Starting phenix.real_space_refine on Sun Mar 24 10:45:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/03_2024/8oo7_17006_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.266 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 243 5.49 5 Mg 2 5.21 5 S 160 5.16 5 C 25026 2.51 5 N 7396 2.21 5 O 8192 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41024 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': 3, 'PTRANS': 30, '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: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4545 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 615} Chain breaks: 5 Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 571 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 32, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 429 Chain: "K" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2306 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2327 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} 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: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: 21.78, per 1000 atoms: 0.53 Number of scatterers: 41024 At special positions: 0 Unit cell: (141.384, 180.018, 191.526, 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 243 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 8192 8.00 N 7396 7.00 C 25026 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: 18.04 Conformation dependent library (CDL) restraints added in 6.9 seconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 31 sheets defined 44.9% alpha, 12.9% beta 61 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 19.95 Creating SS restraints... Processing helix chain 'A' and resid 44 through 58 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.615A pdb=" N ILE A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.699A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) 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 320 removed outlier: 4.041A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (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: 4.377A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.626A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.477A 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: 3.629A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 77 through 87 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 258 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: 3.729A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.511A 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 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.889A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.548A 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 removed outlier: 3.978A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'C' and resid 44 through 58 Processing helix chain 'C' and resid 77 through 88 Processing helix 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: 3.502A pdb=" N ILE C 181 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 182 " --> pdb=" O GLU C 179 " (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 320 removed outlier: 3.823A 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: 4.612A 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: 3.741A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 428 through 437 removed outlier: 4.156A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 4.032A 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 removed outlier: 3.508A pdb=" N ILE D 108 " --> pdb=" O ALA D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.686A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) 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 259 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: 4.883A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 4.310A 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: 4.300A 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 395 removed outlier: 3.585A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.626A pdb=" N ILE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.841A 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: 6.767A pdb=" N GLN E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 removed outlier: 3.774A pdb=" N ILE E 108 " --> pdb=" O ALA E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.640A 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: 5.121A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.518A pdb=" N PHE E 260 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.957A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 4.168A 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: 4.169A 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: 3.998A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (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: 3.603A 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 212 removed outlier: 4.190A 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: 3.728A pdb=" N SER F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 285 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 315 removed outlier: 4.041A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (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: 4.322A 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: 4.031A 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 444 Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'G' and resid 974 through 988 Processing helix chain 'G' and resid 1003 through 1018 Processing helix chain 'G' and resid 1030 through 1043 removed outlier: 4.801A pdb=" N HIS G1034 " --> pdb=" O ALA G1030 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN G1035 " --> pdb=" O SER G1031 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1065 removed outlier: 4.099A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1086 through 1091 removed outlier: 3.754A pdb=" N VAL G1090 " --> pdb=" O TYR G1086 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1098 removed outlier: 4.203A pdb=" N LYS G1098 " --> pdb=" O ALA G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1112 Processing helix chain 'G' and resid 1118 through 1125 removed outlier: 3.693A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1153 removed outlier: 3.708A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1195 removed outlier: 3.953A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS G1195 " --> pdb=" O HIS G1191 " (cutoff:3.500A) Processing helix chain 'G' and resid 1203 through 1206 No H-bonds generated for 'chain 'G' and resid 1203 through 1206' Processing helix chain 'G' and resid 1224 through 1238 removed outlier: 4.049A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1267 removed outlier: 3.654A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (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 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: 4.229A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1358 removed outlier: 3.636A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G1358 " --> pdb=" O ASN G1354 " (cutoff:3.500A) Processing helix chain 'G' and resid 1366 through 1369 removed outlier: 3.769A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1366 through 1369' Processing helix chain 'G' and resid 1375 through 1381 Processing helix chain 'G' and resid 1386 through 1395 removed outlier: 3.958A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1399 through 1406 removed outlier: 3.745A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) 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 1445 Processing helix chain 'G' and resid 1448 through 1455 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 1567 Processing helix chain 'G' and resid 1579 through 1591 Processing helix chain 'G' and resid 1605 through 1617 Processing helix chain 'G' and resid 1652 through 1660 Processing helix chain 'G' and resid 1682 through 1699 removed outlier: 3.570A pdb=" N GLU G1695 " --> pdb=" O LEU G1691 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 removed outlier: 4.305A 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 51 Processing helix chain 'I' and resid 191 through 199 Processing helix chain 'I' and resid 204 through 212 removed outlier: 4.034A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) 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: 3.597A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 281 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 359 Processing helix chain 'J' and resid 362 through 372 removed outlier: 4.528A pdb=" N LYS J 366 " --> pdb=" O LYS J 363 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP J 370 " --> pdb=" O ARG J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 393 removed outlier: 4.411A pdb=" N ARG J 382 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 383 " --> pdb=" O ALA J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 468 Processing helix chain 'J' and resid 470 through 497 Processing helix chain 'J' and resid 502 through 513 removed outlier: 3.626A pdb=" N GLN J 507 " --> pdb=" O LEU J 504 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG J 509 " --> pdb=" O SER J 506 " (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 608 through 614 Processing helix chain 'J' and resid 633 through 638 removed outlier: 3.818A 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 649 No H-bonds generated for 'chain 'J' and resid 646 through 649' Processing helix chain 'J' and resid 657 through 667 Processing helix chain 'J' and resid 669 through 671 No H-bonds generated for 'chain 'J' and resid 669 through 671' Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.327A 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 709 removed outlier: 3.620A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 735 removed outlier: 3.968A pdb=" N GLY J 731 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 742 No H-bonds generated for 'chain 'J' and resid 739 through 742' Processing helix chain 'J' and resid 748 through 754 removed outlier: 3.680A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.334A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 115 removed outlier: 3.637A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS M 115 " --> pdb=" O ALA M 111 " (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 48 through 75 removed outlier: 3.510A pdb=" N TYR N 51 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU N 52 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG N 55 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS N 59 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL N 60 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE N 66 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP N 68 " --> pdb=" O VAL N 65 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU N 74 " --> pdb=" O THR N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 94 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 88 Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 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 34 through 45 removed outlier: 3.503A pdb=" N VAL P 38 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR P 39 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS P 43 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 81 Processing helix chain 'P' and resid 88 through 98 Processing helix chain 'P' and resid 101 through 121 Processing helix chain 'Q' and resid 45 through 54 Processing helix chain 'Q' and resid 64 through 78 removed outlier: 3.946A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 114 Processing helix chain 'Q' and resid 121 through 130 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: 3.507A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 92 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.917A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.641A 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 167 through 174 removed outlier: 3.606A pdb=" N GLY A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 138 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 163 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL A 136 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A 190 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.032A 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 339 removed outlier: 5.655A pdb=" N LEU A 345 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 359 through 364 removed outlier: 6.904A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 364 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 70 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY B 71 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.034A 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: 6.648A pdb=" N LYS B 163 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 136 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 5.800A 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: 5.838A 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: 6.922A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 328 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU C 69 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 330 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLY C 71 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 5.755A 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 168 through 173 removed outlier: 3.589A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 205 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU C 195 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.177A 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 339 removed outlier: 6.042A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 353 through 357 removed outlier: 6.757A pdb=" N ALA D 72 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE D 356 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU D 74 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.173A 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: 3.695A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP D 195 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.053A 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: 6.793A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR E 358 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA E 76 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLY E 77 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER E 327 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 288 through 292 Processing sheet with id= S, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.395A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP E 190 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER E 193 " --> pdb=" O LYS E 203 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS E 203 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASP E 195 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE E 201 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 353 through 358 removed outlier: 6.706A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR F 358 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA F 76 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 323 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE F 75 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET F 325 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLY F 77 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER F 327 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 289 through 292 Processing sheet with id= V, first strand: chain 'F' and resid 168 through 173 removed outlier: 3.606A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS F 163 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL F 142 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP F 190 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 205 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER F 193 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS F 203 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP F 195 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 201 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= X, first strand: chain 'G' and resid 993 through 995 removed outlier: 3.832A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 1214 through 1217 Processing sheet with id= Z, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.783A pdb=" N GLU G1475 " --> pdb=" O TYR G1313 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'H' and resid 449 through 453 Processing sheet with id= AB, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.399A pdb=" N ILE J 296 " --> pdb=" O TYR J 28 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 80 through 82 removed outlier: 7.528A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN J 63 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 159 " --> pdb=" O ASN J 63 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 115 through 117 Processing sheet with id= AE, first strand: chain 'J' and resid 213 through 218 1540 hydrogen bonds defined for protein. 4392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 151 hydrogen bonds 302 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 23.39 Time building geometry restraints manager: 19.28 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: 13101 1.34 - 1.46: 6958 1.46 - 1.58: 21362 1.58 - 1.69: 475 1.69 - 1.81: 279 Bond restraints: 42175 Sorted by residual: bond pdb=" F3 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.685 1.802 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.684 1.800 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" F4 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " ideal model delta sigma weight residual 1.685 1.772 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.83e+00 ... (remaining 42170 not shown) Histogram of bond angle deviations from ideal: 89.51 - 107.59: 3185 107.59 - 125.67: 53679 125.67 - 143.75: 1140 143.75 - 161.82: 0 161.82 - 179.90: 2 Bond angle restraints: 58006 Sorted by residual: angle pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " pdb=" F2 ALF G1901 " ideal model delta sigma weight residual 108.68 179.13 -70.45 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F3 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 109.63 179.90 -70.27 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 110.21 89.69 20.52 3.00e+00 1.11e-01 4.68e+01 angle pdb=" F1 ALF G1901 " pdb="AL ALF G1901 " pdb=" F4 ALF G1901 " ideal model delta sigma weight residual 109.02 89.51 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" F2 ALF G1901 " pdb="AL ALF G1901 " pdb=" F3 ALF G1901 " ideal model delta sigma weight residual 109.59 90.27 19.32 3.00e+00 1.11e-01 4.15e+01 ... (remaining 58001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 23608 33.24 - 66.47: 1404 66.47 - 99.71: 67 99.71 - 132.94: 4 132.94 - 166.18: 9 Dihedral angle restraints: 25092 sinusoidal: 11587 harmonic: 13505 Sorted by residual: dihedral pdb=" O1B ADP G1902 " pdb=" O3A ADP G1902 " pdb=" PB ADP G1902 " pdb=" PA ADP G1902 " ideal model delta sinusoidal sigma weight residual 300.00 133.82 166.18 1 2.00e+01 2.50e-03 4.73e+01 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 -60.00 102.47 -162.48 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 141.22 158.79 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 25089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4397 0.044 - 0.087: 1751 0.087 - 0.131: 412 0.131 - 0.174: 41 0.174 - 0.218: 6 Chirality restraints: 6607 Sorted by residual: chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA THR D 81 " pdb=" N THR D 81 " pdb=" C THR D 81 " pdb=" CB THR D 81 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 6604 not shown) Planarity restraints: 6684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 313 " -0.398 9.50e-02 1.11e+02 1.79e-01 2.49e+01 pdb=" NE ARG E 313 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 313 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG E 313 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.362 9.50e-02 1.11e+02 1.63e-01 2.01e+01 pdb=" NE ARG D 252 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 92 " -0.346 9.50e-02 1.11e+02 1.56e-01 1.86e+01 pdb=" NE ARG N 92 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG N 92 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG N 92 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG N 92 " -0.001 2.00e-02 2.50e+03 ... (remaining 6681 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 58 2.40 - 3.03: 23501 3.03 - 3.65: 63327 3.65 - 4.28: 101696 4.28 - 4.90: 161758 Nonbonded interactions: 350340 Sorted by model distance: nonbonded pdb="MG MG J 801 " pdb=" O1G ATP J 802 " model vdw 1.779 2.170 nonbonded pdb=" F3 ALF G1901 " pdb="MG MG G1903 " model vdw 1.898 2.120 nonbonded pdb=" O2B ADP G1902 " pdb="MG MG G1903 " model vdw 2.018 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1B ATP J 802 " model vdw 2.026 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 801 " model vdw 2.188 2.170 ... (remaining 350335 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 95) selection = (chain 'R' and resid 23 through 95) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.050 Extract box with map and model: 11.940 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 129.280 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.240 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: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 42175 Z= 0.251 Angle : 0.947 70.454 58006 Z= 0.488 Chirality : 0.047 0.218 6607 Planarity : 0.011 0.179 6684 Dihedral : 18.245 166.175 16380 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.13 (0.11), residues: 4639 helix: -1.35 (0.09), residues: 2196 sheet: 0.45 (0.20), residues: 595 loop : -0.09 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G1650 HIS 0.008 0.001 HIS B 21 PHE 0.024 0.002 PHE C 117 TYR 0.031 0.005 TYR A 210 ARG 0.040 0.004 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 897 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7914 (tt0) cc_final: 0.7599 (tp30) REVERT: A 286 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7672 (mtmm) REVERT: A 373 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7810 (ttp80) REVERT: B 269 MET cc_start: 0.7666 (mtm) cc_final: 0.7407 (mtm) REVERT: B 419 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7845 (ttm170) REVERT: B 442 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6975 (mmm160) REVERT: C 106 GLU cc_start: 0.8052 (tt0) cc_final: 0.7671 (mt-10) REVERT: C 303 ASP cc_start: 0.7350 (t0) cc_final: 0.6917 (t0) REVERT: C 368 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 167 MET cc_start: 0.8729 (mtp) cc_final: 0.8438 (ttm) REVERT: D 232 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7792 (mm-40) REVERT: D 235 LYS cc_start: 0.8768 (tttt) cc_final: 0.8550 (ttpp) REVERT: E 263 ASP cc_start: 0.7096 (t0) cc_final: 0.6815 (t0) REVERT: E 273 ASP cc_start: 0.8003 (t0) cc_final: 0.7786 (t0) REVERT: E 302 MET cc_start: 0.8909 (mmm) cc_final: 0.8689 (mmp) REVERT: F 183 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8196 (tptp) REVERT: F 299 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7530 (mm-30) REVERT: G 1235 ASN cc_start: 0.6953 (t0) cc_final: 0.6728 (t0) REVERT: G 1240 MET cc_start: 0.5627 (mmm) cc_final: 0.5227 (mpt) REVERT: G 1406 VAL cc_start: 0.7860 (t) cc_final: 0.7484 (m) REVERT: G 1479 ASP cc_start: 0.7239 (p0) cc_final: 0.6657 (p0) REVERT: G 1534 LYS cc_start: 0.8259 (tttt) cc_final: 0.8042 (mtpp) REVERT: G 1585 MET cc_start: 0.7651 (tpt) cc_final: 0.7143 (tpp) REVERT: J 677 ASP cc_start: 0.7857 (t0) cc_final: 0.7356 (t0) REVERT: N 91 LYS cc_start: 0.8224 (mttt) cc_final: 0.7378 (mptt) REVERT: O 74 LYS cc_start: 0.8135 (mttt) cc_final: 0.7931 (mtpm) REVERT: P 32 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5346 (pt0) REVERT: P 68 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7257 (tp30) REVERT: P 75 SER cc_start: 0.8547 (t) cc_final: 0.8335 (m) REVERT: Q 79 LYS cc_start: 0.8232 (tptm) cc_final: 0.7872 (tmmt) REVERT: R 82 THR cc_start: 0.8094 (p) cc_final: 0.7670 (t) REVERT: R 95 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7372 (mtp-110) outliers start: 0 outliers final: 3 residues processed: 897 average time/residue: 2.0225 time to fit residues: 2107.4243 Evaluate side-chains 504 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 501 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain G residue 1508 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 407 optimal weight: 4.9990 chunk 365 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 377 optimal weight: 40.0000 chunk 146 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS B 255 GLN B 285 GLN B 421 ASN B 429 GLN C 19 HIS C 146 ASN C 237 GLN C 409 GLN D 328 ASN E 65 GLN F 96 GLN F 357 ASN F 394 GLN G1035 ASN G1151 HIS G1269 ASN G1345 HIS I 199 ASN J 73 ASN J 628 HIS M 125 GLN P 60 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS P 81 ASN Q 108 ASN Q 125 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 42175 Z= 0.400 Angle : 0.770 32.986 58006 Z= 0.391 Chirality : 0.047 0.255 6607 Planarity : 0.006 0.076 6684 Dihedral : 21.640 162.081 7689 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.00 % Allowed : 10.57 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.01 (0.12), residues: 4639 helix: -0.01 (0.10), residues: 2205 sheet: 0.32 (0.20), residues: 616 loop : 0.18 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G1036 HIS 0.011 0.002 HIS G1191 PHE 0.027 0.003 PHE G1219 TYR 0.023 0.003 TYR N 88 ARG 0.011 0.001 ARG F 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 501 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8063 (tt0) cc_final: 0.7726 (tp30) REVERT: A 157 THR cc_start: 0.8583 (t) cc_final: 0.8334 (m) REVERT: A 170 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: A 228 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: A 238 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 286 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7835 (mtmm) REVERT: A 373 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7678 (ttp80) REVERT: B 34 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: B 419 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7897 (ttm170) REVERT: B 442 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.7020 (mmm160) REVERT: C 106 GLU cc_start: 0.8197 (tt0) cc_final: 0.7941 (mt-10) REVERT: C 279 GLU cc_start: 0.7444 (tp30) cc_final: 0.7054 (mm-30) REVERT: C 368 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7524 (mm-30) REVERT: D 187 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: D 232 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7860 (mm-40) REVERT: D 235 LYS cc_start: 0.8882 (tttt) cc_final: 0.8656 (pptt) REVERT: D 284 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: E 263 ASP cc_start: 0.7242 (t0) cc_final: 0.6951 (t0) REVERT: E 273 ASP cc_start: 0.7968 (t0) cc_final: 0.7708 (m-30) REVERT: E 302 MET cc_start: 0.8893 (mmm) cc_final: 0.8635 (mmp) REVERT: F 97 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7108 (p0) REVERT: F 136 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: F 183 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8220 (tptp) REVERT: G 997 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7336 (p0) REVERT: G 1017 ARG cc_start: 0.6900 (tpt90) cc_final: 0.6681 (tpp-160) REVERT: G 1235 ASN cc_start: 0.7162 (t0) cc_final: 0.6961 (t0) REVERT: G 1240 MET cc_start: 0.5629 (mmm) cc_final: 0.5261 (mpt) REVERT: G 1312 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: G 1392 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: G 1479 ASP cc_start: 0.6841 (p0) cc_final: 0.6346 (p0) REVERT: G 1585 MET cc_start: 0.7766 (tpt) cc_final: 0.7389 (tpp) REVERT: G 1695 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: H 455 MET cc_start: 0.8340 (mmm) cc_final: 0.7720 (mpp) REVERT: I 42 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7750 (mtmt) REVERT: J 677 ASP cc_start: 0.7948 (t0) cc_final: 0.7549 (t0) REVERT: M 106 ASP cc_start: 0.7353 (m-30) cc_final: 0.7132 (m-30) REVERT: M 133 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: N 88 TYR cc_start: 0.7474 (m-80) cc_final: 0.6956 (m-80) REVERT: N 91 LYS cc_start: 0.8073 (mttt) cc_final: 0.7236 (mptt) REVERT: N 93 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: O 15 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7902 (ptpp) REVERT: O 74 LYS cc_start: 0.8295 (mttt) cc_final: 0.8059 (mtpm) REVERT: P 31 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6516 (tmtm) REVERT: P 32 GLU cc_start: 0.5673 (mt-10) cc_final: 0.5413 (pt0) REVERT: Q 65 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7829 (tt) REVERT: Q 79 LYS cc_start: 0.8272 (tptm) cc_final: 0.7981 (tmmt) REVERT: Q 90 MET cc_start: 0.7478 (mmm) cc_final: 0.7273 (mmp) REVERT: R 59 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7274 (ttmt) REVERT: R 85 ASP cc_start: 0.6705 (m-30) cc_final: 0.6472 (t0) REVERT: R 95 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7367 (mtp-110) outliers start: 113 outliers final: 44 residues processed: 574 average time/residue: 1.8898 time to fit residues: 1277.6947 Evaluate side-chains 497 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 436 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1189 ARG Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1480 SER Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1695 GLU Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 59 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 243 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 438 optimal weight: 5.9990 chunk 473 optimal weight: 3.9990 chunk 390 optimal weight: 9.9990 chunk 434 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN B 429 GLN C 146 ASN D 328 ASN E 419 GLN F 96 GLN F 357 ASN F 394 GLN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 654 GLN J 697 ASN J 722 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 42175 Z= 0.272 Angle : 0.664 30.534 58006 Z= 0.332 Chirality : 0.042 0.164 6607 Planarity : 0.005 0.061 6684 Dihedral : 21.280 171.360 7682 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.19 % Allowed : 12.56 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.40 (0.12), residues: 4639 helix: 0.52 (0.11), residues: 2200 sheet: 0.28 (0.20), residues: 598 loop : 0.17 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G1650 HIS 0.017 0.001 HIS R 75 PHE 0.017 0.002 PHE G1501 TYR 0.025 0.002 TYR P 80 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 487 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8308 (ttmm) REVERT: A 133 GLU cc_start: 0.7987 (tt0) cc_final: 0.7699 (tp30) REVERT: A 238 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: A 286 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7868 (mtmt) REVERT: A 373 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7673 (ttp80) REVERT: B 34 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: B 419 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7869 (ttm170) REVERT: B 429 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: B 442 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7017 (mmm160) REVERT: C 106 GLU cc_start: 0.8124 (tt0) cc_final: 0.7889 (mt-10) REVERT: C 233 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7537 (ptmt) REVERT: C 279 GLU cc_start: 0.7383 (tp30) cc_final: 0.7014 (mm-30) REVERT: C 307 MET cc_start: 0.8687 (mmt) cc_final: 0.8106 (mmt) REVERT: D 61 GLU cc_start: 0.8123 (tp30) cc_final: 0.7916 (tm-30) REVERT: D 163 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8441 (ttpp) REVERT: D 187 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: D 196 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8578 (mtpp) REVERT: D 232 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7464 (mm-40) REVERT: D 284 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: E 263 ASP cc_start: 0.7378 (t0) cc_final: 0.6995 (t0) REVERT: E 302 MET cc_start: 0.8855 (mmm) cc_final: 0.8557 (mmp) REVERT: E 359 HIS cc_start: 0.7091 (m-70) cc_final: 0.6842 (p-80) REVERT: F 136 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: F 183 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8166 (tptp) REVERT: F 313 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7217 (tpp-160) REVERT: F 378 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: G 997 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7268 (p0) REVERT: G 1235 ASN cc_start: 0.7150 (t0) cc_final: 0.6932 (t0) REVERT: G 1240 MET cc_start: 0.5538 (mmm) cc_final: 0.5218 (mpt) REVERT: G 1312 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: G 1328 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8024 (mmmm) REVERT: G 1392 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: G 1479 ASP cc_start: 0.6787 (p0) cc_final: 0.6412 (p0) REVERT: I 30 ARG cc_start: 0.8707 (mtp-110) cc_final: 0.8443 (mtp-110) REVERT: I 48 LEU cc_start: 0.8718 (mt) cc_final: 0.8508 (mm) REVERT: I 167 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8160 (mttm) REVERT: J 174 GLU cc_start: 0.7524 (tt0) cc_final: 0.7279 (pt0) REVERT: J 225 LEU cc_start: 0.9064 (mt) cc_final: 0.8773 (mp) REVERT: J 677 ASP cc_start: 0.7996 (t0) cc_final: 0.7610 (t0) REVERT: M 120 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7356 (mmt) REVERT: M 122 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7739 (pttp) REVERT: M 133 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: N 31 LYS cc_start: 0.7289 (mttt) cc_final: 0.6871 (mtpt) REVERT: N 84 MET cc_start: 0.7769 (tpp) cc_final: 0.6837 (tpp) REVERT: N 88 TYR cc_start: 0.7405 (m-80) cc_final: 0.6870 (m-80) REVERT: N 91 LYS cc_start: 0.8067 (mttt) cc_final: 0.7246 (mptt) REVERT: O 72 ASP cc_start: 0.7300 (m-30) cc_final: 0.6846 (m-30) REVERT: O 74 LYS cc_start: 0.8300 (mttt) cc_final: 0.7976 (mptt) REVERT: P 31 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6555 (tmtm) REVERT: P 32 GLU cc_start: 0.5688 (mt-10) cc_final: 0.5404 (pt0) REVERT: Q 79 LYS cc_start: 0.8347 (tptm) cc_final: 0.8046 (tmmt) REVERT: R 59 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7163 (ttmt) REVERT: R 95 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7303 (mtp-110) outliers start: 120 outliers final: 49 residues processed: 562 average time/residue: 1.8560 time to fit residues: 1233.0325 Evaluate side-chains 508 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 439 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 313 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1189 ARG Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1328 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 59 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 433 optimal weight: 6.9990 chunk 329 optimal weight: 0.0170 chunk 227 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 440 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 417 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 421 ASN C 230 HIS D 301 HIS D 328 ASN E 394 GLN F 96 GLN F 357 ASN G1657 GLN I 199 ASN J 237 HIS ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 42175 Z= 0.399 Angle : 0.725 30.814 58006 Z= 0.364 Chirality : 0.045 0.213 6607 Planarity : 0.005 0.069 6684 Dihedral : 21.371 173.725 7682 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.06 % Allowed : 13.83 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.14 (0.12), residues: 4639 helix: 0.34 (0.11), residues: 2212 sheet: 0.12 (0.19), residues: 619 loop : 0.00 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1650 HIS 0.009 0.002 HIS B 21 PHE 0.026 0.002 PHE D 223 TYR 0.026 0.002 TYR P 80 ARG 0.011 0.001 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 436 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 133 GLU cc_start: 0.8019 (tt0) cc_final: 0.7727 (tp30) REVERT: A 170 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8404 (mttp) REVERT: A 238 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: A 286 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7874 (mtmt) REVERT: A 373 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7654 (ttp80) REVERT: B 34 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: B 419 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7891 (ttm170) REVERT: B 442 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.7049 (mmm160) REVERT: C 307 MET cc_start: 0.8728 (mmt) cc_final: 0.8312 (mmt) REVERT: D 187 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8594 (mmm) REVERT: D 196 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8574 (mtpp) REVERT: D 232 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7391 (mm-40) REVERT: D 284 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: E 112 GLU cc_start: 0.7685 (tt0) cc_final: 0.7481 (tt0) REVERT: E 132 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8306 (tppt) REVERT: E 263 ASP cc_start: 0.7342 (t0) cc_final: 0.6789 (t0) REVERT: E 302 MET cc_start: 0.8886 (mmm) cc_final: 0.8658 (mmp) REVERT: E 359 HIS cc_start: 0.7166 (m-70) cc_final: 0.6923 (p-80) REVERT: F 97 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7407 (p0) REVERT: F 136 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: F 183 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8195 (tptp) REVERT: F 333 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: F 378 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: G 997 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7315 (p0) REVERT: G 1235 ASN cc_start: 0.7284 (t0) cc_final: 0.7056 (t0) REVERT: G 1240 MET cc_start: 0.5560 (mmm) cc_final: 0.5213 (mpt) REVERT: G 1392 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: G 1479 ASP cc_start: 0.6902 (p0) cc_final: 0.6552 (p0) REVERT: I 35 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6805 (ttm110) REVERT: I 48 LEU cc_start: 0.8718 (mt) cc_final: 0.8518 (mm) REVERT: J 174 GLU cc_start: 0.7544 (tt0) cc_final: 0.7277 (pt0) REVERT: J 295 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.5997 (mtm-85) REVERT: J 677 ASP cc_start: 0.8042 (t0) cc_final: 0.7613 (t0) REVERT: J 740 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: M 120 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: M 122 LYS cc_start: 0.7948 (ptmm) cc_final: 0.7736 (pttp) REVERT: M 133 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: N 84 MET cc_start: 0.7857 (tpp) cc_final: 0.7613 (tpp) REVERT: N 91 LYS cc_start: 0.8075 (mttt) cc_final: 0.7250 (mptt) REVERT: O 74 LYS cc_start: 0.8362 (mttt) cc_final: 0.8020 (mptt) REVERT: P 31 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6631 (tttm) REVERT: Q 59 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6531 (pt0) REVERT: Q 79 LYS cc_start: 0.8376 (tptm) cc_final: 0.8073 (tmmt) REVERT: R 85 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5839 (t0) REVERT: R 95 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7329 (mtp-110) outliers start: 153 outliers final: 71 residues processed: 545 average time/residue: 1.8522 time to fit residues: 1197.0430 Evaluate side-chains 507 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 415 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 740 GLU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 388 optimal weight: 30.0000 chunk 264 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 346 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 397 optimal weight: 0.6980 chunk 322 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 418 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS B 263 GLN B 421 ASN B 429 GLN C 146 ASN D 328 ASN F 357 ASN G1140 GLN ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 GLN M 125 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 93 GLN Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42175 Z= 0.162 Angle : 0.602 29.628 58006 Z= 0.296 Chirality : 0.039 0.171 6607 Planarity : 0.004 0.055 6684 Dihedral : 20.818 177.590 7682 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.26 % Allowed : 16.43 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.72 (0.12), residues: 4639 helix: 0.94 (0.11), residues: 2211 sheet: 0.17 (0.19), residues: 631 loop : 0.20 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1147 HIS 0.007 0.001 HIS G1191 PHE 0.014 0.001 PHE G1219 TYR 0.023 0.001 TYR J 167 ARG 0.012 0.000 ARG G1234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 486 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7371 (mmm-85) REVERT: A 133 GLU cc_start: 0.7943 (tt0) cc_final: 0.7682 (tp30) REVERT: A 238 ASP cc_start: 0.7825 (m-30) cc_final: 0.7605 (m-30) REVERT: A 261 MET cc_start: 0.8837 (tpp) cc_final: 0.8581 (mpp) REVERT: A 286 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7854 (mtmt) REVERT: A 373 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7690 (ttp80) REVERT: B 34 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: B 129 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7280 (tttp) REVERT: B 419 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7862 (ttm170) REVERT: B 421 ASN cc_start: 0.8265 (m-40) cc_final: 0.8019 (m110) REVERT: B 429 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: B 442 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.7056 (mmm160) REVERT: C 307 MET cc_start: 0.8631 (mmt) cc_final: 0.8160 (mmt) REVERT: D 61 GLU cc_start: 0.8150 (tp30) cc_final: 0.7944 (tm-30) REVERT: D 167 MET cc_start: 0.8325 (ttm) cc_final: 0.7964 (mtp) REVERT: D 175 SER cc_start: 0.8075 (p) cc_final: 0.7754 (t) REVERT: D 184 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7435 (tt0) REVERT: D 187 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: D 196 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8485 (mtpt) REVERT: D 284 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: E 112 GLU cc_start: 0.7649 (tt0) cc_final: 0.7413 (tt0) REVERT: E 264 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7459 (t) REVERT: F 136 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: F 183 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8162 (tptp) REVERT: F 333 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: G 997 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7202 (p0) REVERT: G 1240 MET cc_start: 0.5620 (mmm) cc_final: 0.5310 (mpt) REVERT: G 1377 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7359 (mt-10) REVERT: G 1392 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: G 1479 ASP cc_start: 0.6870 (p0) cc_final: 0.6485 (p0) REVERT: G 1581 MET cc_start: 0.7461 (tpt) cc_final: 0.7033 (tpt) REVERT: H 455 MET cc_start: 0.8207 (mmm) cc_final: 0.7875 (mtm) REVERT: I 35 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6818 (ttm110) REVERT: J 677 ASP cc_start: 0.8111 (t0) cc_final: 0.7688 (t0) REVERT: J 684 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (mtt90) REVERT: J 740 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: M 122 LYS cc_start: 0.7866 (ptmm) cc_final: 0.7654 (pttp) REVERT: M 133 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: N 31 LYS cc_start: 0.7306 (mttt) cc_final: 0.7042 (ptmt) REVERT: N 84 MET cc_start: 0.7742 (tpp) cc_final: 0.7445 (tpp) REVERT: N 91 LYS cc_start: 0.7963 (mttt) cc_final: 0.7130 (mptt) REVERT: N 93 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: O 74 LYS cc_start: 0.8313 (mttt) cc_final: 0.8080 (mtpm) REVERT: P 31 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6690 (tttm) REVERT: P 32 GLU cc_start: 0.5771 (mt-10) cc_final: 0.5506 (pt0) REVERT: P 68 GLU cc_start: 0.7463 (tp30) cc_final: 0.7026 (tt0) REVERT: Q 53 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: Q 59 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: Q 79 LYS cc_start: 0.8322 (tptm) cc_final: 0.8048 (tmmt) REVERT: R 78 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6557 (mtm-85) REVERT: R 85 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5600 (t0) REVERT: R 95 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7278 (mtp-110) outliers start: 85 outliers final: 31 residues processed: 536 average time/residue: 1.9098 time to fit residues: 1216.7715 Evaluate side-chains 492 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 442 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 684 ARG Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 740 GLU Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 156 optimal weight: 7.9990 chunk 419 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 466 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN E 24 HIS E 359 HIS F 357 ASN F 419 GLN G1235 ASN I 199 ASN M 68 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN R 25 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 42175 Z= 0.408 Angle : 0.722 30.782 58006 Z= 0.361 Chirality : 0.045 0.179 6607 Planarity : 0.005 0.076 6684 Dihedral : 21.160 179.529 7682 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.85 % Allowed : 15.87 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.27 (0.12), residues: 4639 helix: 0.51 (0.11), residues: 2221 sheet: 0.01 (0.19), residues: 636 loop : 0.04 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1650 HIS 0.008 0.001 HIS B 21 PHE 0.026 0.002 PHE D 223 TYR 0.027 0.002 TYR P 80 ARG 0.009 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 435 time to evaluate : 4.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8007 (tt0) cc_final: 0.7728 (tp30) REVERT: A 238 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: A 286 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7856 (mtmt) REVERT: A 373 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7672 (ttp80) REVERT: A 401 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7217 (mtm180) REVERT: B 34 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: B 269 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7159 (ttm) REVERT: B 419 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7873 (ttm170) REVERT: B 429 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: B 442 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7126 (mmm160) REVERT: C 307 MET cc_start: 0.8698 (mmt) cc_final: 0.8273 (mmt) REVERT: D 167 MET cc_start: 0.8467 (ttm) cc_final: 0.8211 (mtp) REVERT: D 175 SER cc_start: 0.8190 (p) cc_final: 0.7879 (t) REVERT: D 184 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7447 (tt0) REVERT: D 187 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: D 228 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: D 284 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: E 112 GLU cc_start: 0.7708 (tt0) cc_final: 0.7446 (tt0) REVERT: E 264 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7719 (t) REVERT: F 136 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: F 177 MET cc_start: 0.9039 (tpp) cc_final: 0.8626 (tpp) REVERT: F 183 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8044 (tptp) REVERT: F 184 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: F 185 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7903 (ptm-80) REVERT: F 333 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7894 (ttp80) REVERT: G 997 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7354 (p0) REVERT: G 1098 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7957 (mttp) REVERT: G 1240 MET cc_start: 0.5663 (mmm) cc_final: 0.5308 (mpt) REVERT: G 1392 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: G 1479 ASP cc_start: 0.6880 (p0) cc_final: 0.6506 (p0) REVERT: G 1585 MET cc_start: 0.7704 (tpp) cc_final: 0.7221 (tpp) REVERT: I 35 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6828 (ttm110) REVERT: I 167 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (mttm) REVERT: J 626 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: J 677 ASP cc_start: 0.8052 (t0) cc_final: 0.7625 (t0) REVERT: J 740 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: M 90 MET cc_start: 0.7504 (mmm) cc_final: 0.7274 (mmt) REVERT: M 120 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7435 (mmt) REVERT: M 133 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: N 84 MET cc_start: 0.7866 (tpp) cc_final: 0.7546 (tpp) REVERT: N 91 LYS cc_start: 0.8050 (mttt) cc_final: 0.7242 (mptt) REVERT: O 74 LYS cc_start: 0.8344 (mttt) cc_final: 0.8099 (mtpm) REVERT: Q 53 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7306 (ttm170) REVERT: Q 79 LYS cc_start: 0.8375 (tptm) cc_final: 0.8052 (tmmm) REVERT: R 85 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5736 (t0) REVERT: R 95 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7166 (mtp85) outliers start: 145 outliers final: 72 residues processed: 531 average time/residue: 1.8357 time to fit residues: 1153.8949 Evaluate side-chains 508 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 412 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 968 LEU Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1098 LYS Chi-restraints excluded: chain G residue 1110 GLN Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 740 GLU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 449 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 340 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 392 optimal weight: 30.0000 chunk 260 optimal weight: 2.9990 chunk 464 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 283 optimal weight: 0.0770 chunk 214 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN D 328 ASN E 359 HIS F 357 ASN ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 42175 Z= 0.247 Angle : 0.643 30.778 58006 Z= 0.319 Chirality : 0.041 0.174 6607 Planarity : 0.004 0.066 6684 Dihedral : 20.921 179.755 7682 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.68 % Allowed : 17.47 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.51 (0.12), residues: 4639 helix: 0.77 (0.11), residues: 2214 sheet: 0.04 (0.19), residues: 634 loop : 0.10 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G1650 HIS 0.006 0.001 HIS G1191 PHE 0.027 0.002 PHE D 223 TYR 0.026 0.002 TYR J 167 ARG 0.008 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 436 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7963 (tt0) cc_final: 0.7725 (tp30) REVERT: A 238 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 286 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7824 (mtmt) REVERT: A 373 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7670 (ttp80) REVERT: B 34 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: B 429 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: B 442 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7116 (mmm160) REVERT: C 307 MET cc_start: 0.8665 (mmt) cc_final: 0.8216 (mmt) REVERT: D 61 GLU cc_start: 0.8178 (tp30) cc_final: 0.7974 (tm-30) REVERT: D 175 SER cc_start: 0.8121 (p) cc_final: 0.7857 (t) REVERT: D 187 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8466 (mmm) REVERT: D 228 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8115 (mm-30) REVERT: D 235 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8625 (tttt) REVERT: D 284 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: E 112 GLU cc_start: 0.7704 (tt0) cc_final: 0.7448 (tt0) REVERT: E 264 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7492 (t) REVERT: F 136 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: F 183 LYS cc_start: 0.8353 (mmmm) cc_final: 0.7999 (tptp) REVERT: F 185 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7921 (ptm-80) REVERT: F 333 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7847 (ttp80) REVERT: G 997 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7323 (p0) REVERT: G 1131 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6630 (mtt90) REVERT: G 1143 MET cc_start: 0.7535 (mmm) cc_final: 0.7318 (tpp) REVERT: G 1240 MET cc_start: 0.5795 (mmm) cc_final: 0.5474 (mpt) REVERT: G 1377 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7381 (mt-10) REVERT: G 1392 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: G 1479 ASP cc_start: 0.6874 (p0) cc_final: 0.6515 (p0) REVERT: J 677 ASP cc_start: 0.8010 (t0) cc_final: 0.7651 (t0) REVERT: J 740 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: M 90 MET cc_start: 0.7426 (mmm) cc_final: 0.7205 (mmt) REVERT: M 133 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: N 31 LYS cc_start: 0.7346 (mttt) cc_final: 0.7088 (ptmt) REVERT: N 84 MET cc_start: 0.7830 (tpp) cc_final: 0.7495 (tpp) REVERT: N 91 LYS cc_start: 0.7944 (mttt) cc_final: 0.7117 (mptt) REVERT: N 93 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6036 (mp10) REVERT: O 74 LYS cc_start: 0.8360 (mttt) cc_final: 0.8100 (mtpm) REVERT: P 32 GLU cc_start: 0.5738 (mt-10) cc_final: 0.5490 (pt0) REVERT: P 68 GLU cc_start: 0.7577 (tp30) cc_final: 0.7155 (tt0) REVERT: Q 53 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7285 (ttm170) REVERT: Q 59 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6527 (pt0) REVERT: Q 79 LYS cc_start: 0.8351 (tptm) cc_final: 0.8044 (tmmm) REVERT: R 95 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7364 (mtp-110) outliers start: 101 outliers final: 50 residues processed: 498 average time/residue: 1.8859 time to fit residues: 1111.1371 Evaluate side-chains 483 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 416 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1131 ARG Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 740 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 287 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 277 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 295 optimal weight: 0.0030 chunk 316 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 365 optimal weight: 0.6980 overall best weight: 1.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN D 328 ASN D 375 GLN E 24 HIS E 96 GLN E 359 HIS F 357 ASN ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.004 0.043 42175 Z= 0.252 Angle : 0.643 31.433 58006 Z= 0.318 Chirality : 0.041 0.170 6607 Planarity : 0.005 0.066 6684 Dihedral : 20.831 178.472 7682 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.55 % Allowed : 18.13 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.57 (0.12), residues: 4639 helix: 0.86 (0.11), residues: 2204 sheet: 0.05 (0.19), residues: 632 loop : 0.08 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G1650 HIS 0.006 0.001 HIS G1191 PHE 0.027 0.002 PHE D 223 TYR 0.029 0.002 TYR P 80 ARG 0.010 0.000 ARG Q 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 429 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7430 (mmm-85) REVERT: A 133 GLU cc_start: 0.7960 (tt0) cc_final: 0.7730 (tp30) REVERT: A 238 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: A 286 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7820 (mtmt) REVERT: A 373 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7668 (ttp80) REVERT: B 34 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: B 429 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: B 442 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7123 (mmm160) REVERT: C 8 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5412 (mpt180) REVERT: C 307 MET cc_start: 0.8667 (mmt) cc_final: 0.8205 (mmt) REVERT: D 175 SER cc_start: 0.8121 (p) cc_final: 0.7870 (t) REVERT: D 187 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: D 228 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8106 (mm-30) REVERT: D 235 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8631 (tttt) REVERT: D 284 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: E 112 GLU cc_start: 0.7711 (tt0) cc_final: 0.7462 (tt0) REVERT: E 252 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8028 (ptt180) REVERT: E 264 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (t) REVERT: F 136 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: F 183 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7997 (tptp) REVERT: F 185 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7925 (ptm-80) REVERT: F 333 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7852 (ttp80) REVERT: G 997 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7322 (p0) REVERT: G 1131 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6678 (mtt90) REVERT: G 1143 MET cc_start: 0.7513 (mmm) cc_final: 0.7294 (tpp) REVERT: G 1240 MET cc_start: 0.5820 (mmm) cc_final: 0.5500 (mpt) REVERT: G 1353 GLU cc_start: 0.7504 (pm20) cc_final: 0.7236 (mp0) REVERT: G 1377 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7355 (mt-10) REVERT: G 1392 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: G 1479 ASP cc_start: 0.6877 (p0) cc_final: 0.6508 (p0) REVERT: H 455 MET cc_start: 0.8267 (mmm) cc_final: 0.7857 (mtm) REVERT: J 626 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: J 677 ASP cc_start: 0.8014 (t0) cc_final: 0.7640 (t0) REVERT: J 740 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: M 90 MET cc_start: 0.7422 (mmm) cc_final: 0.7209 (mmt) REVERT: M 133 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: N 31 LYS cc_start: 0.7343 (mttt) cc_final: 0.7087 (ptmt) REVERT: N 84 MET cc_start: 0.7839 (tpp) cc_final: 0.7523 (tpp) REVERT: N 91 LYS cc_start: 0.8000 (mttt) cc_final: 0.7170 (mptt) REVERT: N 93 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6122 (mp10) REVERT: O 74 LYS cc_start: 0.8371 (mttt) cc_final: 0.8111 (mtpm) REVERT: P 32 GLU cc_start: 0.5800 (mt-10) cc_final: 0.5444 (pt0) REVERT: P 68 GLU cc_start: 0.7509 (tp30) cc_final: 0.7114 (tt0) REVERT: Q 53 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7295 (ttm170) REVERT: Q 59 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: Q 79 LYS cc_start: 0.8330 (tptm) cc_final: 0.8034 (tmmm) REVERT: R 95 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7368 (mtp-110) outliers start: 96 outliers final: 56 residues processed: 490 average time/residue: 1.8928 time to fit residues: 1095.6528 Evaluate side-chains 493 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 417 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1110 GLN Chi-restraints excluded: chain G residue 1131 ARG Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1591 TYR Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 740 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 422 optimal weight: 4.9990 chunk 445 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 chunk 444 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 339 optimal weight: 0.0570 chunk 132 optimal weight: 6.9990 chunk 391 optimal weight: 30.0000 chunk 409 optimal weight: 0.0270 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN D 328 ASN D 419 GLN E 24 HIS E 359 HIS F 357 ASN G1235 ASN ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42175 Z= 0.214 Angle : 0.628 31.103 58006 Z= 0.309 Chirality : 0.040 0.158 6607 Planarity : 0.004 0.067 6684 Dihedral : 20.698 178.864 7682 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 18.34 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.70 (0.12), residues: 4639 helix: 1.00 (0.11), residues: 2197 sheet: 0.07 (0.20), residues: 632 loop : 0.11 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G1147 HIS 0.006 0.001 HIS G1191 PHE 0.027 0.001 PHE D 223 TYR 0.028 0.001 TYR J 167 ARG 0.009 0.000 ARG Q 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 428 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7367 (mmm-85) REVERT: A 133 GLU cc_start: 0.7939 (tt0) cc_final: 0.7722 (tp30) REVERT: A 238 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 286 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7851 (mtmt) REVERT: A 373 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7674 (ttp80) REVERT: B 34 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: B 129 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7193 (tptp) REVERT: B 195 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 429 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: B 442 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7093 (mmm160) REVERT: C 8 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5382 (mpt180) REVERT: C 307 MET cc_start: 0.8671 (mmt) cc_final: 0.8186 (mmt) REVERT: D 139 GLU cc_start: 0.7225 (pm20) cc_final: 0.6845 (pm20) REVERT: D 175 SER cc_start: 0.8110 (p) cc_final: 0.7863 (t) REVERT: D 187 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8576 (mpt) REVERT: D 228 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8112 (mm-30) REVERT: D 234 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7798 (mmt90) REVERT: D 235 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8646 (tttt) REVERT: D 284 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: E 112 GLU cc_start: 0.7702 (tt0) cc_final: 0.7463 (tt0) REVERT: E 252 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7985 (ptt180) REVERT: E 264 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7436 (t) REVERT: F 136 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: F 183 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7988 (tptp) REVERT: F 185 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7944 (ptm-80) REVERT: F 208 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: F 333 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7827 (ttp80) REVERT: G 997 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7315 (p0) REVERT: G 1131 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6622 (mtt90) REVERT: G 1143 MET cc_start: 0.7469 (mmm) cc_final: 0.7265 (tpp) REVERT: G 1240 MET cc_start: 0.5857 (mmm) cc_final: 0.5555 (mpt) REVERT: G 1353 GLU cc_start: 0.7474 (pm20) cc_final: 0.7214 (mp0) REVERT: G 1377 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7356 (mt-10) REVERT: G 1392 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: G 1479 ASP cc_start: 0.6866 (p0) cc_final: 0.6490 (p0) REVERT: H 455 MET cc_start: 0.8194 (mmm) cc_final: 0.7796 (mtm) REVERT: J 39 ILE cc_start: 0.6864 (pp) cc_final: 0.6383 (pt) REVERT: J 626 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: J 677 ASP cc_start: 0.8024 (t0) cc_final: 0.7652 (t0) REVERT: M 133 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: N 31 LYS cc_start: 0.7361 (mttt) cc_final: 0.7117 (ptmt) REVERT: N 84 MET cc_start: 0.7852 (tpp) cc_final: 0.7459 (tpp) REVERT: N 91 LYS cc_start: 0.7988 (mttt) cc_final: 0.7165 (mptt) REVERT: N 93 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.6108 (mp10) REVERT: O 74 LYS cc_start: 0.8351 (mttt) cc_final: 0.8108 (mtpm) REVERT: P 32 GLU cc_start: 0.5793 (mt-10) cc_final: 0.5467 (pt0) REVERT: P 82 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7498 (mttm) REVERT: Q 53 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: Q 59 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6480 (pt0) REVERT: Q 79 LYS cc_start: 0.8306 (tptm) cc_final: 0.8048 (tmmt) REVERT: R 78 ARG cc_start: 0.7061 (mtm110) cc_final: 0.6512 (mtm-85) REVERT: R 95 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7377 (mtp-110) outliers start: 92 outliers final: 56 residues processed: 489 average time/residue: 1.8392 time to fit residues: 1066.3045 Evaluate side-chains 488 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 411 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1019 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1110 GLN Chi-restraints excluded: chain G residue 1131 ARG Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 431 optimal weight: 7.9990 chunk 284 optimal weight: 0.6980 chunk 457 optimal weight: 0.5980 chunk 279 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 480 optimal weight: 6.9990 chunk 441 optimal weight: 6.9990 chunk 382 optimal weight: 50.0000 chunk 39 optimal weight: 0.7980 chunk 295 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 429 GLN D 328 ASN E 96 GLN E 359 HIS F 357 ASN ** G1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1692 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42175 Z= 0.170 Angle : 0.606 30.533 58006 Z= 0.296 Chirality : 0.039 0.226 6607 Planarity : 0.004 0.064 6684 Dihedral : 20.452 179.031 7682 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.96 % Allowed : 19.06 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 4639 helix: 1.20 (0.11), residues: 2198 sheet: 0.13 (0.20), residues: 642 loop : 0.18 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1147 HIS 0.006 0.001 HIS G1191 PHE 0.012 0.001 PHE C 117 TYR 0.047 0.001 TYR P 80 ARG 0.009 0.000 ARG Q 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 447 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7287 (mmm-85) REVERT: A 261 MET cc_start: 0.8774 (tpp) cc_final: 0.8552 (tpp) REVERT: A 286 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7848 (mtmm) REVERT: A 373 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7660 (ttp80) REVERT: A 401 ARG cc_start: 0.7140 (mtm180) cc_final: 0.6895 (ptt90) REVERT: B 34 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: B 168 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: B 429 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: B 442 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7116 (mmm160) REVERT: C 159 LEU cc_start: 0.8721 (mp) cc_final: 0.8100 (mt) REVERT: C 307 MET cc_start: 0.8614 (mmt) cc_final: 0.8109 (mmt) REVERT: C 327 ILE cc_start: 0.8769 (tt) cc_final: 0.8489 (tt) REVERT: D 139 GLU cc_start: 0.7228 (pm20) cc_final: 0.6804 (pm20) REVERT: D 175 SER cc_start: 0.8089 (p) cc_final: 0.7841 (t) REVERT: D 187 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8573 (mpt) REVERT: D 234 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7838 (mmt90) REVERT: D 235 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8649 (tttt) REVERT: E 112 GLU cc_start: 0.7691 (tt0) cc_final: 0.7452 (tt0) REVERT: E 252 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7989 (ptt180) REVERT: E 264 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7163 (t) REVERT: E 378 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6862 (mm-30) REVERT: F 40 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8248 (ptt-90) REVERT: F 136 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: F 183 LYS cc_start: 0.8346 (mmmm) cc_final: 0.7988 (tptp) REVERT: F 185 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7956 (ptm-80) REVERT: F 284 GLU cc_start: 0.8023 (tp30) cc_final: 0.7813 (tp30) REVERT: F 333 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7836 (ttp80) REVERT: G 997 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7237 (p0) REVERT: G 1131 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6338 (mtt90) REVERT: G 1240 MET cc_start: 0.5823 (mmm) cc_final: 0.5569 (mpt) REVERT: G 1353 GLU cc_start: 0.7469 (pm20) cc_final: 0.7204 (mp0) REVERT: G 1377 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7326 (mt-10) REVERT: G 1392 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: G 1479 ASP cc_start: 0.6869 (p0) cc_final: 0.6468 (p0) REVERT: G 1581 MET cc_start: 0.7417 (tpt) cc_final: 0.7075 (tpt) REVERT: J 39 ILE cc_start: 0.6900 (pp) cc_final: 0.6399 (pt) REVERT: J 626 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: J 677 ASP cc_start: 0.8065 (t0) cc_final: 0.7654 (t0) REVERT: M 133 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: N 31 LYS cc_start: 0.7332 (mttt) cc_final: 0.7097 (ptmt) REVERT: N 84 MET cc_start: 0.7851 (tpp) cc_final: 0.7478 (tpp) REVERT: N 91 LYS cc_start: 0.8003 (mttt) cc_final: 0.7147 (mptt) REVERT: O 74 LYS cc_start: 0.8359 (mttt) cc_final: 0.8106 (mtpm) REVERT: P 32 GLU cc_start: 0.5777 (mt-10) cc_final: 0.5473 (pt0) REVERT: P 68 GLU cc_start: 0.7594 (tp30) cc_final: 0.7181 (tt0) REVERT: P 76 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7586 (ttm110) REVERT: P 82 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7487 (mttm) REVERT: Q 53 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7281 (ttm170) REVERT: Q 59 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: Q 79 LYS cc_start: 0.8258 (tptm) cc_final: 0.8013 (tmmt) REVERT: R 78 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6516 (mtm-85) REVERT: R 95 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7380 (mtp-110) outliers start: 74 outliers final: 40 residues processed: 500 average time/residue: 1.9058 time to fit residues: 1140.9087 Evaluate side-chains 473 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 416 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 997 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1110 GLN Chi-restraints excluded: chain G residue 1131 ARG Chi-restraints excluded: chain G residue 1220 CYS Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1579 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 92 ARG Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 234 optimal weight: 0.1980 chunk 303 optimal weight: 0.9990 chunk 407 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 382 optimal weight: 50.0000 chunk 160 optimal weight: 0.8980 chunk 393 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN C 43 GLN D 328 ASN E 359 HIS F 357 ASN ** G1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094375 restraints weight = 65925.595| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.50 r_work: 0.3262 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42175 Z= 0.171 Angle : 0.608 30.616 58006 Z= 0.296 Chirality : 0.039 0.155 6607 Planarity : 0.004 0.066 6684 Dihedral : 20.360 176.717 7682 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.67 % Allowed : 19.75 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: 0.97 (0.12), residues: 4639 helix: 1.28 (0.11), residues: 2201 sheet: 0.13 (0.20), residues: 647 loop : 0.20 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1147 HIS 0.005 0.001 HIS G1191 PHE 0.027 0.001 PHE D 223 TYR 0.051 0.001 TYR P 80 ARG 0.008 0.000 ARG Q 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18812.37 seconds wall clock time: 330 minutes 27.37 seconds (19827.37 seconds total)