: 0.8373 (tp30) cc_final: 0.8084 (tp30) REVERT: H 470 GLN cc_start: 0.8622 (pp30) cc_final: 0.8185 (pp30) REVERT: Q 17 GLU cc_start: 0.8102 (pm20) cc_final: 0.7438 (mt-10) REVERT: Q 249 MET cc_start: 0.8588 (pmm) cc_final: 0.8018 (pmm) REVERT: Q 250 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8237 (tp) REVERT: Q 311 MET cc_start: 0.9263 (ttt) cc_final: 0.8988 (ttt) REVERT: Z 17 GLN cc_start: 0.8892 (mt0) cc_final: 0.8596 (mp10) REVERT: Z 46 MET cc_start: 0.9434 (ttm) cc_final: 0.9071 (ttm) REVERT: Z 53 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: a 416 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: b 17 ASP cc_start: 0.7676 (t0) cc_final: 0.7333 (t0) REVERT: b 242 THR cc_start: 0.9187 (p) cc_final: 0.8983 (p) REVERT: b 445 MET cc_start: 0.8425 (tpp) cc_final: 0.8099 (tpp) REVERT: d 331 GLU cc_start: 0.8915 (pm20) cc_final: 0.8658 (pm20) REVERT: e 24 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8366 (ttm-80) REVERT: h 2 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: h 423 TYR cc_start: 0.9173 (t80) cc_final: 0.8881 (t80) REVERT: h 455 PHE cc_start: 0.8249 (m-10) cc_final: 0.7989 (m-10) REVERT: h 482 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8077 (mm-30) REVERT: q 55 MET cc_start: 0.8932 (mtm) cc_final: 0.8423 (mtm) REVERT: q 117 GLU cc_start: 0.8492 (tp30) cc_final: 0.8090 (tm-30) REVERT: q 322 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8261 (mtm180) REVERT: q 443 GLU cc_start: 0.9033 (tt0) cc_final: 0.8690 (tt0) REVERT: z 241 LYS cc_start: 0.8847 (tttp) cc_final: 0.8282 (tppp) REVERT: z 244 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8335 (t) REVERT: z 364 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: z 526 MET cc_start: 0.7643 (pmm) cc_final: 0.7160 (pmm) REVERT: P 93 MET cc_start: 0.5850 (mmm) cc_final: 0.4628 (pp-130) REVERT: P 158 PHE cc_start: 0.5858 (m-80) cc_final: 0.5529 (m-10) REVERT: P 198 MET cc_start: 0.8073 (ptt) cc_final: 0.7845 (ppp) outliers start: 47 outliers final: 32 residues processed: 534 average time/residue: 1.4626 time to fit residues: 1033.0027 Evaluate side-chains 538 residues out of total 7238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 498 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 ILE 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 G residue 144 VAL Chi-restraints excluded: chain G residue 519 ILE 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 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 163 GLU Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 10 ASP 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 h residue 2 MET Chi-restraints excluded: chain h residue 211 VAL 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 364 GLU 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 490 optimal weight: 0.9990 chunk 611 optimal weight: 0.6980 chunk 714 optimal weight: 4.9990 chunk 733 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 458 optimal weight: 7.9990 chunk 90 optimal weight: 0.0980 chunk 640 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 597 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.067954 restraints weight = 153950.872| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.80 r_work: 0.2756 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 67596 Z= 0.172 Angle : 0.560 12.353 91263 Z= 0.271 Chirality : 0.041 0.176 10867 Planarity : 0.003 0.054 11652 Dihedral : 6.581 166.460 9386 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.54 % Allowed : 14.37 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8639 helix: 2.50 (0.08), residues: 4502 sheet: -0.05 (0.16), residues: 1116 loop : -0.52 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP q 319 HIS 0.005 0.001 HIS a 201 PHE 0.019 0.001 PHE q 178 TYR 0.031 0.001 TYR Z 498 ARG 0.014 0.000 ARG h 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32218.54 seconds wall clock time: 555 minutes 10.73 seconds (33310.73 seconds total)