Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 15:05:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/08_2023/8oo7_17006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/08_2023/8oo7_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_17006/08_2023/8oo7_17006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/08_2023/8oo7_17006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/08_2023/8oo7_17006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo7_17006/08_2023/8oo7_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 19.12, per 1000 atoms: 0.47 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: 17.05 Conformation dependent library (CDL) restraints added in 5.6 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: 17.50 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: 23.73 Time building geometry restraints manager: 18.29 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: 23417 33.24 - 66.47: 1380 66.47 - 99.71: 67 99.71 - 132.94: 4 132.94 - 166.18: 9 Dihedral angle restraints: 24877 sinusoidal: 11372 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 24874 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: 4.250 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: 0.070 Extract box with map and model: 13.450 Check model and map are aligned: 0.600 Set scattering table: 0.330 Process input model: 119.620 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.950 ------------------------------------------------------------------------------- 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 : 18.161 166.175 16165 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 % 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 *********************** 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 : 4.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 897 average time/residue: 2.0572 time to fit residues: 2151.3514 Evaluate side-chains 495 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 492 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 1.1244 time to fit residues: 8.8256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 0.9990 chunk 229 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 146 ASN C 237 GLN C 409 GLN D 328 ASN F 96 GLN F 357 ASN F 394 GLN G1035 ASN G1151 HIS G1207 GLN G1345 HIS I 199 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 42175 Z= 0.292 Angle : 0.715 32.984 58006 Z= 0.363 Chirality : 0.044 0.238 6607 Planarity : 0.005 0.066 6684 Dihedral : 21.411 159.330 7467 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.81 % 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: 0.23 (0.12), residues: 4639 helix: 0.17 (0.11), residues: 2210 sheet: 0.32 (0.20), residues: 621 loop : 0.34 (0.14), residues: 1808 *********************** 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 603 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 497 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 39 residues processed: 560 average time/residue: 1.9678 time to fit residues: 1301.0258 Evaluate side-chains 466 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 427 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 10 average time/residue: 0.8637 time to fit residues: 17.8764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 364 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 438 optimal weight: 5.9990 chunk 473 optimal weight: 5.9990 chunk 390 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 B 429 GLN C 19 HIS C 146 ASN C 230 HIS D 328 ASN E 394 GLN E 419 GLN F 96 GLN F 357 ASN G1269 ASN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 645 GLN J 654 GLN J 697 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 42175 Z= 0.447 Angle : 0.772 30.696 58006 Z= 0.389 Chirality : 0.047 0.247 6607 Planarity : 0.006 0.082 6684 Dihedral : 21.592 169.577 7467 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 3.45 % 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: 0.12 (0.11), residues: 2195 sheet: 0.17 (0.20), residues: 609 loop : 0.05 (0.14), residues: 1835 *********************** 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 592 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 462 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 56 residues processed: 545 average time/residue: 1.8889 time to fit residues: 1225.9202 Evaluate side-chains 467 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 411 time to evaluate : 4.292 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 13 average time/residue: 0.9101 time to fit residues: 22.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 433 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 440 optimal weight: 3.9990 chunk 465 optimal weight: 0.8980 chunk 229 optimal weight: 0.0470 chunk 417 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN C 146 ASN D 328 ASN F 96 GLN F 357 ASN I 199 ASN J 73 ASN M 125 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 42175 Z= 0.216 Angle : 0.635 30.134 58006 Z= 0.315 Chirality : 0.040 0.177 6607 Planarity : 0.004 0.056 6684 Dihedral : 21.197 173.609 7467 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 3.24 % 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: 0.49 (0.12), residues: 4639 helix: 0.65 (0.11), residues: 2203 sheet: 0.17 (0.20), residues: 617 loop : 0.19 (0.14), residues: 1819 *********************** 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 587 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 465 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 54 residues processed: 546 average time/residue: 1.8054 time to fit residues: 1175.5693 Evaluate side-chains 471 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 417 time to evaluate : 4.054 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 44 residues processed: 11 average time/residue: 0.7729 time to fit residues: 17.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 6 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 397 optimal weight: 0.9980 chunk 322 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 418 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 421 ASN D 301 HIS D 328 ASN E 359 HIS F 357 ASN F 419 GLN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 42175 Z= 0.262 Angle : 0.649 30.319 58006 Z= 0.322 Chirality : 0.041 0.199 6607 Planarity : 0.005 0.058 6684 Dihedral : 21.080 174.568 7467 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.89 % 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: 0.53 (0.12), residues: 4639 helix: 0.73 (0.11), residues: 2212 sheet: 0.14 (0.19), residues: 631 loop : 0.16 (0.14), residues: 1796 *********************** 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 542 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 433 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 55 residues processed: 511 average time/residue: 1.8409 time to fit residues: 1125.9266 Evaluate side-chains 466 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 411 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 13 average time/residue: 0.6114 time to fit residues: 18.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 156 optimal weight: 8.9990 chunk 419 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 466 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS C 146 ASN D 328 ASN E 359 HIS F 357 ASN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3452 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= 0.235 Angle : 0.633 30.291 58006 Z= 0.312 Chirality : 0.041 0.196 6607 Planarity : 0.004 0.059 6684 Dihedral : 20.914 176.390 7467 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.81 % 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: 0.64 (0.12), residues: 4639 helix: 0.86 (0.11), residues: 2210 sheet: 0.13 (0.19), residues: 631 loop : 0.19 (0.14), residues: 1798 *********************** 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 547 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 441 time to evaluate : 4.673 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 59 residues processed: 516 average time/residue: 1.8214 time to fit residues: 1126.0122 Evaluate side-chains 466 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 407 time to evaluate : 4.338 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 49 residues processed: 12 average time/residue: 0.5848 time to fit residues: 17.1490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 449 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 chunk 260 optimal weight: 2.9990 chunk 464 optimal weight: 0.9980 chunk 290 optimal weight: 5.9990 chunk 283 optimal weight: 0.0980 chunk 214 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN D 375 GLN E 24 HIS E 359 HIS F 357 ASN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 42175 Z= 0.319 Angle : 0.675 30.879 58006 Z= 0.336 Chirality : 0.043 0.180 6607 Planarity : 0.005 0.067 6684 Dihedral : 21.001 179.414 7467 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 2.87 % 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: 0.46 (0.12), residues: 4639 helix: 0.70 (0.11), residues: 2209 sheet: 0.08 (0.19), residues: 629 loop : 0.09 (0.14), residues: 1801 *********************** 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 532 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 424 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 72 residues processed: 496 average time/residue: 1.8223 time to fit residues: 1083.0331 Evaluate side-chains 475 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 403 time to evaluate : 4.274 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 53 residues processed: 21 average time/residue: 0.7136 time to fit residues: 27.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 287 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 365 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN E 24 HIS E 96 GLN E 359 HIS F 357 ASN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 42175 Z= 0.370 Angle : 0.706 32.999 58006 Z= 0.353 Chirality : 0.044 0.210 6607 Planarity : 0.005 0.075 6684 Dihedral : 21.082 176.736 7467 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.63 % 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: 0.23 (0.12), residues: 4639 helix: 0.51 (0.11), residues: 2212 sheet: -0.01 (0.19), residues: 629 loop : -0.02 (0.14), residues: 1798 *********************** 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 511 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 412 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 68 residues processed: 485 average time/residue: 1.8977 time to fit residues: 1101.7654 Evaluate side-chains 465 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 397 time to evaluate : 4.758 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 56 residues processed: 13 average time/residue: 0.7379 time to fit residues: 20.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 406 optimal weight: 2.9990 chunk 432 optimal weight: 0.3980 chunk 444 optimal weight: 0.9990 chunk 260 optimal weight: 0.0470 chunk 188 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 391 optimal weight: 30.0000 chunk 409 optimal weight: 8.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN D 328 ASN E 359 HIS F 357 ASN G1035 ASN G1692 GLN 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** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 42175 Z= 0.172 Angle : 0.611 30.768 58006 Z= 0.300 Chirality : 0.039 0.203 6607 Planarity : 0.004 0.063 6684 Dihedral : 20.649 179.200 7467 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.94 % 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: 0.77 (0.12), residues: 4639 helix: 1.06 (0.11), residues: 2191 sheet: 0.06 (0.20), residues: 644 loop : 0.17 (0.14), residues: 1804 *********************** 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 509 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 436 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 55 residues processed: 494 average time/residue: 1.8406 time to fit residues: 1090.6368 Evaluate side-chains 458 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 403 time to evaluate : 4.453 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 9 average time/residue: 0.5789 time to fit residues: 14.2876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 457 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 chunk 480 optimal weight: 5.9990 chunk 441 optimal weight: 0.9980 chunk 382 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN E 24 HIS E 359 HIS F 357 ASN G1035 ASN G1692 GLN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 42175 Z= 0.367 Angle : 0.709 33.101 58006 Z= 0.352 Chirality : 0.044 0.212 6607 Planarity : 0.005 0.078 6684 Dihedral : 20.915 176.341 7467 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.91 % 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: 0.39 (0.12), residues: 4639 helix: 0.70 (0.11), residues: 2209 sheet: 0.00 (0.20), residues: 634 loop : 0.00 (0.14), residues: 1796 ********************** 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 476 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 404 time to evaluate : 4.580 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 54 residues processed: 464 average time/residue: 1.9292 time to fit residues: 1072.6110 Evaluate side-chains 449 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 395 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 49 residues processed: 6 average time/residue: 0.5039 time to fit residues: 10.5704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 234 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 407 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 352 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 382 optimal weight: 50.0000 chunk 160 optimal weight: 0.7980 chunk 393 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 328 ASN E 359 HIS F 357 ASN G1035 ASN I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092346 restraints weight = 66213.336| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.54 r_work: 0.3222 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 42175 Z= 0.225 Angle : 0.642 31.552 58006 Z= 0.316 Chirality : 0.040 0.187 6607 Planarity : 0.005 0.073 6684 Dihedral : 20.740 178.821 7467 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.57 % 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: 0.63 (0.12), residues: 4639 helix: 0.93 (0.11), residues: 2196 sheet: 0.09 (0.20), residues: 629 loop : 0.07 (0.14), residues: 1814 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18130.67 seconds wall clock time: 320 minutes 37.19 seconds (19237.19 seconds total)