Starting phenix.real_space_refine on Sun Mar 24 09:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oop_17025/03_2024/8oop_17025_updated.pdb" } resolution = 2.7 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= 0.013 sd= 0.324 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 1 5.89 5 P 234 5.49 5 Mg 2 5.21 5 S 160 5.16 5 C 24886 2.51 5 N 7340 2.21 5 O 8120 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40747 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5736 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 670} Chain breaks: 2 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4472 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 601} Chain breaks: 5 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 807 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 32, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 415 Chain: "K" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2243 Classifications: {'DNA': 110} Link IDs: {'rna3p': 109} Chain: "L" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2201 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.35, per 1000 atoms: 0.50 Number of scatterers: 40747 At special positions: 0 Unit cell: (134.808, 180.018, 192.348, 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 160 16.00 P 234 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 8120 8.00 N 7340 7.00 C 24886 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.83 Conformation dependent library (CDL) restraints added in 7.4 seconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 207 helices and 32 sheets defined 45.3% alpha, 13.1% beta 61 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 17.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 58 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.667A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.494A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.085A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.653A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.050A pdb=" N GLU A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.564A pdb=" N ILE B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.662A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.669A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.580A pdb=" N HIS B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.759A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.561A pdb=" N ILE C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.546A pdb=" N GLN C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 184 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 274 through 290 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.847A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.751A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 389 through 401 Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.066A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix removed outlier: 3.692A pdb=" N ASN C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.973A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.837A pdb=" N GLU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.729A pdb=" N SER D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.179A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 347 through 352 removed outlier: 4.293A pdb=" N ARG D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.870A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 435 through 445 Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 83 through 97 removed outlier: 6.299A pdb=" N GLN E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.607A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 208 through 213 removed outlier: 5.705A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 Processing helix chain 'E' and resid 255 through 261 removed outlier: 4.226A pdb=" N SER E 261 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 305 through 316 removed outlier: 4.180A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 347 through 352 removed outlier: 4.805A pdb=" N ARG E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 376 Processing helix chain 'E' and resid 383 through 396 Processing helix chain 'E' and resid 398 through 414 removed outlier: 4.081A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 105 through 108 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.791A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 183 Processing helix chain 'F' and resid 208 through 213 removed outlier: 4.376A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 255 through 261 removed outlier: 3.513A pdb=" N LEU F 259 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.818A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 347 through 352 removed outlier: 4.279A pdb=" N ARG F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 376 Processing helix chain 'F' and resid 383 through 396 Processing helix chain 'F' and resid 398 through 415 removed outlier: 4.121A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 435 through 445 Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 974 through 988 removed outlier: 3.729A pdb=" N GLY G 979 " --> pdb=" O TYR G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 1003 through 1018 removed outlier: 3.543A pdb=" N ILE G1008 " --> pdb=" O THR G1004 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET G1011 " --> pdb=" O SER G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1030 through 1043 removed outlier: 3.611A pdb=" N LEU G1033 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N HIS G1034 " --> pdb=" O SER G1031 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN G1037 " --> pdb=" O HIS G1034 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL G1040 " --> pdb=" O GLN G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1065 removed outlier: 3.859A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1088 through 1091 No H-bonds generated for 'chain 'G' and resid 1088 through 1091' Processing helix chain 'G' and resid 1093 through 1096 No H-bonds generated for 'chain 'G' and resid 1093 through 1096' Processing helix chain 'G' and resid 1109 through 1112 Processing helix chain 'G' and resid 1118 through 1125 removed outlier: 3.674A pdb=" N LEU G1123 " --> pdb=" O ARG G1119 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1144 through 1153 removed outlier: 4.480A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1193 removed outlier: 4.152A pdb=" N HIS G1191 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1224 through 1239 removed outlier: 3.517A pdb=" N SER G1232 " --> pdb=" O ALA G1228 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1269 removed outlier: 4.979A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G1267 " --> pdb=" O GLN G1263 " (cutoff:3.500A) Processing helix chain 'G' and resid 1271 through 1274 No H-bonds generated for 'chain 'G' and resid 1271 through 1274' Processing helix chain 'G' and resid 1295 through 1297 No H-bonds generated for 'chain 'G' and resid 1295 through 1297' Processing helix chain 'G' and resid 1317 through 1320 No H-bonds generated for 'chain 'G' and resid 1317 through 1320' Processing helix chain 'G' and resid 1334 through 1344 removed outlier: 4.217A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1357 removed outlier: 3.758A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1366 through 1370 removed outlier: 3.735A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1375 through 1383 removed outlier: 3.516A pdb=" N HIS G1383 " --> pdb=" O TYR G1379 " (cutoff:3.500A) Processing helix chain 'G' and resid 1386 through 1395 removed outlier: 3.766A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1399 through 1406 removed outlier: 3.692A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1410 through 1412 No H-bonds generated for 'chain 'G' and resid 1410 through 1412' Processing helix chain 'G' and resid 1418 through 1420 No H-bonds generated for 'chain 'G' and resid 1418 through 1420' Processing helix chain 'G' and resid 1424 through 1427 No H-bonds generated for 'chain 'G' and resid 1424 through 1427' Processing helix chain 'G' and resid 1430 through 1434 Processing helix chain 'G' and resid 1441 through 1455 removed outlier: 5.874A pdb=" N ALA G1449 " --> pdb=" O LEU G1445 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG G1450 " --> pdb=" O MET G1446 " (cutoff:3.500A) Processing helix chain 'G' and resid 1481 through 1491 Processing helix chain 'G' and resid 1494 through 1501 Processing helix chain 'G' and resid 1505 through 1513 Processing helix chain 'G' and resid 1545 through 1550 Processing helix chain 'G' and resid 1553 through 1568 Processing helix chain 'G' and resid 1579 through 1590 Processing helix chain 'G' and resid 1605 through 1617 Processing helix chain 'G' and resid 1628 through 1631 No H-bonds generated for 'chain 'G' and resid 1628 through 1631' Processing helix chain 'G' and resid 1652 through 1662 removed outlier: 3.893A pdb=" N ALA G1662 " --> pdb=" O ALA G1658 " (cutoff:3.500A) Processing helix chain 'G' and resid 1682 through 1699 Processing helix chain 'H' and resid 469 through 474 removed outlier: 4.037A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 20 Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 191 through 199 Processing helix chain 'I' and resid 204 through 211 Processing helix chain 'J' and resid 18 through 21 No H-bonds generated for 'chain 'J' and resid 18 through 21' Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 227 No H-bonds generated for 'chain 'J' and resid 225 through 227' Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 removed outlier: 3.708A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 290 through 293 No H-bonds generated for 'chain 'J' and resid 290 through 293' Processing helix chain 'J' and resid 312 through 357 Processing helix chain 'J' and resid 362 through 371 Processing helix chain 'J' and resid 377 through 393 removed outlier: 4.165A pdb=" N ARG J 393 " --> pdb=" O ARG J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 468 Processing helix chain 'J' and resid 470 through 498 removed outlier: 4.204A pdb=" N LEU J 494 " --> pdb=" O GLU J 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP J 497 " --> pdb=" O ARG J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 588 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 598 through 602 Processing helix chain 'J' and resid 604 through 606 No H-bonds generated for 'chain 'J' and resid 604 through 606' Processing helix chain 'J' and resid 609 through 614 Processing helix chain 'J' and resid 633 through 638 removed outlier: 3.883A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 646 through 650 Processing helix chain 'J' and resid 657 through 666 Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.517A pdb=" N ASP J 685 " --> pdb=" O ALA J 681 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 693 No H-bonds generated for 'chain 'J' and resid 691 through 693' Processing helix chain 'J' and resid 698 through 707 Processing helix chain 'J' and resid 726 through 735 removed outlier: 3.607A pdb=" N GLY J 731 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 744 Processing helix chain 'J' and resid 748 through 754 Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.296A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 113 removed outlier: 3.612A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'N' and resid 25 through 28 Processing helix chain 'N' and resid 31 through 40 Processing helix chain 'N' and resid 50 through 74 removed outlier: 3.626A pdb=" N ARG N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 Processing helix chain 'O' and resid 17 through 21 Processing helix chain 'O' and resid 27 through 36 Processing helix chain 'O' and resid 47 through 72 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 35 through 45 removed outlier: 3.843A pdb=" N GLN P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 80 Processing helix chain 'P' and resid 88 through 98 Processing helix chain 'P' and resid 101 through 118 Processing helix chain 'Q' and resid 45 through 54 removed outlier: 3.548A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 76 Processing helix chain 'Q' and resid 86 through 113 removed outlier: 3.583A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 131 Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 50 through 75 removed outlier: 3.542A pdb=" N VAL R 60 " --> pdb=" O GLY R 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 93 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.947A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 330 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 297 Processing sheet with id= C, first strand: chain 'A' and resid 168 through 174 removed outlier: 3.765A pdb=" N GLU A 138 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS A 163 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL A 136 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 190 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= E, first strand: chain 'B' and resid 359 through 364 removed outlier: 6.932A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 364 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 70 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY B 71 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 332 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 293 through 297 Processing sheet with id= G, first strand: chain 'B' and resid 167 through 173 removed outlier: 3.629A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 138 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS B 163 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL B 136 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.707A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 359 through 364 removed outlier: 6.896A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 328 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 69 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 330 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY C 71 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C 332 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 293 through 297 Processing sheet with id= K, first strand: chain 'C' and resid 167 through 173 removed outlier: 3.550A pdb=" N THR C 157 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 195 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS C 201 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 336 through 338 Processing sheet with id= M, first strand: chain 'D' and resid 353 through 357 removed outlier: 6.736A pdb=" N ALA D 72 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE D 356 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 74 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET D 325 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 288 through 292 Processing sheet with id= O, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.536A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 205 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP D 195 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE D 201 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 331 through 333 Processing sheet with id= Q, first strand: chain 'E' and resid 353 through 358 removed outlier: 6.846A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR E 358 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA E 76 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY E 77 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER E 327 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 289 through 292 Processing sheet with id= S, first strand: chain 'E' and resid 167 through 173 removed outlier: 3.626A pdb=" N MET E 167 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY E 158 " --> pdb=" O MET E 173 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 157 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP E 190 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER E 193 " --> pdb=" O LYS E 203 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS E 203 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP E 195 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE E 201 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 331 through 333 Processing sheet with id= U, first strand: chain 'F' and resid 353 through 357 removed outlier: 6.652A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL F 323 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE F 75 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F 325 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 288 through 292 Processing sheet with id= W, first strand: chain 'F' and resid 168 through 173 removed outlier: 3.641A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN F 157 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS F 163 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL F 142 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP F 190 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER F 193 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS F 203 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP F 195 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 201 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= Y, first strand: chain 'G' and resid 993 through 995 removed outlier: 3.757A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1214 through 1217 Processing sheet with id= AA, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.262A pdb=" N GLU G1475 " --> pdb=" O TYR G1313 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'H' and resid 449 through 453 Processing sheet with id= AC, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.546A pdb=" N ILE J 296 " --> pdb=" O TYR J 28 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 185 through 189 removed outlier: 6.763A pdb=" N ILE J 156 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY J 188 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET J 158 " --> pdb=" O GLY J 188 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE J 59 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR J 159 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE J 61 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 115 through 117 Processing sheet with id= AF, first strand: chain 'J' and resid 213 through 218 1553 hydrogen bonds defined for protein. 4494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 300 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 22.70 Time building geometry restraints manager: 20.11 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: 12427 1.34 - 1.46: 6695 1.46 - 1.57: 22013 1.57 - 1.69: 460 1.69 - 1.81: 279 Bond restraints: 41874 Sorted by residual: bond pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" F4 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.686 1.776 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.770 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.523 1.578 -0.055 2.00e-02 2.50e+03 7.64e+00 ... (remaining 41869 not shown) Histogram of bond angle deviations from ideal: 89.49 - 107.54: 3120 107.54 - 125.59: 53317 125.59 - 143.64: 1116 143.64 - 161.69: 0 161.69 - 179.74: 2 Bond angle restraints: 57555 Sorted by residual: angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F2 ALF G2003 " ideal model delta sigma weight residual 108.68 179.71 -71.03 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.63 179.74 -70.11 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 110.21 89.49 20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.69 89.50 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.59 90.27 19.32 3.00e+00 1.11e-01 4.15e+01 ... (remaining 57550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 23664 35.30 - 70.59: 1203 70.59 - 105.89: 64 105.89 - 141.18: 5 141.18 - 176.48: 5 Dihedral angle restraints: 24941 sinusoidal: 11482 harmonic: 13459 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 123.52 176.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 126.85 173.14 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 139.58 160.41 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 24938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4927 0.061 - 0.122: 1412 0.122 - 0.182: 201 0.182 - 0.243: 15 0.243 - 0.304: 1 Chirality restraints: 6556 Sorted by residual: chirality pdb=" CB ILE O 79 " pdb=" CA ILE O 79 " pdb=" CG1 ILE O 79 " pdb=" CG2 ILE O 79 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU G1626 " pdb=" CB LEU G1626 " pdb=" CD1 LEU G1626 " pdb=" CD2 LEU G1626 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE F 356 " pdb=" N ILE F 356 " pdb=" C ILE F 356 " pdb=" CB ILE F 356 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 6553 not shown) Planarity restraints: 6657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G1086 " 0.003 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR G1086 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR G1086 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR G1086 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G1086 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR G1086 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G1086 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR G1086 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.382 9.50e-02 1.11e+02 1.72e-01 2.27e+01 pdb=" NE ARG F 437 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -25 " 0.053 2.00e-02 2.50e+03 3.11e-02 2.18e+01 pdb=" N1 DC L -25 " -0.075 2.00e-02 2.50e+03 pdb=" C2 DC L -25 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC L -25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC L -25 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC L -25 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC L -25 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DC L -25 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC L -25 " -0.002 2.00e-02 2.50e+03 ... (remaining 6654 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 12 2.40 - 3.03: 23311 3.03 - 3.65: 62255 3.65 - 4.28: 101388 4.28 - 4.90: 161075 Nonbonded interactions: 348041 Sorted by model distance: nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.775 2.170 nonbonded pdb="MG MG G2002 " pdb=" F3 ALF G2003 " model vdw 1.877 2.120 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 1.997 2.170 nonbonded pdb=" O2B ADP G2001 " pdb="MG MG G2002 " model vdw 2.018 2.170 nonbonded pdb=" N2 DG K -68 " pdb=" O2 DT L 69 " model vdw 2.193 2.520 ... (remaining 348036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 462 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 462 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 460 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 460 or resid 501)) selection = (chain 'F' and (resid 20 through 460 or resid 501)) } ncs_group { reference = (chain 'N' and resid 23 through 93) selection = (chain 'R' and resid 23 through 93) } 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: 3.400 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: 0.030 Extract box with map and model: 11.960 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 125.950 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.230 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 41874 Z= 0.333 Angle : 1.065 71.033 57555 Z= 0.561 Chirality : 0.055 0.304 6556 Planarity : 0.011 0.172 6657 Dihedral : 18.299 176.478 16259 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -1.11 (0.11), residues: 4623 helix: -1.31 (0.09), residues: 2169 sheet: 0.49 (0.20), residues: 617 loop : -0.14 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP G1650 HIS 0.012 0.002 HIS B 242 PHE 0.049 0.003 PHE G1047 TYR 0.053 0.006 TYR G1086 ARG 0.038 0.004 ARG F 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7787 (mtm) cc_final: 0.7556 (mmp) REVERT: B 133 GLU cc_start: 0.8112 (tt0) cc_final: 0.7835 (tp30) REVERT: B 250 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.6944 (tmt90) REVERT: B 421 ASN cc_start: 0.7254 (m-40) cc_final: 0.6978 (m-40) REVERT: C 394 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7804 (ttt-90) REVERT: C 458 HIS cc_start: 0.7634 (m-70) cc_final: 0.7389 (m-70) REVERT: E 217 MET cc_start: 0.8478 (mmm) cc_final: 0.8274 (mmm) REVERT: F 263 ASP cc_start: 0.7940 (t70) cc_final: 0.7691 (t0) REVERT: G 1099 MET cc_start: 0.7799 (tpt) cc_final: 0.7508 (tpt) REVERT: G 1145 GLU cc_start: 0.6855 (tt0) cc_final: 0.6604 (mm-30) REVERT: G 1258 MET cc_start: 0.4807 (mmm) cc_final: 0.2897 (tpt) REVERT: G 1262 MET cc_start: 0.6363 (tpp) cc_final: 0.6039 (tpt) REVERT: J 19 TRP cc_start: 0.8958 (p90) cc_final: 0.8446 (p90) REVERT: J 174 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7776 (mt-10) REVERT: M 106 ASP cc_start: 0.7492 (m-30) cc_final: 0.7208 (m-30) REVERT: M 129 ARG cc_start: 0.7585 (tpt-90) cc_final: 0.7148 (tpt90) REVERT: N 25 ASN cc_start: 0.6830 (m-40) cc_final: 0.6371 (m-40) REVERT: N 31 LYS cc_start: 0.7873 (mttt) cc_final: 0.7650 (mttp) REVERT: N 93 GLN cc_start: 0.6398 (mt0) cc_final: 0.6004 (mm-40) REVERT: O 38 ASN cc_start: 0.8247 (t0) cc_final: 0.8036 (t0) REVERT: O 74 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7544 (mmtt) REVERT: O 94 ASN cc_start: 0.7859 (t0) cc_final: 0.7604 (t0) REVERT: O 99 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.6888 (mtp85) REVERT: P 40 LYS cc_start: 0.7785 (mttt) cc_final: 0.7099 (mmtt) REVERT: P 54 LYS cc_start: 0.7396 (ttmt) cc_final: 0.7151 (mtmm) REVERT: P 59 MET cc_start: 0.8089 (mmm) cc_final: 0.7700 (mmm) REVERT: P 65 ASP cc_start: 0.8145 (t70) cc_final: 0.7721 (t0) REVERT: Q 68 GLN cc_start: 0.7529 (mt0) cc_final: 0.7317 (mt0) REVERT: R 53 GLU cc_start: 0.8305 (tp30) cc_final: 0.7903 (tp30) REVERT: R 77 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7963 (mttm) REVERT: R 95 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7126 (mtp85) outliers start: 0 outliers final: 1 residues processed: 810 average time/residue: 1.9518 time to fit residues: 1846.0583 Evaluate side-chains 457 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 112 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 376 optimal weight: 50.0000 chunk 145 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 280 optimal weight: 0.6980 chunk 435 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 146 ASN A 168 GLN A 248 ASN A 421 ASN B 19 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 230 HIS C 421 ASN C 425 GLN D 24 HIS D 328 ASN D 359 HIS E 24 HIS E 225 GLN F 452 ASN G1034 HIS ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN G1345 HIS G1657 GLN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN J 628 HIS J 633 ASN J 654 GLN J 667 GLN J 696 GLN N 93 GLN O 110 ASN P 44 GLN P 60 ASN P 81 ASN Q 125 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 41874 Z= 0.219 Angle : 0.687 30.641 57555 Z= 0.349 Chirality : 0.043 0.182 6556 Planarity : 0.004 0.057 6657 Dihedral : 20.799 162.497 7571 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.15 % Allowed : 9.30 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.48 (0.12), residues: 4623 helix: 0.50 (0.11), residues: 2200 sheet: 0.60 (0.20), residues: 605 loop : 0.20 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G1021 HIS 0.009 0.001 HIS G1345 PHE 0.022 0.002 PHE G1264 TYR 0.023 0.002 TYR A 193 ARG 0.011 0.001 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 524 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.6130 (tm-30) cc_final: 0.5752 (tm-30) REVERT: A 263 GLN cc_start: 0.8277 (mt0) cc_final: 0.8065 (mt0) REVERT: A 265 MET cc_start: 0.7705 (mtm) cc_final: 0.7430 (mmt) REVERT: A 381 GLN cc_start: 0.8362 (tt0) cc_final: 0.8004 (tm-30) REVERT: B 60 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7849 (m90) REVERT: B 133 GLU cc_start: 0.8087 (tt0) cc_final: 0.7802 (tp30) REVERT: B 250 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.6985 (tmt90) REVERT: B 423 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7286 (mpp80) REVERT: C 6 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 260 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8526 (mtp) REVERT: D 200 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: D 222 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: D 235 LYS cc_start: 0.8676 (tttt) cc_final: 0.8457 (ptmt) REVERT: E 273 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: F 133 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5838 (tm-30) REVERT: F 263 ASP cc_start: 0.7760 (t70) cc_final: 0.7469 (t0) REVERT: G 1009 SER cc_start: 0.7951 (p) cc_final: 0.7687 (t) REVERT: G 1099 MET cc_start: 0.7642 (tpt) cc_final: 0.7354 (tpt) REVERT: G 1145 GLU cc_start: 0.7082 (tt0) cc_final: 0.6622 (mm-30) REVERT: G 1258 MET cc_start: 0.4383 (mmm) cc_final: 0.2510 (tpt) REVERT: H 463 GLU cc_start: 0.7288 (pm20) cc_final: 0.6936 (pm20) REVERT: I 31 ASN cc_start: 0.8996 (t0) cc_final: 0.7808 (t0) REVERT: J 19 TRP cc_start: 0.8852 (p90) cc_final: 0.8628 (p90) REVERT: J 34 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7251 (ptp90) REVERT: J 94 MET cc_start: 0.7034 (ttm) cc_final: 0.6780 (ttm) REVERT: M 129 ARG cc_start: 0.7414 (tpt-90) cc_final: 0.6984 (tpt90) REVERT: N 31 LYS cc_start: 0.7860 (mttt) cc_final: 0.7636 (mttp) REVERT: N 88 TYR cc_start: 0.7380 (m-80) cc_final: 0.6862 (m-80) REVERT: N 92 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7316 (mtp-110) REVERT: N 93 GLN cc_start: 0.6342 (mt0) cc_final: 0.6128 (mm-40) REVERT: O 74 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7585 (mmtt) REVERT: O 94 ASN cc_start: 0.7620 (t0) cc_final: 0.7353 (t0) REVERT: O 99 ARG cc_start: 0.7524 (mmt-90) cc_final: 0.6897 (mtp85) REVERT: O 104 GLN cc_start: 0.7706 (mt0) cc_final: 0.7459 (mt0) REVERT: P 54 LYS cc_start: 0.6921 (ttmt) cc_final: 0.6501 (mtpt) REVERT: P 56 MET cc_start: 0.7533 (tpp) cc_final: 0.7187 (mmm) REVERT: P 83 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.7232 (mtt90) REVERT: Q 49 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7761 (ttm170) REVERT: R 53 GLU cc_start: 0.8029 (tp30) cc_final: 0.7755 (tp30) REVERT: R 95 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7299 (mtp85) outliers start: 81 outliers final: 19 residues processed: 572 average time/residue: 1.9162 time to fit residues: 1293.7166 Evaluate side-chains 444 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 418 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1299 THR Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 0.6980 chunk 471 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 433 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 409 GLN A 421 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN C 86 GLN C 237 GLN C 458 HIS D 359 HIS D 452 ASN E 65 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1037 GLN ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 41874 Z= 0.308 Angle : 0.703 30.321 57555 Z= 0.351 Chirality : 0.044 0.271 6556 Planarity : 0.005 0.069 6657 Dihedral : 20.694 147.828 7567 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.13 % Allowed : 11.50 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.55 (0.12), residues: 4623 helix: 0.67 (0.11), residues: 2191 sheet: 0.57 (0.20), residues: 622 loop : 0.11 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1650 HIS 0.008 0.001 HIS G1345 PHE 0.022 0.002 PHE G1079 TYR 0.024 0.002 TYR A 193 ARG 0.010 0.001 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 453 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9039 (tp) cc_final: 0.8759 (tp) REVERT: A 265 MET cc_start: 0.7738 (mtm) cc_final: 0.7402 (mmt) REVERT: A 419 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7640 (ttm170) REVERT: A 421 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8306 (t0) REVERT: A 423 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7008 (ptp-170) REVERT: B 60 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (m90) REVERT: B 133 GLU cc_start: 0.8093 (tt0) cc_final: 0.7806 (tp30) REVERT: B 250 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7166 (tmt90) REVERT: B 373 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (mtm-85) REVERT: B 397 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: B 423 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7257 (mpp80) REVERT: C 8 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7312 (mmm160) REVERT: D 200 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8434 (mmpt) REVERT: D 283 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8696 (tttm) REVERT: E 273 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: F 133 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5887 (tm-30) REVERT: F 263 ASP cc_start: 0.7684 (t70) cc_final: 0.7449 (t0) REVERT: F 364 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: F 446 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: G 1009 SER cc_start: 0.8048 (p) cc_final: 0.7843 (t) REVERT: G 1083 ILE cc_start: 0.8081 (mm) cc_final: 0.7838 (mp) REVERT: G 1104 MET cc_start: 0.7339 (ttm) cc_final: 0.6914 (ttt) REVERT: G 1145 GLU cc_start: 0.7218 (tt0) cc_final: 0.6813 (mp0) REVERT: G 1258 MET cc_start: 0.4079 (mmm) cc_final: 0.2075 (tpt) REVERT: G 1262 MET cc_start: 0.5980 (tpp) cc_final: 0.5746 (tpt) REVERT: G 1450 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7243 (mmm160) REVERT: H 464 GLU cc_start: 0.8064 (mp0) cc_final: 0.7483 (mp0) REVERT: J 19 TRP cc_start: 0.8798 (p90) cc_final: 0.8583 (p90) REVERT: J 174 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7915 (mt-10) REVERT: J 751 TYR cc_start: 0.8237 (t80) cc_final: 0.7986 (t80) REVERT: M 129 ARG cc_start: 0.7494 (tpt-90) cc_final: 0.7026 (tpt90) REVERT: N 39 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6740 (ttp-110) REVERT: N 84 MET cc_start: 0.7570 (tpp) cc_final: 0.7348 (tpp) REVERT: N 88 TYR cc_start: 0.7478 (m-80) cc_final: 0.6932 (m-80) REVERT: N 91 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7131 (mptt) REVERT: N 92 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7498 (mtp-110) REVERT: N 93 GLN cc_start: 0.6472 (mt0) cc_final: 0.6023 (mm-40) REVERT: O 74 LYS cc_start: 0.7880 (mtmm) cc_final: 0.7616 (mmtt) REVERT: O 99 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.6924 (mtp85) REVERT: P 56 MET cc_start: 0.7465 (tpp) cc_final: 0.7112 (mmm) REVERT: Q 92 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6542 (mt) REVERT: R 53 GLU cc_start: 0.8003 (tp30) cc_final: 0.7778 (tp30) REVERT: R 95 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7277 (mtp85) outliers start: 118 outliers final: 38 residues processed: 528 average time/residue: 1.8192 time to fit residues: 1135.3258 Evaluate side-chains 464 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 410 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1144 GLN Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1450 ARG Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 438 optimal weight: 0.7980 chunk 463 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN C 458 HIS D 359 HIS E 65 GLN E 254 GLN E 359 HIS F 301 HIS ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN N 93 GLN O 38 ASN P 79 HIS Q 68 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41874 Z= 0.183 Angle : 0.627 29.771 57555 Z= 0.308 Chirality : 0.040 0.274 6556 Planarity : 0.004 0.055 6657 Dihedral : 20.289 122.640 7567 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.58 % Allowed : 13.25 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.91 (0.12), residues: 4623 helix: 1.09 (0.11), residues: 2184 sheet: 0.56 (0.20), residues: 625 loop : 0.19 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G1021 HIS 0.008 0.001 HIS G1080 PHE 0.016 0.001 PHE D 223 TYR 0.022 0.001 TYR A 193 ARG 0.010 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 441 time to evaluate : 4.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9031 (tp) cc_final: 0.8817 (tp) REVERT: A 263 GLN cc_start: 0.8271 (mt0) cc_final: 0.8006 (mt0) REVERT: A 265 MET cc_start: 0.7734 (mtm) cc_final: 0.7349 (mmp) REVERT: A 421 ASN cc_start: 0.8574 (t0) cc_final: 0.8372 (t0) REVERT: B 250 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7107 (tmt90) REVERT: B 397 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: C 8 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7122 (mmm160) REVERT: D 200 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8432 (mmpt) REVERT: D 224 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (tt) REVERT: E 67 LYS cc_start: 0.8286 (mtmp) cc_final: 0.7841 (mmtt) REVERT: E 183 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8039 (ttpt) REVERT: E 273 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: E 418 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8375 (tptt) REVERT: F 133 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5876 (tm-30) REVERT: F 171 TYR cc_start: 0.9052 (m-80) cc_final: 0.8708 (m-80) REVERT: F 217 MET cc_start: 0.8206 (mmt) cc_final: 0.7893 (mmt) REVERT: F 263 ASP cc_start: 0.7553 (t70) cc_final: 0.7346 (t0) REVERT: F 384 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7908 (t70) REVERT: F 437 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8263 (ttp80) REVERT: G 1009 SER cc_start: 0.8042 (p) cc_final: 0.7806 (t) REVERT: G 1080 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6539 (m90) REVERT: G 1083 ILE cc_start: 0.8062 (mm) cc_final: 0.7830 (mp) REVERT: G 1192 MET cc_start: 0.5552 (mpt) cc_final: 0.5245 (mmt) REVERT: G 1222 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6453 (mt) REVERT: G 1262 MET cc_start: 0.5915 (tpp) cc_final: 0.5667 (tpt) REVERT: G 1629 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5262 (mtm180) REVERT: I 14 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8260 (tp-100) REVERT: J 19 TRP cc_start: 0.8743 (p90) cc_final: 0.8516 (p90) REVERT: J 34 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7232 (ptp90) REVERT: J 90 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7563 (tpt-90) REVERT: J 96 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7713 (pttt) REVERT: J 740 GLU cc_start: 0.7518 (tp30) cc_final: 0.7307 (tp30) REVERT: M 129 ARG cc_start: 0.7581 (tpt-90) cc_final: 0.7105 (tpt90) REVERT: N 88 TYR cc_start: 0.7444 (m-80) cc_final: 0.7055 (m-80) REVERT: N 91 LYS cc_start: 0.7578 (mtmm) cc_final: 0.7038 (mptt) REVERT: N 92 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7394 (mtp-110) REVERT: N 93 GLN cc_start: 0.6393 (mt0) cc_final: 0.5996 (mm-40) REVERT: O 74 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7549 (mmtt) REVERT: O 99 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.6878 (mtp85) REVERT: P 56 MET cc_start: 0.7502 (tpp) cc_final: 0.7238 (mmm) REVERT: P 79 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.7110 (t-90) REVERT: Q 92 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6541 (mt) REVERT: R 77 LYS cc_start: 0.8030 (mttm) cc_final: 0.7753 (mttt) REVERT: R 95 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7256 (mtp85) outliers start: 97 outliers final: 39 residues processed: 503 average time/residue: 1.7823 time to fit residues: 1069.4425 Evaluate side-chains 459 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 407 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1055 THR Chi-restraints excluded: chain G residue 1080 HIS Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1222 LEU Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1447 ASN Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN C 19 HIS C 458 HIS D 359 HIS D 375 GLN E 65 GLN E 96 GLN E 232 GLN F 24 HIS F 96 GLN F 419 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1636 ASN G1692 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 259 ASN J 298 GLN O 38 ASN P 60 ASN P 79 HIS Q 68 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 41874 Z= 0.520 Angle : 0.792 32.177 57555 Z= 0.396 Chirality : 0.049 0.289 6556 Planarity : 0.006 0.083 6657 Dihedral : 20.839 126.555 7567 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.72 % Allowed : 14.29 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.20 (0.12), residues: 4623 helix: 0.43 (0.11), residues: 2194 sheet: 0.33 (0.20), residues: 632 loop : -0.12 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP G1021 HIS 0.009 0.002 HIS B 242 PHE 0.036 0.003 PHE G1079 TYR 0.027 0.003 TYR O 50 ARG 0.008 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 417 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7134 (tmt90) REVERT: B 373 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7841 (mtm-85) REVERT: B 397 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: B 423 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7412 (mpp80) REVERT: D 200 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8435 (mmpt) REVERT: D 231 LEU cc_start: 0.8954 (mm) cc_final: 0.8712 (mp) REVERT: D 283 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8692 (tttm) REVERT: E 183 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8144 (ttpt) REVERT: E 212 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (ttp-110) REVERT: E 273 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: F 133 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6046 (tm-30) REVERT: F 217 MET cc_start: 0.8274 (mmt) cc_final: 0.7967 (mmt) REVERT: F 263 ASP cc_start: 0.7676 (t70) cc_final: 0.7434 (t0) REVERT: F 364 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: F 384 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7967 (t70) REVERT: G 1145 GLU cc_start: 0.7175 (tt0) cc_final: 0.6886 (mp0) REVERT: G 1258 MET cc_start: 0.3962 (mtt) cc_final: 0.2183 (tpt) REVERT: G 1262 MET cc_start: 0.6013 (tpp) cc_final: 0.5806 (tpt) REVERT: G 1435 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: G 1629 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5312 (mtm180) REVERT: G 1665 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7402 (mt) REVERT: I 14 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8349 (tp-100) REVERT: I 18 GLU cc_start: 0.8617 (pt0) cc_final: 0.8399 (pt0) REVERT: J 19 TRP cc_start: 0.8742 (p90) cc_final: 0.8477 (p90) REVERT: M 129 ARG cc_start: 0.7530 (tpt-90) cc_final: 0.7058 (tpt90) REVERT: N 39 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6722 (ttp-110) REVERT: N 78 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6434 (ptm160) REVERT: N 88 TYR cc_start: 0.7529 (m-80) cc_final: 0.7121 (m-80) REVERT: N 91 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7179 (mptt) REVERT: N 92 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7399 (mtp-110) REVERT: N 93 GLN cc_start: 0.6639 (mt0) cc_final: 0.6059 (mm-40) REVERT: O 74 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7658 (mmtt) REVERT: O 99 ARG cc_start: 0.7622 (mmt-90) cc_final: 0.6942 (mtp85) REVERT: P 56 MET cc_start: 0.7503 (tpp) cc_final: 0.7098 (mmm) REVERT: P 79 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7065 (t-90) REVERT: R 95 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7279 (mtp85) outliers start: 140 outliers final: 68 residues processed: 509 average time/residue: 1.8218 time to fit residues: 1102.7940 Evaluate side-chains 477 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 392 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1055 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1416 THR Chi-restraints excluded: chain G residue 1435 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain G residue 1701 ILE Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 122 LYS Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 1.9990 chunk 417 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 464 optimal weight: 0.9980 chunk 385 optimal weight: 20.0000 chunk 215 optimal weight: 0.4980 chunk 38 optimal weight: 0.0980 chunk 153 optimal weight: 8.9990 chunk 243 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 43 GLN A 146 ASN A 421 ASN C 458 HIS D 65 GLN E 65 GLN E 96 GLN F 96 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 60 ASN P 79 HIS Q 68 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41874 Z= 0.165 Angle : 0.627 29.869 57555 Z= 0.307 Chirality : 0.040 0.272 6556 Planarity : 0.004 0.053 6657 Dihedral : 20.308 121.214 7567 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.42 % Allowed : 15.91 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.82 (0.12), residues: 4623 helix: 1.09 (0.11), residues: 2185 sheet: 0.51 (0.21), residues: 613 loop : 0.04 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G1021 HIS 0.028 0.001 HIS P 79 PHE 0.022 0.001 PHE G1264 TYR 0.025 0.001 TYR P 80 ARG 0.016 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 440 time to evaluate : 4.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9020 (tp) cc_final: 0.8807 (tp) REVERT: A 263 GLN cc_start: 0.8302 (mt0) cc_final: 0.8051 (mt0) REVERT: A 265 MET cc_start: 0.7831 (mtm) cc_final: 0.7569 (mmp) REVERT: B 138 GLU cc_start: 0.8101 (mp0) cc_final: 0.7815 (mp0) REVERT: B 250 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7092 (tmt90) REVERT: B 373 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7765 (mtm-85) REVERT: B 397 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: B 423 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7452 (mpp80) REVERT: C 8 ARG cc_start: 0.7337 (mmm160) cc_final: 0.6928 (mmm160) REVERT: D 200 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: E 273 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: E 418 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8350 (tptt) REVERT: F 109 PHE cc_start: 0.8821 (m-80) cc_final: 0.8537 (m-80) REVERT: F 133 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6042 (tm-30) REVERT: F 217 MET cc_start: 0.8166 (mmt) cc_final: 0.7816 (mmt) REVERT: F 263 ASP cc_start: 0.7498 (t70) cc_final: 0.7283 (t0) REVERT: F 384 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7994 (t70) REVERT: F 437 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8277 (ttp80) REVERT: G 1083 ILE cc_start: 0.8042 (mm) cc_final: 0.7825 (mp) REVERT: G 1158 PHE cc_start: 0.8161 (m-80) cc_final: 0.7886 (m-80) REVERT: G 1195 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6713 (ptmt) REVERT: G 1262 MET cc_start: 0.5974 (tpp) cc_final: 0.5727 (tpt) REVERT: G 1629 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5281 (mtm180) REVERT: I 14 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8216 (tp-100) REVERT: I 18 GLU cc_start: 0.8579 (pt0) cc_final: 0.8223 (pt0) REVERT: J 19 TRP cc_start: 0.8736 (p90) cc_final: 0.8474 (p90) REVERT: M 129 ARG cc_start: 0.7605 (tpt-90) cc_final: 0.7126 (tpt90) REVERT: N 31 LYS cc_start: 0.7860 (mttp) cc_final: 0.7658 (mttm) REVERT: N 88 TYR cc_start: 0.7415 (m-80) cc_final: 0.7018 (m-80) REVERT: N 91 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7098 (mptt) REVERT: N 92 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7348 (mtp-110) REVERT: N 93 GLN cc_start: 0.6502 (mt0) cc_final: 0.5997 (mm-40) REVERT: O 20 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: O 74 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7619 (mmtt) REVERT: O 99 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.6892 (mtp85) REVERT: P 56 MET cc_start: 0.7478 (tpp) cc_final: 0.7233 (mmm) REVERT: Q 92 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6531 (mt) REVERT: R 77 LYS cc_start: 0.7951 (mttm) cc_final: 0.7719 (mttt) REVERT: R 95 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7287 (mtp85) outliers start: 91 outliers final: 41 residues processed: 499 average time/residue: 1.8638 time to fit residues: 1106.5072 Evaluate side-chains 458 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 406 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1055 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1195 LYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1408 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 264 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 390 optimal weight: 50.0000 chunk 259 optimal weight: 0.1980 chunk 462 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 282 optimal weight: 0.3980 chunk 213 optimal weight: 3.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN C 60 HIS C 317 ASN C 458 HIS E 65 GLN F 96 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 60 ASN P 79 HIS Q 68 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41874 Z= 0.206 Angle : 0.638 30.217 57555 Z= 0.311 Chirality : 0.040 0.290 6556 Planarity : 0.004 0.072 6657 Dihedral : 20.231 120.327 7567 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.36 % Allowed : 16.44 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.89 (0.12), residues: 4623 helix: 1.19 (0.11), residues: 2188 sheet: 0.56 (0.20), residues: 625 loop : 0.00 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G1021 HIS 0.013 0.001 HIS C 60 PHE 0.023 0.001 PHE G1264 TYR 0.038 0.001 TYR P 80 ARG 0.012 0.000 ARG J 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 429 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9035 (tp) cc_final: 0.8827 (tp) REVERT: A 263 GLN cc_start: 0.8355 (mt0) cc_final: 0.8069 (mt0) REVERT: A 265 MET cc_start: 0.7831 (mtm) cc_final: 0.7551 (mmp) REVERT: B 138 GLU cc_start: 0.8110 (mp0) cc_final: 0.7789 (mp0) REVERT: B 250 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7079 (tmt90) REVERT: B 373 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7791 (mtm-85) REVERT: B 397 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: B 423 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7496 (mpp80) REVERT: C 8 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7112 (mmm160) REVERT: D 200 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8408 (mmpt) REVERT: D 285 GLU cc_start: 0.7347 (tt0) cc_final: 0.6972 (mt-10) REVERT: E 148 ASP cc_start: 0.7199 (m-30) cc_final: 0.6962 (p0) REVERT: E 157 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6901 (pp30) REVERT: E 273 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: E 418 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8389 (tptt) REVERT: F 133 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: F 217 MET cc_start: 0.8168 (mmt) cc_final: 0.7871 (mmt) REVERT: F 384 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8017 (t70) REVERT: F 437 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8252 (ttp80) REVERT: G 1009 SER cc_start: 0.8010 (p) cc_final: 0.7733 (t) REVERT: G 1195 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6706 (ptmt) REVERT: G 1327 ASP cc_start: 0.7577 (p0) cc_final: 0.7371 (p0) REVERT: G 1629 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5264 (mtm180) REVERT: G 1665 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7188 (tt) REVERT: I 14 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8156 (tp-100) REVERT: I 18 GLU cc_start: 0.8632 (pt0) cc_final: 0.8285 (pt0) REVERT: J 19 TRP cc_start: 0.8728 (p90) cc_final: 0.8472 (p90) REVERT: J 90 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7623 (tpt-90) REVERT: M 129 ARG cc_start: 0.7509 (tpt-90) cc_final: 0.7073 (tpt90) REVERT: N 31 LYS cc_start: 0.7859 (mttp) cc_final: 0.7654 (mttm) REVERT: N 85 ASP cc_start: 0.7474 (m-30) cc_final: 0.7041 (m-30) REVERT: N 88 TYR cc_start: 0.7491 (m-80) cc_final: 0.7028 (m-80) REVERT: N 91 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7111 (mptt) REVERT: N 92 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7347 (mtp-110) REVERT: N 93 GLN cc_start: 0.6513 (mt0) cc_final: 0.5981 (mm-40) REVERT: O 74 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7600 (mmtt) REVERT: O 99 ARG cc_start: 0.7578 (mmt-90) cc_final: 0.6891 (mtp85) REVERT: P 56 MET cc_start: 0.7528 (tpp) cc_final: 0.7268 (mmm) REVERT: P 79 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7041 (t-90) REVERT: Q 92 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6588 (mt) REVERT: R 77 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7730 (mttt) REVERT: R 95 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7252 (mtp85) outliers start: 89 outliers final: 47 residues processed: 486 average time/residue: 1.7944 time to fit residues: 1042.7333 Evaluate side-chains 467 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 405 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1195 LYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 77 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 294 optimal weight: 0.0770 chunk 315 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS C 458 HIS E 65 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 60 ASN P 79 HIS Q 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41874 Z= 0.259 Angle : 0.666 30.588 57555 Z= 0.326 Chirality : 0.041 0.281 6556 Planarity : 0.004 0.055 6657 Dihedral : 20.312 118.789 7567 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.52 % Allowed : 16.97 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.81 (0.12), residues: 4623 helix: 1.11 (0.11), residues: 2187 sheet: 0.57 (0.21), residues: 621 loop : -0.05 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G1021 HIS 0.014 0.001 HIS P 79 PHE 0.026 0.002 PHE G1264 TYR 0.048 0.002 TYR P 80 ARG 0.013 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 420 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9030 (tp) cc_final: 0.8820 (tp) REVERT: A 265 MET cc_start: 0.7849 (mtm) cc_final: 0.7611 (mmp) REVERT: B 138 GLU cc_start: 0.8113 (mp0) cc_final: 0.7799 (mp0) REVERT: B 250 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7092 (tmt90) REVERT: B 397 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: B 423 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7516 (mpp80) REVERT: C 8 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6905 (mmm160) REVERT: C 427 ASP cc_start: 0.8425 (t0) cc_final: 0.8218 (t0) REVERT: D 200 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: D 283 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8843 (tttm) REVERT: D 285 GLU cc_start: 0.7404 (tt0) cc_final: 0.7010 (mt-10) REVERT: E 112 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: E 148 ASP cc_start: 0.7265 (m-30) cc_final: 0.6997 (p0) REVERT: E 157 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6861 (pp30) REVERT: E 273 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: E 418 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8312 (tptt) REVERT: F 133 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: F 217 MET cc_start: 0.8191 (mmt) cc_final: 0.7917 (mmt) REVERT: F 384 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8023 (t70) REVERT: F 437 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8275 (ttp80) REVERT: G 1009 SER cc_start: 0.8027 (p) cc_final: 0.7765 (t) REVERT: G 1195 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6647 (ptmt) REVERT: G 1327 ASP cc_start: 0.7603 (p0) cc_final: 0.7364 (p0) REVERT: G 1629 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5258 (mtm180) REVERT: G 1665 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7235 (tt) REVERT: I 14 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8103 (tp-100) REVERT: I 18 GLU cc_start: 0.8600 (pt0) cc_final: 0.8236 (pt0) REVERT: J 19 TRP cc_start: 0.8729 (p90) cc_final: 0.8467 (p90) REVERT: J 34 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7337 (ptp90) REVERT: J 90 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7605 (tpt-90) REVERT: J 174 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7944 (mt-10) REVERT: M 129 ARG cc_start: 0.7522 (tpt-90) cc_final: 0.7089 (tpt90) REVERT: N 31 LYS cc_start: 0.7876 (mttp) cc_final: 0.7673 (mttm) REVERT: N 85 ASP cc_start: 0.7518 (m-30) cc_final: 0.7122 (m-30) REVERT: N 88 TYR cc_start: 0.7508 (m-80) cc_final: 0.7098 (m-80) REVERT: N 91 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7127 (mptt) REVERT: N 92 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7355 (mtp-110) REVERT: N 93 GLN cc_start: 0.6527 (mt0) cc_final: 0.5988 (mm-40) REVERT: O 74 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7618 (mmtt) REVERT: O 99 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.6900 (mtp85) REVERT: P 56 MET cc_start: 0.7554 (tpp) cc_final: 0.7279 (mmm) REVERT: Q 92 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6551 (mt) REVERT: R 77 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7723 (mttt) REVERT: R 95 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7244 (mtp85) outliers start: 95 outliers final: 56 residues processed: 483 average time/residue: 1.7703 time to fit residues: 1019.1423 Evaluate side-chains 472 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 401 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1195 LYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 77 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 4.9990 chunk 443 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 431 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 389 optimal weight: 50.0000 chunk 407 optimal weight: 0.9990 chunk 429 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS C 458 HIS E 65 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 60 ASN Q 68 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41874 Z= 0.256 Angle : 0.669 30.513 57555 Z= 0.326 Chirality : 0.042 0.311 6556 Planarity : 0.004 0.076 6657 Dihedral : 20.335 118.322 7567 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.66 % Allowed : 17.21 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.78 (0.12), residues: 4623 helix: 1.10 (0.11), residues: 2186 sheet: 0.55 (0.21), residues: 625 loop : -0.07 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G1021 HIS 0.013 0.001 HIS C 60 PHE 0.028 0.002 PHE G1264 TYR 0.052 0.002 TYR P 80 ARG 0.022 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 411 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9033 (tp) cc_final: 0.8823 (tp) REVERT: A 265 MET cc_start: 0.7859 (mtm) cc_final: 0.7588 (mmp) REVERT: A 321 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: B 138 GLU cc_start: 0.8098 (mp0) cc_final: 0.7816 (mp0) REVERT: B 250 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7092 (tmt90) REVERT: B 397 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: B 423 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7517 (mpp80) REVERT: C 8 ARG cc_start: 0.7352 (mmm160) cc_final: 0.6888 (mmm160) REVERT: C 427 ASP cc_start: 0.8434 (t0) cc_final: 0.8229 (t0) REVERT: D 200 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: D 285 GLU cc_start: 0.7432 (tt0) cc_final: 0.7036 (mt-10) REVERT: E 112 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: E 148 ASP cc_start: 0.7215 (m-30) cc_final: 0.6968 (p0) REVERT: E 157 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6840 (pp30) REVERT: E 273 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: E 418 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8303 (tptt) REVERT: F 133 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: F 217 MET cc_start: 0.8197 (mmt) cc_final: 0.7911 (mmt) REVERT: F 384 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (t70) REVERT: F 437 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: G 1009 SER cc_start: 0.8043 (p) cc_final: 0.7795 (t) REVERT: G 1195 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6627 (ptmt) REVERT: G 1327 ASP cc_start: 0.7589 (p0) cc_final: 0.7356 (p0) REVERT: G 1545 MET cc_start: 0.7413 (tpt) cc_final: 0.7048 (tpt) REVERT: G 1629 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5254 (mtm180) REVERT: G 1665 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7217 (tt) REVERT: I 14 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8155 (tp-100) REVERT: I 18 GLU cc_start: 0.8596 (pt0) cc_final: 0.8250 (pt0) REVERT: J 19 TRP cc_start: 0.8717 (p90) cc_final: 0.8448 (p90) REVERT: J 34 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7437 (ptp90) REVERT: J 90 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7588 (tpt-90) REVERT: J 94 MET cc_start: 0.8479 (tmm) cc_final: 0.7865 (pp-130) REVERT: J 174 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7938 (mt-10) REVERT: J 751 TYR cc_start: 0.8055 (t80) cc_final: 0.7844 (t80) REVERT: M 129 ARG cc_start: 0.7523 (tpt-90) cc_final: 0.7088 (tpt90) REVERT: N 31 LYS cc_start: 0.7872 (mttp) cc_final: 0.7668 (mttm) REVERT: N 84 MET cc_start: 0.7548 (tpp) cc_final: 0.6868 (tpp) REVERT: N 85 ASP cc_start: 0.7490 (m-30) cc_final: 0.7099 (m-30) REVERT: N 88 TYR cc_start: 0.7518 (m-80) cc_final: 0.7057 (m-80) REVERT: N 91 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7126 (mptt) REVERT: N 92 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7345 (mtp-110) REVERT: N 93 GLN cc_start: 0.6485 (mt0) cc_final: 0.5974 (mm-40) REVERT: O 74 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7631 (mmtt) REVERT: O 99 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.6895 (mtp85) REVERT: O 104 GLN cc_start: 0.7969 (mt0) cc_final: 0.7727 (pt0) REVERT: P 56 MET cc_start: 0.7542 (tpp) cc_final: 0.7257 (mmm) REVERT: Q 92 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6579 (mt) REVERT: R 77 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7725 (mttt) REVERT: R 95 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7239 (mtp85) outliers start: 100 outliers final: 58 residues processed: 478 average time/residue: 1.8135 time to fit residues: 1037.6224 Evaluate side-chains 474 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 401 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1195 LYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 77 LYS Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.6980 chunk 455 optimal weight: 0.3980 chunk 278 optimal weight: 0.0670 chunk 216 optimal weight: 0.0570 chunk 316 optimal weight: 0.9990 chunk 478 optimal weight: 3.9990 chunk 440 optimal weight: 1.9990 chunk 380 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 294 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS C 168 GLN C 458 HIS D 274 GLN E 65 GLN E 96 GLN E 419 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 60 ASN P 79 HIS Q 68 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41874 Z= 0.148 Angle : 0.621 29.655 57555 Z= 0.299 Chirality : 0.039 0.334 6556 Planarity : 0.004 0.078 6657 Dihedral : 19.866 120.710 7567 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.46 % Allowed : 18.27 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.20 (0.12), residues: 4623 helix: 1.51 (0.11), residues: 2181 sheet: 0.72 (0.21), residues: 621 loop : 0.05 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP G1021 HIS 0.004 0.001 HIS G1080 PHE 0.024 0.001 PHE G1264 TYR 0.058 0.001 TYR P 80 ARG 0.020 0.000 ARG F 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 468 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8988 (tp) cc_final: 0.8647 (tp) REVERT: A 263 GLN cc_start: 0.8145 (mt0) cc_final: 0.7918 (mt0) REVERT: A 265 MET cc_start: 0.7836 (mtm) cc_final: 0.7579 (mmp) REVERT: A 381 GLN cc_start: 0.8427 (tt0) cc_final: 0.8059 (tm-30) REVERT: B 138 GLU cc_start: 0.8043 (mp0) cc_final: 0.7806 (mp0) REVERT: B 250 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7126 (tmt90) REVERT: B 397 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 8 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6919 (mmm160) REVERT: C 44 CYS cc_start: 0.8469 (m) cc_final: 0.8121 (m) REVERT: D 200 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8509 (tppt) REVERT: D 257 LEU cc_start: 0.8136 (tp) cc_final: 0.7935 (tp) REVERT: D 285 GLU cc_start: 0.7186 (tt0) cc_final: 0.6854 (mt-10) REVERT: D 337 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7853 (p) REVERT: E 228 GLU cc_start: 0.7837 (tt0) cc_final: 0.7589 (tp30) REVERT: E 418 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8366 (tptt) REVERT: F 109 PHE cc_start: 0.8693 (m-80) cc_final: 0.8403 (m-80) REVERT: F 133 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6034 (tm-30) REVERT: F 217 MET cc_start: 0.8095 (mmt) cc_final: 0.7787 (mmt) REVERT: F 437 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8233 (ttp80) REVERT: G 1009 SER cc_start: 0.8166 (p) cc_final: 0.7894 (t) REVERT: G 1158 PHE cc_start: 0.8141 (m-80) cc_final: 0.7881 (m-80) REVERT: G 1195 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6637 (ptmt) REVERT: G 1258 MET cc_start: 0.3346 (mtt) cc_final: 0.2601 (ptm) REVERT: G 1327 ASP cc_start: 0.7528 (p0) cc_final: 0.7314 (p0) REVERT: G 1629 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5210 (mtm180) REVERT: G 1665 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7106 (tt) REVERT: I 14 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8143 (tp-100) REVERT: I 18 GLU cc_start: 0.8617 (pt0) cc_final: 0.8289 (pt0) REVERT: J 19 TRP cc_start: 0.8674 (p90) cc_final: 0.8411 (p90) REVERT: J 34 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7428 (ptp90) REVERT: J 90 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7684 (tpt-90) REVERT: J 94 MET cc_start: 0.8480 (tmm) cc_final: 0.7873 (pp-130) REVERT: J 174 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7857 (mt-10) REVERT: M 129 ARG cc_start: 0.7473 (tpt-90) cc_final: 0.7058 (tpt90) REVERT: N 57 VAL cc_start: 0.7507 (t) cc_final: 0.7244 (m) REVERT: N 84 MET cc_start: 0.7350 (tpp) cc_final: 0.6610 (tpp) REVERT: N 88 TYR cc_start: 0.7454 (m-80) cc_final: 0.6970 (m-80) REVERT: N 91 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7051 (mptt) REVERT: N 92 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7364 (mtp-110) REVERT: N 93 GLN cc_start: 0.6319 (mt0) cc_final: 0.5917 (mm-40) REVERT: O 74 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7518 (mmtt) REVERT: O 99 ARG cc_start: 0.7560 (mmt-90) cc_final: 0.6857 (mtp85) REVERT: P 56 MET cc_start: 0.7520 (tpp) cc_final: 0.7300 (mmm) REVERT: P 60 ASN cc_start: 0.7804 (m-40) cc_final: 0.7580 (m110) REVERT: P 79 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.7003 (t-90) REVERT: R 77 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7728 (mttt) REVERT: R 78 ARG cc_start: 0.6554 (mtt180) cc_final: 0.6039 (ttp-110) REVERT: R 95 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7182 (mtp85) outliers start: 55 outliers final: 26 residues processed: 504 average time/residue: 1.8126 time to fit residues: 1093.2870 Evaluate side-chains 448 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 412 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1195 LYS Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1672 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain R residue 77 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 351 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 391 optimal weight: 0.0060 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN C 60 HIS C 458 HIS D 157 GLN D 375 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1034 HIS G1191 HIS ** G1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN O 38 ASN P 79 HIS ** P 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088602 restraints weight = 69540.326| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.77 r_work: 0.3214 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41874 Z= 0.241 Angle : 0.667 30.327 57555 Z= 0.324 Chirality : 0.042 0.314 6556 Planarity : 0.004 0.064 6657 Dihedral : 20.084 117.206 7567 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 18.99 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.04 (0.12), residues: 4623 helix: 1.35 (0.11), residues: 2181 sheet: 0.65 (0.20), residues: 644 loop : 0.01 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G1021 HIS 0.007 0.001 HIS C 60 PHE 0.036 0.002 PHE G1264 TYR 0.060 0.002 TYR P 80 ARG 0.014 0.000 ARG J 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17859.87 seconds wall clock time: 314 minutes 6.15 seconds (18846.15 seconds total)