Starting phenix.real_space_refine on Sun Mar 24 12:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8h_16476/03_2024/8c8h_16476_updated.pdb" } resolution = 3.84 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= 0.008 sd= 0.061 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 191 5.16 5 C 26243 2.51 5 N 6851 2.21 5 O 7939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41296 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5603 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 646} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "R" Number of atoms: 1056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1065 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "U" Number of atoms: 1362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 48} Conformer: "B" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 48} bond proxies already assigned to first conformer: 1468 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1013 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4347 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 11, 'TRANS': 527} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "S" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1311 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8500 SG CYS B1087 85.709 97.908 101.216 1.00102.55 S ATOM 8523 SG CYS B1090 84.965 94.300 100.234 1.00101.00 S ATOM 8612 SG CYS B1103 83.277 95.829 103.116 1.00102.96 S ATOM 8637 SG CYS B1106 86.922 94.911 103.456 1.00 98.80 S ATOM 14373 SG CYS I 326 51.754 114.296 100.278 1.00118.79 S ATOM 14686 SG CYS I 363 50.713 111.521 97.306 1.00102.22 S ATOM 14710 SG CYS I 366 53.512 114.200 96.871 1.00106.34 S ATOM 22247 SG CYS A 49 68.897 93.362 103.568 1.00119.06 S ATOM 22269 SG CYS A 52 69.622 97.116 103.368 1.00114.14 S ATOM 22321 SG CYS A 59 69.853 95.025 100.227 1.00112.49 S ATOM 22581 SG CYS A 90 106.249 63.550 92.795 1.00130.69 S ATOM 22605 SG CYS A 93 108.056 64.595 96.017 1.00129.42 S ATOM 22903 SG CYS A 130 109.932 63.085 93.113 1.00134.49 S ATOM 22946 SG CYS A 135 107.934 60.850 95.193 1.00140.78 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A G U 36 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G U 36 " occ=0.50 Time building chain proxies: 21.58, per 1000 atoms: 0.52 Number of scatterers: 41296 At special positions: 0 Unit cell: (154.208, 161.652, 190.367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 191 16.00 P 67 15.00 Mg 1 11.99 O 7939 8.00 N 6851 7.00 C 26243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 441 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 438 " - pdb=" SG CYS K 456 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 15.45 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " Number of angles added : 18 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 45 sheets defined 34.0% alpha, 12.0% beta 20 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 18.42 Creating SS restraints... Processing helix chain 'B' and resid 9 through 16 Processing helix chain 'B' and resid 29 through 50 removed outlier: 5.429A pdb=" N PHE B 33 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 36 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 43 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 45 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 46 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 50 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 258 through 277 removed outlier: 4.109A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 324 through 343 removed outlier: 3.873A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 362 through 391 removed outlier: 3.536A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.522A pdb=" N ASN B 437 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 499 through 514 removed outlier: 3.650A pdb=" N ASP B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.707A pdb=" N ILE B 545 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N CYS B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 547 " --> pdb=" O MET B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 613 No H-bonds generated for 'chain 'B' and resid 611 through 613' Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 644 through 648 Processing helix chain 'B' and resid 655 through 657 No H-bonds generated for 'chain 'B' and resid 655 through 657' Processing helix chain 'B' and resid 665 through 668 Processing helix chain 'B' and resid 684 through 694 removed outlier: 3.974A pdb=" N ILE B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 899 through 901 No H-bonds generated for 'chain 'B' and resid 899 through 901' Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1022 through 1024 No H-bonds generated for 'chain 'B' and resid 1022 through 1024' Processing helix chain 'B' and resid 1055 through 1063 Processing helix chain 'B' and resid 1067 through 1073 Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1104 through 1108 Processing helix chain 'B' and resid 1122 through 1133 Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.656A pdb=" N CYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 79 through 95 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 144 through 160 Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 168 through 185 removed outlier: 3.645A pdb=" N LEU I 171 " --> pdb=" O MET I 168 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU I 172 " --> pdb=" O LYS I 169 " (cutoff:3.500A) Proline residue: I 173 - end of helix removed outlier: 5.158A pdb=" N LEU I 179 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP I 180 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'I' and resid 255 through 266 removed outlier: 4.379A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 270 through 278 removed outlier: 3.550A pdb=" N TYR I 273 " --> pdb=" O ARG I 270 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER I 274 " --> pdb=" O HIS I 271 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR I 275 " --> pdb=" O LEU I 272 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 276 " --> pdb=" O TYR I 273 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU I 278 " --> pdb=" O TYR I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 290 removed outlier: 4.616A pdb=" N THR I 288 " --> pdb=" O SER I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 335 Processing helix chain 'I' and resid 342 through 353 Processing helix chain 'I' and resid 371 through 373 No H-bonds generated for 'chain 'I' and resid 371 through 373' Processing helix chain 'I' and resid 405 through 420 removed outlier: 3.522A pdb=" N ARG I 408 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE I 411 " --> pdb=" O ARG I 408 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN I 412 " --> pdb=" O PHE I 409 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE I 420 " --> pdb=" O PHE I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 removed outlier: 3.650A pdb=" N LYS I 429 " --> pdb=" O TRP I 426 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR I 430 " --> pdb=" O VAL I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 453 removed outlier: 3.756A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 460 removed outlier: 3.590A pdb=" N ARG I 460 " --> pdb=" O SER I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 500 Processing helix chain 'I' and resid 504 through 513 Processing helix chain 'I' and resid 523 through 537 Processing helix chain 'I' and resid 546 through 556 Processing helix chain 'I' and resid 562 through 580 removed outlier: 3.753A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 Processing helix chain 'I' and resid 706 through 709 No H-bonds generated for 'chain 'I' and resid 706 through 709' Processing helix chain 'I' and resid 724 through 741 Processing helix chain 'I' and resid 757 through 770 removed outlier: 3.656A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 774 through 792 removed outlier: 5.890A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 19 No H-bonds generated for 'chain 'J' and resid 16 through 19' Processing helix chain 'J' and resid 28 through 35 removed outlier: 4.559A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 45 Processing helix chain 'R' and resid 27 through 39 removed outlier: 4.548A pdb=" N ASN R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'K' and resid 451 through 456 Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.100A pdb=" N ILE A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.521A pdb=" N TRP A 177 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix No H-bonds generated for 'chain 'A' and resid 174 through 180' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.236A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 476 through 487 removed outlier: 6.597A pdb=" N LYS A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 551 through 571 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 586 through 614 Processing helix chain 'A' and resid 623 through 655 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 728 through 762 Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.706A pdb=" N SER A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'A' and resid 985 through 995 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1036 through 1045 Processing helix chain 'A' and resid 1078 through 1092 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1130 through 1135 removed outlier: 4.348A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1154 Processing helix chain 'A' and resid 1156 through 1171 Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 4.233A pdb=" N GLN A1180 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Proline residue: A1181 - end of helix Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1219 through 1226 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1259 through 1262 No H-bonds generated for 'chain 'A' and resid 1259 through 1262' Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Y' and resid 5 through 16 Processing helix chain 'Y' and resid 33 through 44 Processing helix chain 'Y' and resid 61 through 74 removed outlier: 4.853A pdb=" N LYS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 89 No H-bonds generated for 'chain 'Y' and resid 87 through 89' Processing helix chain 'Y' and resid 93 through 101 Processing helix chain 'Y' and resid 103 through 105 No H-bonds generated for 'chain 'Y' and resid 103 through 105' Processing helix chain 'Y' and resid 119 through 128 Processing helix chain 'Y' and resid 143 through 151 Processing helix chain 'Y' and resid 162 through 174 removed outlier: 3.890A pdb=" N LYS Y 170 " --> pdb=" O ASN Y 166 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 192 through 201 Processing helix chain 'Y' and resid 220 through 226 Processing helix chain 'Y' and resid 265 through 281 Processing helix chain 'Y' and resid 288 through 295 Processing helix chain 'Y' and resid 322 through 327 Processing helix chain 'Y' and resid 335 through 341 Processing helix chain 'Y' and resid 352 through 364 Processing helix chain 'Y' and resid 366 through 377 Processing helix chain 'Y' and resid 393 through 404 Processing helix chain 'Y' and resid 419 through 426 Processing helix chain 'Y' and resid 467 through 477 Processing helix chain 'Y' and resid 480 through 483 Processing helix chain 'Y' and resid 509 through 533 removed outlier: 3.869A pdb=" N PHE Y 514 " --> pdb=" O ASP Y 510 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN Y 526 " --> pdb=" O LYS Y 522 " (cutoff:3.500A) Processing helix chain 'Y' and resid 536 through 542 Processing helix chain 'Y' and resid 555 through 559 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 49 through 58 removed outlier: 4.263A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 66 through 73 removed outlier: 4.029A pdb=" N ILE C 69 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS C 70 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 71 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 208 through 228 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 284 through 301 Processing helix chain 'S' and resid 37 through 50 Processing helix chain 'S' and resid 73 through 79 Processing helix chain 'S' and resid 82 through 84 No H-bonds generated for 'chain 'S' and resid 82 through 84' Processing helix chain 'S' and resid 103 through 107 Processing helix chain 'S' and resid 113 through 130 Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'B' and resid 54 through 59 removed outlier: 6.519A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= D, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.823A pdb=" N THR B 189 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL B 182 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER B 191 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 180 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 443 through 445 Processing sheet with id= F, first strand: chain 'B' and resid 567 through 571 removed outlier: 7.815A pdb=" N ILE B 578 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 588 through 592 Processing sheet with id= H, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.812A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 892 through 897 removed outlier: 7.600A pdb=" N ILE B 760 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 896 " --> pdb=" O ILE B 760 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 1095 through 1097 removed outlier: 3.511A pdb=" N ILE B1097 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.313A pdb=" N ILE E 82 " --> pdb=" O PHE E 64 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 113 through 115 removed outlier: 7.328A pdb=" N ILE E 181 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 3 through 15 Processing sheet with id= N, first strand: chain 'G' and resid 136 through 140 removed outlier: 5.213A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE G 152 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LYS G 107 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE G 154 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL G 153 " --> pdb=" O GLN G 145 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN G 157 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU G 141 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 124 through 126 Processing sheet with id= P, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.620A pdb=" N THR G 75 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE G 48 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.115A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 242 " --> pdb=" O LEU I 237 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 198 through 200 removed outlier: 6.581A pdb=" N LYS I 162 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL I 132 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE I 164 " --> pdb=" O VAL I 132 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 210 through 217 Processing sheet with id= T, first strand: chain 'I' and resid 354 through 357 Processing sheet with id= U, first strand: chain 'I' and resid 656 through 658 Processing sheet with id= V, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.250A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 14 through 16 removed outlier: 6.118A pdb=" N ALA R 113 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE R 96 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE R 115 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL R 98 " --> pdb=" O ILE R 115 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL R 117 " --> pdb=" O VAL R 98 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 48 through 54 Processing sheet with id= Y, first strand: chain 'K' and resid 383 through 385 removed outlier: 4.060A pdb=" N MET K 415 " --> pdb=" O ILE K 385 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 399 through 401 Processing sheet with id= AA, first strand: chain 'K' and resid 427 through 431 removed outlier: 3.831A pdb=" N LYS K 427 " --> pdb=" O PHE K 443 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE K 439 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= AC, first strand: chain 'A' and resid 22 through 24 removed outlier: 4.279A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.196A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 285 through 289 removed outlier: 3.525A pdb=" N SER A 288 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.256A pdb=" N ILE A 402 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'A' and resid 312 through 316 removed outlier: 6.999A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 796 through 799 Processing sheet with id= AI, first strand: chain 'A' and resid 976 through 978 Processing sheet with id= AJ, first strand: chain 'A' and resid 979 through 981 Processing sheet with id= AK, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 3.690A pdb=" N LYS A1015 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Q' and resid 48 through 54 Processing sheet with id= AM, first strand: chain 'Q' and resid 113 through 118 removed outlier: 6.482A pdb=" N GLU Q 9 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL Q 94 " --> pdb=" O PHE Q 7 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE Q 7 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id= AO, first strand: chain 'Y' and resid 231 through 234 removed outlier: 8.111A pdb=" N SER Y 232 " --> pdb=" O SER Y 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU Y 52 " --> pdb=" O SER Y 232 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE Y 234 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE Y 54 " --> pdb=" O ILE Y 234 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET Y 179 " --> pdb=" O LEU Y 51 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU Y 53 " --> pdb=" O MET Y 179 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS Y 181 " --> pdb=" O LEU Y 53 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS Y 55 " --> pdb=" O CYS Y 181 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Y' and resid 253 through 262 removed outlier: 4.423A pdb=" N ASN Y 456 " --> pdb=" O TYR Y 492 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS Y 381 " --> pdb=" O ASN Y 456 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE Y 458 " --> pdb=" O LYS Y 381 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU Y 383 " --> pdb=" O ILE Y 458 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE Y 460 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE Y 385 " --> pdb=" O ILE Y 460 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS Y 440 " --> pdb=" O CYS Y 382 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL Y 384 " --> pdb=" O CYS Y 440 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 5 through 13 Processing sheet with id= AR, first strand: chain 'C' and resid 99 through 104 removed outlier: 7.170A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 251 through 253 1296 hydrogen bonds defined for protein. 3444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 18.98 Time building geometry restraints manager: 16.77 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: 12924 1.34 - 1.46: 10086 1.46 - 1.59: 18755 1.59 - 1.71: 139 1.71 - 1.83: 299 Bond restraints: 42203 Sorted by residual: bond pdb=" C3' U U 20 " pdb=" C2' U U 20 " ideal model delta sigma weight residual 1.525 1.544 -0.019 1.50e-02 4.44e+03 1.63e+00 bond pdb=" C4' G U 18 " pdb=" C3' G U 18 " ideal model delta sigma weight residual 1.527 1.510 0.017 1.50e-02 4.44e+03 1.36e+00 bond pdb=" O4' U U 20 " pdb=" C1' U U 20 " ideal model delta sigma weight residual 1.415 1.398 0.017 1.50e-02 4.44e+03 1.25e+00 bond pdb=" CA THR A1109 " pdb=" CB THR A1109 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.15e+00 bond pdb=" C VAL C 173 " pdb=" O VAL C 173 " ideal model delta sigma weight residual 1.236 1.223 0.014 1.35e-02 5.49e+03 1.05e+00 ... (remaining 42198 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.62: 1298 106.62 - 113.79: 24247 113.79 - 120.97: 19846 120.97 - 128.14: 11691 128.14 - 135.32: 264 Bond angle restraints: 57346 Sorted by residual: angle pdb=" N CYS E 14 " pdb=" CA CYS E 14 " pdb=" C CYS E 14 " ideal model delta sigma weight residual 113.18 104.94 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" C2' A U 31 " pdb=" C1' A U 31 " pdb=" N9 A U 31 " ideal model delta sigma weight residual 112.00 117.32 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C THR A 695 " pdb=" N ARG A 696 " pdb=" CA ARG A 696 " ideal model delta sigma weight residual 122.15 112.96 9.19 2.83e+00 1.25e-01 1.05e+01 angle pdb=" C4' G U 18 " pdb=" C3' G U 18 " pdb=" C2' G U 18 " ideal model delta sigma weight residual 102.60 99.44 3.16 1.00e+00 1.00e+00 9.96e+00 angle pdb=" O4' G U 18 " pdb=" C4' G U 18 " pdb=" C3' G U 18 " ideal model delta sigma weight residual 106.10 103.07 3.03 1.00e+00 1.00e+00 9.18e+00 ... (remaining 57341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 24657 29.18 - 58.36: 918 58.36 - 87.54: 123 87.54 - 116.72: 4 116.72 - 145.90: 1 Dihedral angle restraints: 25703 sinusoidal: 11151 harmonic: 14552 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -158.84 72.84 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" O4' U U 19 " pdb=" C1' U U 19 " pdb=" N1 U U 19 " pdb=" C2 U U 19 " ideal model delta sinusoidal sigma weight residual 232.00 86.10 145.90 1 1.70e+01 3.46e-03 6.07e+01 dihedral pdb=" O4' U U 16 " pdb=" C1' U U 16 " pdb=" N1 U U 16 " pdb=" C2 U U 16 " ideal model delta sinusoidal sigma weight residual -160.00 -68.93 -91.07 1 1.50e+01 4.44e-03 4.35e+01 ... (remaining 25700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4962 0.046 - 0.091: 1187 0.091 - 0.137: 391 0.137 - 0.182: 10 0.182 - 0.228: 2 Chirality restraints: 6552 Sorted by residual: chirality pdb=" C1' C U 23 " pdb=" O4' C U 23 " pdb=" C2' C U 23 " pdb=" N1 C U 23 " both_signs ideal model delta sigma weight residual False 2.45 2.22 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' C U 44 " pdb=" O4' C U 44 " pdb=" C2' C U 44 " pdb=" N1 C U 44 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR E 136 " pdb=" N THR E 136 " pdb=" C THR E 136 " pdb=" CB THR E 136 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 6549 not shown) Planarity restraints: 7012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 42 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ILE B 42 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 42 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU B 43 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 18 " 0.040 2.00e-02 2.50e+03 2.52e-02 1.91e+01 pdb=" N9 G U 18 " -0.071 2.00e-02 2.50e+03 pdb=" C8 G U 18 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G U 18 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G U 18 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G U 18 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G U 18 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G U 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G U 18 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G U 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G U 18 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G U 18 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U 44 " -0.035 2.00e-02 2.50e+03 2.41e-02 1.30e+01 pdb=" N1 C U 44 " 0.059 2.00e-02 2.50e+03 pdb=" C2 C U 44 " -0.021 2.00e-02 2.50e+03 pdb=" O2 C U 44 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C U 44 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C U 44 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C U 44 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C U 44 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C U 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 7009 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 756 2.66 - 3.22: 37412 3.22 - 3.78: 65456 3.78 - 4.34: 94514 4.34 - 4.90: 150602 Nonbonded interactions: 348740 Sorted by model distance: nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.105 2.170 nonbonded pdb=" OH TYR A 606 " pdb=" OE2 GLU A 626 " model vdw 2.147 2.440 nonbonded pdb=" O VAL A 619 " pdb=" OH TYR S 144 " model vdw 2.173 2.440 nonbonded pdb=" O GLU I 398 " pdb=" OG SER Y 547 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR B 208 " pdb=" O PHE B 315 " model vdw 2.179 2.440 ... (remaining 348735 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 'Q' and (resid 1 through 15 or resid 17 through 124)) selection = (chain 'R' and (resid 1 through 15 or resid 17 through 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 124)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.190 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 125.710 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 146.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.002 0.036 42203 Z= 0.148 Angle : 0.557 13.908 57346 Z= 0.314 Chirality : 0.042 0.228 6552 Planarity : 0.006 0.073 7012 Dihedral : 14.853 145.902 16269 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 7.66 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: -3.34 (0.10), residues: 4859 helix: -2.18 (0.09), residues: 1813 sheet: -1.64 (0.18), residues: 712 loop : -2.37 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 777 HIS 0.007 0.001 HIS B 44 PHE 0.037 0.001 PHE A 938 TYR 0.025 0.001 TYR C 170 ARG 0.018 0.001 ARG I 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1240 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 TYR cc_start: 0.7888 (t80) cc_final: 0.7500 (t80) REVERT: B 209 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7947 (tttt) REVERT: B 237 SER cc_start: 0.9036 (m) cc_final: 0.8596 (t) REVERT: B 307 PHE cc_start: 0.7801 (t80) cc_final: 0.7361 (t80) REVERT: B 474 ASP cc_start: 0.8102 (t70) cc_final: 0.7716 (t0) REVERT: B 614 MET cc_start: 0.7332 (mtm) cc_final: 0.7120 (mtm) REVERT: B 627 ILE cc_start: 0.9067 (mt) cc_final: 0.8864 (tp) REVERT: B 680 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.6833 (p0) REVERT: B 704 ASP cc_start: 0.7246 (m-30) cc_final: 0.6839 (m-30) REVERT: B 719 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7155 (mt-10) REVERT: B 721 PRO cc_start: 0.8827 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: B 777 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8438 (ttmt) REVERT: B 785 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: B 790 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7398 (ptpp) REVERT: B 794 ARG cc_start: 0.6427 (mtm110) cc_final: 0.6193 (mmt180) REVERT: B 1014 TYR cc_start: 0.7983 (t80) cc_final: 0.6202 (t80) REVERT: B 1085 TYR cc_start: 0.8723 (m-80) cc_final: 0.8271 (m-80) REVERT: B 1131 MET cc_start: 0.8744 (mmt) cc_final: 0.8448 (mmp) REVERT: B 1141 ASP cc_start: 0.8044 (m-30) cc_final: 0.7823 (m-30) REVERT: E 51 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8359 (tmt-80) REVERT: E 152 LEU cc_start: 0.8719 (mt) cc_final: 0.7345 (mt) REVERT: F 94 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8608 (mm-40) REVERT: F 147 LEU cc_start: 0.9151 (tp) cc_final: 0.8949 (tt) REVERT: F 152 ASP cc_start: 0.7922 (m-30) cc_final: 0.7634 (m-30) REVERT: G 83 ASP cc_start: 0.7003 (m-30) cc_final: 0.6724 (m-30) REVERT: G 103 ASP cc_start: 0.7858 (p0) cc_final: 0.6689 (m-30) REVERT: G 104 LEU cc_start: 0.9108 (tp) cc_final: 0.8880 (tp) REVERT: G 125 PHE cc_start: 0.8442 (t80) cc_final: 0.8090 (t80) REVERT: I 205 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8020 (tttt) REVERT: I 214 LEU cc_start: 0.8276 (tp) cc_final: 0.7540 (pt) REVERT: I 376 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7472 (t70) REVERT: I 384 THR cc_start: 0.3824 (OUTLIER) cc_final: 0.2615 (m) REVERT: I 487 MET cc_start: 0.6754 (mmp) cc_final: 0.6386 (mmm) REVERT: I 646 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8739 (mmmt) REVERT: J 10 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (p) REVERT: A 73 ILE cc_start: 0.9179 (mm) cc_final: 0.8966 (mm) REVERT: A 105 ASP cc_start: 0.8088 (m-30) cc_final: 0.7572 (p0) REVERT: A 151 PHE cc_start: 0.8167 (m-80) cc_final: 0.7917 (m-80) REVERT: A 266 THR cc_start: 0.8786 (p) cc_final: 0.8479 (p) REVERT: A 287 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.8209 (ttm-80) REVERT: A 389 VAL cc_start: 0.8460 (t) cc_final: 0.8221 (p) REVERT: A 423 MET cc_start: 0.8540 (mtt) cc_final: 0.8299 (mtt) REVERT: A 530 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8615 (t) REVERT: A 545 LEU cc_start: 0.8685 (mt) cc_final: 0.8443 (tp) REVERT: A 675 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 765 ASP cc_start: 0.7389 (m-30) cc_final: 0.7002 (m-30) REVERT: A 836 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9146 (p) REVERT: A 998 VAL cc_start: 0.8534 (t) cc_final: 0.8271 (p) REVERT: A 1068 PHE cc_start: 0.9094 (m-80) cc_final: 0.8722 (m-80) REVERT: A 1199 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: A 1234 ASP cc_start: 0.7983 (m-30) cc_final: 0.7761 (m-30) REVERT: A 1241 PHE cc_start: 0.9031 (m-80) cc_final: 0.8742 (m-80) REVERT: A 1242 SER cc_start: 0.8966 (m) cc_final: 0.8573 (p) REVERT: Y 182 LEU cc_start: 0.8447 (mp) cc_final: 0.8179 (mt) REVERT: Y 218 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.5273 (m) REVERT: Y 258 MET cc_start: 0.2983 (mtt) cc_final: 0.2612 (mmm) REVERT: Y 565 LEU cc_start: 0.6610 (mt) cc_final: 0.5976 (mp) REVERT: C 29 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 31 LYS cc_start: 0.8233 (mtmt) cc_final: 0.8012 (mtmm) REVERT: C 42 SER cc_start: 0.7819 (t) cc_final: 0.7135 (p) REVERT: C 98 ASP cc_start: 0.7645 (m-30) cc_final: 0.7155 (t0) REVERT: C 101 TYR cc_start: 0.8723 (m-80) cc_final: 0.8419 (m-10) REVERT: C 151 ASN cc_start: 0.8831 (p0) cc_final: 0.8297 (p0) REVERT: C 239 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: C 244 TYR cc_start: 0.7760 (t80) cc_final: 0.7066 (t80) REVERT: C 250 MET cc_start: 0.8601 (tpp) cc_final: 0.8171 (tpt) REVERT: S 78 TYR cc_start: 0.7500 (t80) cc_final: 0.7253 (t80) REVERT: S 118 LEU cc_start: 0.7554 (mt) cc_final: 0.7079 (mp) REVERT: S 125 ILE cc_start: 0.7640 (mt) cc_final: 0.7412 (tt) outliers start: 194 outliers final: 24 residues processed: 1374 average time/residue: 0.5524 time to fit residues: 1221.5342 Evaluate side-chains 656 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 619 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 218 VAL Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain S residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 414 optimal weight: 8.9990 chunk 372 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 384 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 445 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 169 ASN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 387 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 639 ASN B 681 HIS ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 HIS B 789 ASN B 971 GLN B1040 GLN B1101 ASN B1122 HIS E 129 GLN F 115 HIS G 100 GLN G 133 ASN I 253 ASN I 348 ASN I 419 ASN ** I 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 ASN I 567 HIS ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 GLN ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 753 ASN ** I 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 GLN ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 167 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 255 ASN A 309 ASN A 318 ASN A 359 HIS A 385 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 548 HIS A 589 ASN A 611 ASN A 636 ASN A 641 ASN A 741 GLN A 865 HIS A 994 ASN A1065 ASN A1094 ASN A1142 ASN A1149 ASN A1169 ASN A1199 ASN A1226 HIS ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 HIS Q 111 ASN Y 78 ASN ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 144 HIS Y 189 ASN Y 236 ASN Y 272 GLN Y 391 GLN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 24 GLN C 129 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 171 ASN S 58 ASN S 72 ASN S 73 ASN S 135 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 42203 Z= 0.378 Angle : 0.728 14.740 57346 Z= 0.381 Chirality : 0.047 0.244 6552 Planarity : 0.005 0.060 7012 Dihedral : 11.984 147.253 6417 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.94 % Allowed : 15.81 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.11), residues: 4859 helix: -0.56 (0.11), residues: 1781 sheet: -1.31 (0.19), residues: 679 loop : -1.82 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 43 HIS 0.011 0.002 HIS B 318 PHE 0.033 0.002 PHE G 154 TYR 0.040 0.002 TYR I 734 ARG 0.012 0.001 ARG B1058 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 602 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8883 (p0) REVERT: B 188 PHE cc_start: 0.8536 (m-80) cc_final: 0.8326 (m-80) REVERT: B 217 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8640 (tp) REVERT: B 237 SER cc_start: 0.9182 (m) cc_final: 0.8735 (t) REVERT: B 307 PHE cc_start: 0.7709 (t80) cc_final: 0.7132 (t80) REVERT: B 319 MET cc_start: 0.7555 (mmt) cc_final: 0.6361 (mmm) REVERT: B 474 ASP cc_start: 0.8192 (t70) cc_final: 0.7897 (t0) REVERT: B 513 ILE cc_start: 0.8807 (mt) cc_final: 0.8604 (tp) REVERT: B 575 MET cc_start: 0.8940 (mpp) cc_final: 0.8739 (mpp) REVERT: B 666 GLU cc_start: 0.8383 (pm20) cc_final: 0.8183 (pm20) REVERT: B 680 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.6637 (p0) REVERT: B 716 MET cc_start: 0.7686 (mtp) cc_final: 0.7355 (mtp) REVERT: B 777 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8327 (ttmt) REVERT: B 785 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: B 1108 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (ttmm) REVERT: B 1141 ASP cc_start: 0.8118 (m-30) cc_final: 0.7817 (m-30) REVERT: E 51 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8328 (tmt-80) REVERT: E 113 PHE cc_start: 0.8560 (p90) cc_final: 0.8161 (p90) REVERT: E 142 MET cc_start: 0.7724 (ttp) cc_final: 0.7507 (ttp) REVERT: F 74 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8854 (p) REVERT: F 81 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: F 94 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8589 (mm-40) REVERT: G 83 ASP cc_start: 0.7357 (m-30) cc_final: 0.6858 (m-30) REVERT: G 96 ASN cc_start: 0.6439 (OUTLIER) cc_final: 0.5818 (p0) REVERT: G 103 ASP cc_start: 0.7908 (p0) cc_final: 0.6731 (m-30) REVERT: G 104 LEU cc_start: 0.9173 (tp) cc_final: 0.8842 (tp) REVERT: G 141 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8388 (mp) REVERT: I 168 MET cc_start: 0.8604 (mtp) cc_final: 0.8196 (mmm) REVERT: I 169 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8535 (tppt) REVERT: I 205 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8139 (tttt) REVERT: I 372 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7698 (mm) REVERT: I 376 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7593 (t70) REVERT: I 422 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7851 (mmtt) REVERT: I 487 MET cc_start: 0.7117 (mmp) cc_final: 0.6473 (mmm) REVERT: I 593 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: I 595 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.7432 (mmt180) REVERT: I 646 LYS cc_start: 0.9283 (mtpp) cc_final: 0.9019 (mtmt) REVERT: I 695 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7866 (p0) REVERT: I 790 MET cc_start: 0.7848 (mmt) cc_final: 0.7639 (mpp) REVERT: A 105 ASP cc_start: 0.8231 (m-30) cc_final: 0.7561 (p0) REVERT: A 107 ASN cc_start: 0.7335 (t0) cc_final: 0.6838 (t0) REVERT: A 266 THR cc_start: 0.8735 (p) cc_final: 0.8515 (p) REVERT: A 287 ARG cc_start: 0.8732 (ttp-170) cc_final: 0.8214 (ttm-80) REVERT: A 536 MET cc_start: 0.9154 (mmm) cc_final: 0.8943 (mmt) REVERT: A 675 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8026 (mm-30) REVERT: A 765 ASP cc_start: 0.7379 (m-30) cc_final: 0.7072 (m-30) REVERT: A 836 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9261 (p) REVERT: A 1026 TYR cc_start: 0.8165 (m-80) cc_final: 0.7944 (m-80) REVERT: A 1040 MET cc_start: 0.7231 (mtm) cc_final: 0.6981 (mtp) REVERT: A 1103 ILE cc_start: 0.8903 (mp) cc_final: 0.8584 (mt) REVERT: A 1192 SER cc_start: 0.8461 (t) cc_final: 0.8258 (t) REVERT: A 1242 SER cc_start: 0.9027 (m) cc_final: 0.8710 (p) REVERT: Y 101 TYR cc_start: 0.6916 (m-80) cc_final: 0.6545 (m-80) REVERT: Y 182 LEU cc_start: 0.8499 (mp) cc_final: 0.8294 (mt) REVERT: Y 258 MET cc_start: 0.3169 (mtt) cc_final: 0.2906 (mmp) REVERT: Y 391 GLN cc_start: 0.1577 (OUTLIER) cc_final: 0.1155 (pm20) REVERT: Y 531 PHE cc_start: 0.8370 (m-80) cc_final: 0.8015 (m-80) REVERT: C 42 SER cc_start: 0.7799 (t) cc_final: 0.7569 (m) REVERT: C 98 ASP cc_start: 0.7776 (m-30) cc_final: 0.7459 (t0) REVERT: C 142 ILE cc_start: 0.8904 (tt) cc_final: 0.8574 (tp) REVERT: C 170 TYR cc_start: 0.7724 (t80) cc_final: 0.7477 (t80) REVERT: S 39 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8337 (p0) REVERT: S 243 LEU cc_start: 0.7494 (mp) cc_final: 0.7248 (mm) outliers start: 178 outliers final: 102 residues processed: 736 average time/residue: 0.5248 time to fit residues: 639.7399 Evaluate side-chains 599 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 479 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1108 LYS Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain A residue 1235 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 45 ASP Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 33 ASP Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 441 VAL Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 150 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 247 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 371 optimal weight: 0.7980 chunk 303 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 446 optimal weight: 0.8980 chunk 482 optimal weight: 9.9990 chunk 397 optimal weight: 0.9990 chunk 442 optimal weight: 4.9990 chunk 152 optimal weight: 0.0030 chunk 358 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 714 HIS B1110 ASN E 125 ASN I 253 ASN I 448 GLN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 GLN ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42203 Z= 0.173 Angle : 0.581 11.352 57346 Z= 0.303 Chirality : 0.044 0.260 6552 Planarity : 0.004 0.047 7012 Dihedral : 11.648 150.544 6395 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.43 % Allowed : 17.09 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 4859 helix: -0.12 (0.12), residues: 1776 sheet: -0.89 (0.20), residues: 670 loop : -1.63 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 365 HIS 0.009 0.001 HIS B 318 PHE 0.029 0.001 PHE A 938 TYR 0.022 0.001 TYR A 306 ARG 0.010 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 570 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 ASN cc_start: 0.8627 (t0) cc_final: 0.8419 (t0) REVERT: B 237 SER cc_start: 0.9119 (m) cc_final: 0.8686 (t) REVERT: B 311 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: B 319 MET cc_start: 0.7337 (mmt) cc_final: 0.7043 (mmm) REVERT: B 386 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8016 (mpp) REVERT: B 474 ASP cc_start: 0.8047 (t70) cc_final: 0.7832 (t0) REVERT: B 482 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 544 MET cc_start: 0.8493 (mtp) cc_final: 0.8005 (mtm) REVERT: B 565 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: B 627 ILE cc_start: 0.9172 (mm) cc_final: 0.8939 (tp) REVERT: B 666 GLU cc_start: 0.8240 (pm20) cc_final: 0.7709 (pm20) REVERT: B 680 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.6817 (p0) REVERT: B 785 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: B 862 THR cc_start: 0.8533 (m) cc_final: 0.8288 (t) REVERT: B 1069 THR cc_start: 0.8851 (m) cc_final: 0.8647 (p) REVERT: B 1085 TYR cc_start: 0.8543 (m-80) cc_final: 0.7686 (m-10) REVERT: B 1141 ASP cc_start: 0.8000 (m-30) cc_final: 0.7734 (m-30) REVERT: E 51 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8306 (tmt-80) REVERT: E 123 ILE cc_start: 0.7970 (mt) cc_final: 0.7736 (mt) REVERT: E 152 LEU cc_start: 0.8750 (mt) cc_final: 0.8342 (mt) REVERT: F 74 THR cc_start: 0.9061 (m) cc_final: 0.8745 (p) REVERT: F 81 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: F 88 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8489 (mm-30) REVERT: F 94 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8425 (mt0) REVERT: F 131 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7270 (tm-30) REVERT: G 83 ASP cc_start: 0.7378 (m-30) cc_final: 0.6814 (m-30) REVERT: G 96 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.5930 (p0) REVERT: G 103 ASP cc_start: 0.7745 (p0) cc_final: 0.6633 (m-30) REVERT: G 104 LEU cc_start: 0.9101 (tp) cc_final: 0.8703 (tp) REVERT: I 168 MET cc_start: 0.8490 (mtp) cc_final: 0.8088 (mmm) REVERT: I 169 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8598 (tppt) REVERT: I 205 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8060 (tttt) REVERT: I 259 TRP cc_start: 0.8688 (m-10) cc_final: 0.8470 (m-10) REVERT: I 372 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7609 (mm) REVERT: I 376 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7324 (t70) REVERT: I 486 LYS cc_start: 0.8681 (mttt) cc_final: 0.8209 (ptmt) REVERT: I 487 MET cc_start: 0.7104 (mmp) cc_final: 0.6862 (mmm) REVERT: I 593 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: I 595 ARG cc_start: 0.7844 (mmt-90) cc_final: 0.7491 (mmt180) REVERT: I 599 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4805 (pp) REVERT: I 646 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8925 (mtmt) REVERT: I 695 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7892 (p0) REVERT: I 715 MET cc_start: 0.8248 (mmm) cc_final: 0.7863 (tpt) REVERT: A 105 ASP cc_start: 0.8287 (m-30) cc_final: 0.7649 (p0) REVERT: A 266 THR cc_start: 0.8743 (p) cc_final: 0.8541 (p) REVERT: A 287 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8294 (ttm-80) REVERT: A 422 TRP cc_start: 0.8472 (p-90) cc_final: 0.7970 (p-90) REVERT: A 423 MET cc_start: 0.8372 (mtp) cc_final: 0.7653 (mtt) REVERT: A 633 MET cc_start: 0.8471 (mtp) cc_final: 0.8186 (mtp) REVERT: A 675 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 677 MET cc_start: 0.8685 (ttp) cc_final: 0.8055 (ttp) REVERT: A 836 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 837 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8527 (tt) REVERT: A 1026 TYR cc_start: 0.8067 (m-80) cc_final: 0.7857 (m-80) REVERT: A 1028 LYS cc_start: 0.9380 (ttpp) cc_final: 0.9030 (ttpp) REVERT: A 1128 MET cc_start: 0.6499 (tmm) cc_final: 0.6267 (tmm) REVERT: A 1242 SER cc_start: 0.8979 (m) cc_final: 0.8512 (p) REVERT: Q 78 PHE cc_start: 0.4155 (m-10) cc_final: 0.3586 (m-10) REVERT: Y 182 LEU cc_start: 0.8449 (mp) cc_final: 0.8244 (mt) REVERT: Y 192 GLN cc_start: 0.8610 (pt0) cc_final: 0.8214 (pt0) REVERT: Y 196 MET cc_start: 0.8248 (ttp) cc_final: 0.8041 (ttp) REVERT: Y 258 MET cc_start: 0.3284 (mtt) cc_final: 0.3036 (mmp) REVERT: Y 531 PHE cc_start: 0.8299 (m-80) cc_final: 0.7884 (m-80) REVERT: C 98 ASP cc_start: 0.7655 (m-30) cc_final: 0.7385 (t0) REVERT: C 142 ILE cc_start: 0.8700 (tt) cc_final: 0.8419 (tp) REVERT: S 39 ASP cc_start: 0.8659 (p0) cc_final: 0.7803 (p0) outliers start: 155 outliers final: 77 residues processed: 683 average time/residue: 0.5056 time to fit residues: 571.7283 Evaluate side-chains 579 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 485 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1068 ASN Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 45 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 33 ASP Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 441 optimal weight: 6.9990 chunk 335 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 213 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 chunk 448 optimal weight: 0.1980 chunk 474 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 424 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN I 253 ASN I 589 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 ASN ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42203 Z= 0.174 Angle : 0.562 10.609 57346 Z= 0.292 Chirality : 0.044 0.261 6552 Planarity : 0.004 0.055 7012 Dihedral : 11.440 153.979 6387 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.30 % Allowed : 17.95 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4859 helix: 0.21 (0.12), residues: 1765 sheet: -0.77 (0.20), residues: 670 loop : -1.52 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.013 0.001 HIS R 112 PHE 0.028 0.001 PHE A 938 TYR 0.033 0.001 TYR R 41 ARG 0.013 0.000 ARG R 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 530 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.7057 (tpp) cc_final: 0.6767 (tpp) REVERT: B 237 SER cc_start: 0.9158 (m) cc_final: 0.8742 (t) REVERT: B 319 MET cc_start: 0.7506 (mmt) cc_final: 0.7157 (mmm) REVERT: B 474 ASP cc_start: 0.8138 (t70) cc_final: 0.7869 (t0) REVERT: B 482 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8549 (m) REVERT: B 565 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: B 627 ILE cc_start: 0.9185 (mm) cc_final: 0.8918 (tp) REVERT: B 666 GLU cc_start: 0.8194 (pm20) cc_final: 0.7923 (pm20) REVERT: B 680 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6750 (p0) REVERT: B 698 ILE cc_start: 0.8841 (mm) cc_final: 0.8636 (mt) REVERT: B 771 ASP cc_start: 0.8642 (t0) cc_final: 0.8247 (t70) REVERT: B 785 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: B 794 ARG cc_start: 0.6351 (mtm110) cc_final: 0.5909 (mmt-90) REVERT: B 862 THR cc_start: 0.8521 (m) cc_final: 0.8234 (t) REVERT: B 1021 LEU cc_start: 0.9160 (mt) cc_final: 0.8877 (mm) REVERT: B 1141 ASP cc_start: 0.7991 (m-30) cc_final: 0.7784 (m-30) REVERT: E 51 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8251 (tmt-80) REVERT: E 169 MET cc_start: 0.8084 (ttp) cc_final: 0.7840 (ttp) REVERT: F 74 THR cc_start: 0.9039 (m) cc_final: 0.8714 (p) REVERT: F 81 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: F 94 GLN cc_start: 0.8869 (mt0) cc_final: 0.8433 (mt0) REVERT: F 131 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7278 (tm-30) REVERT: G 74 ILE cc_start: 0.8952 (pt) cc_final: 0.8353 (tt) REVERT: G 83 ASP cc_start: 0.7426 (m-30) cc_final: 0.6849 (m-30) REVERT: G 96 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.6022 (p0) REVERT: G 103 ASP cc_start: 0.7768 (p0) cc_final: 0.6578 (m-30) REVERT: G 104 LEU cc_start: 0.9068 (tp) cc_final: 0.8680 (tp) REVERT: I 168 MET cc_start: 0.8411 (mtp) cc_final: 0.7975 (mmm) REVERT: I 169 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8559 (tppt) REVERT: I 205 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8020 (tttt) REVERT: I 255 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.7824 (t) REVERT: I 259 TRP cc_start: 0.8700 (m-10) cc_final: 0.8144 (m-10) REVERT: I 372 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7757 (mm) REVERT: I 376 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7435 (t70) REVERT: I 486 LYS cc_start: 0.8644 (mttt) cc_final: 0.8194 (ptmt) REVERT: I 487 MET cc_start: 0.7246 (mmp) cc_final: 0.6988 (tpt) REVERT: I 593 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: I 595 ARG cc_start: 0.7879 (mmt-90) cc_final: 0.7384 (mmt180) REVERT: I 599 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5081 (pp) REVERT: I 695 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7930 (p0) REVERT: I 715 MET cc_start: 0.8360 (mmm) cc_final: 0.8106 (tpt) REVERT: A 105 ASP cc_start: 0.8275 (m-30) cc_final: 0.7642 (p0) REVERT: A 287 ARG cc_start: 0.8780 (ttp-170) cc_final: 0.8287 (ttm-80) REVERT: A 423 MET cc_start: 0.8364 (mtp) cc_final: 0.8007 (mtt) REVERT: A 631 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 675 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 771 TYR cc_start: 0.8650 (m-80) cc_final: 0.8423 (m-80) REVERT: A 790 ILE cc_start: 0.8297 (mt) cc_final: 0.8093 (mm) REVERT: A 836 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9093 (p) REVERT: A 837 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8495 (tt) REVERT: A 1026 TYR cc_start: 0.8065 (m-80) cc_final: 0.7699 (m-80) REVERT: A 1242 SER cc_start: 0.8992 (m) cc_final: 0.8513 (p) REVERT: Y 220 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7740 (mm-30) REVERT: Y 258 MET cc_start: 0.3162 (mtt) cc_final: 0.2854 (mmp) REVERT: Y 531 PHE cc_start: 0.8291 (m-80) cc_final: 0.7885 (m-80) REVERT: C 98 ASP cc_start: 0.7691 (m-30) cc_final: 0.7387 (t0) REVERT: C 101 TYR cc_start: 0.8852 (m-10) cc_final: 0.8628 (m-10) REVERT: C 142 ILE cc_start: 0.8735 (tt) cc_final: 0.8466 (tp) REVERT: C 250 MET cc_start: 0.7296 (mmm) cc_final: 0.7035 (mmm) REVERT: C 279 MET cc_start: 0.8425 (mmm) cc_final: 0.7715 (mmt) REVERT: S 39 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.7908 (p0) outliers start: 149 outliers final: 94 residues processed: 644 average time/residue: 0.5051 time to fit residues: 543.9329 Evaluate side-chains 589 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 479 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 777 LYS Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 395 optimal weight: 4.9990 chunk 269 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 328 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 792 ASN J 53 ASN ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 42203 Z= 0.278 Angle : 0.616 13.395 57346 Z= 0.318 Chirality : 0.045 0.321 6552 Planarity : 0.004 0.052 7012 Dihedral : 11.356 156.435 6383 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.18 % Allowed : 17.95 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4859 helix: 0.34 (0.12), residues: 1761 sheet: -0.81 (0.20), residues: 661 loop : -1.42 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 79 HIS 0.009 0.001 HIS Y 533 PHE 0.028 0.002 PHE A 938 TYR 0.024 0.002 TYR G 76 ARG 0.005 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 508 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.6959 (m-30) cc_final: 0.5797 (p0) REVERT: B 140 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8880 (p0) REVERT: B 159 ASN cc_start: 0.8636 (t0) cc_final: 0.7871 (p0) REVERT: B 237 SER cc_start: 0.9230 (m) cc_final: 0.8810 (t) REVERT: B 319 MET cc_start: 0.7627 (mmt) cc_final: 0.6526 (mmm) REVERT: B 474 ASP cc_start: 0.8294 (t70) cc_final: 0.8009 (t0) REVERT: B 513 ILE cc_start: 0.8649 (mt) cc_final: 0.8443 (tp) REVERT: B 565 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: B 627 ILE cc_start: 0.9245 (mm) cc_final: 0.9003 (tp) REVERT: B 666 GLU cc_start: 0.8291 (pm20) cc_final: 0.8056 (pm20) REVERT: B 680 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6547 (p0) REVERT: B 771 ASP cc_start: 0.8710 (t0) cc_final: 0.8319 (t70) REVERT: B 794 ARG cc_start: 0.6411 (mtm110) cc_final: 0.5929 (mmt-90) REVERT: B 862 THR cc_start: 0.8535 (m) cc_final: 0.8245 (t) REVERT: B 1085 TYR cc_start: 0.8494 (m-80) cc_final: 0.7631 (m-10) REVERT: B 1141 ASP cc_start: 0.8096 (m-30) cc_final: 0.7808 (m-30) REVERT: E 51 ARG cc_start: 0.8604 (ttm170) cc_final: 0.8378 (tmt-80) REVERT: E 80 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: E 116 LEU cc_start: 0.7596 (mm) cc_final: 0.7126 (tp) REVERT: F 81 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: F 94 GLN cc_start: 0.8958 (mt0) cc_final: 0.8522 (mt0) REVERT: F 131 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7521 (tm-30) REVERT: G 83 ASP cc_start: 0.7343 (m-30) cc_final: 0.6800 (m-30) REVERT: G 96 ASN cc_start: 0.6639 (OUTLIER) cc_final: 0.6066 (p0) REVERT: G 103 ASP cc_start: 0.7749 (p0) cc_final: 0.6452 (m-30) REVERT: G 104 LEU cc_start: 0.8990 (tp) cc_final: 0.8592 (tp) REVERT: I 168 MET cc_start: 0.8386 (mtp) cc_final: 0.7985 (mmm) REVERT: I 169 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8574 (tppt) REVERT: I 205 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8021 (tttt) REVERT: I 255 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.7982 (t) REVERT: I 259 TRP cc_start: 0.8731 (m-10) cc_final: 0.8476 (m-10) REVERT: I 372 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7600 (mm) REVERT: I 376 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7466 (t70) REVERT: I 487 MET cc_start: 0.7293 (mmp) cc_final: 0.6701 (tpt) REVERT: I 560 MET cc_start: 0.6914 (ttp) cc_final: 0.6531 (tmm) REVERT: I 593 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: I 595 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7461 (mmt180) REVERT: R 41 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7273 (t80) REVERT: R 101 THR cc_start: 0.7494 (p) cc_final: 0.7224 (p) REVERT: K 392 MET cc_start: 0.5854 (tpp) cc_final: 0.5509 (mmm) REVERT: A 105 ASP cc_start: 0.8412 (m-30) cc_final: 0.7722 (p0) REVERT: A 107 ASN cc_start: 0.7014 (t0) cc_final: 0.6451 (t0) REVERT: A 287 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8330 (ttm-80) REVERT: A 423 MET cc_start: 0.8421 (mtp) cc_final: 0.8043 (mtt) REVERT: A 675 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 771 TYR cc_start: 0.8682 (m-80) cc_final: 0.8025 (m-80) REVERT: A 1024 ARG cc_start: 0.9367 (ptp-110) cc_final: 0.8912 (ttm110) REVERT: A 1026 TYR cc_start: 0.8073 (m-10) cc_final: 0.7633 (m-80) REVERT: A 1128 MET cc_start: 0.6597 (tmm) cc_final: 0.6350 (tmm) REVERT: A 1242 SER cc_start: 0.8981 (m) cc_final: 0.8503 (p) REVERT: Y 258 MET cc_start: 0.3142 (mtt) cc_final: 0.2875 (mmt) REVERT: Y 531 PHE cc_start: 0.8397 (m-80) cc_final: 0.7998 (m-80) REVERT: C 98 ASP cc_start: 0.7855 (m-30) cc_final: 0.7553 (t0) REVERT: C 142 ILE cc_start: 0.8691 (tt) cc_final: 0.8416 (tp) REVERT: C 250 MET cc_start: 0.7530 (mmm) cc_final: 0.7304 (tpp) REVERT: S 39 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.7985 (p0) REVERT: S 105 ASP cc_start: 0.5451 (m-30) cc_final: 0.4402 (t0) REVERT: S 119 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6773 (ttp-110) outliers start: 189 outliers final: 128 residues processed: 651 average time/residue: 0.5060 time to fit residues: 550.2538 Evaluate side-chains 604 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 463 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 LYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1068 ASN Chi-restraints excluded: chain B residue 1071 THR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 41 TYR Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 102 MET Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 33 ASP Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 63 MET Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 159 optimal weight: 7.9990 chunk 427 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 475 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 39 optimal weight: 0.0870 chunk 157 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 126 ASN ** Y 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 526 GLN ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42203 Z= 0.249 Angle : 0.596 10.373 57346 Z= 0.310 Chirality : 0.044 0.214 6552 Planarity : 0.004 0.042 7012 Dihedral : 11.277 158.832 6379 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.98 % Allowed : 18.86 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4859 helix: 0.40 (0.12), residues: 1755 sheet: -0.84 (0.20), residues: 670 loop : -1.36 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 538 HIS 0.010 0.001 HIS Y 533 PHE 0.032 0.002 PHE Y 123 TYR 0.039 0.002 TYR A 306 ARG 0.005 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 488 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.8387 (mmm) cc_final: 0.8171 (mmm) REVERT: B 93 ASP cc_start: 0.6965 (m-30) cc_final: 0.5776 (p0) REVERT: B 159 ASN cc_start: 0.8626 (t0) cc_final: 0.7944 (p0) REVERT: B 237 SER cc_start: 0.9241 (m) cc_final: 0.8826 (t) REVERT: B 319 MET cc_start: 0.7563 (mmt) cc_final: 0.6066 (mmm) REVERT: B 320 ASN cc_start: 0.6506 (t0) cc_final: 0.6188 (p0) REVERT: B 474 ASP cc_start: 0.8278 (t70) cc_final: 0.7993 (t0) REVERT: B 544 MET cc_start: 0.8537 (ptp) cc_final: 0.8324 (ptp) REVERT: B 565 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: B 680 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6459 (p0) REVERT: B 794 ARG cc_start: 0.6555 (mtm110) cc_final: 0.6052 (mmt-90) REVERT: B 862 THR cc_start: 0.8518 (m) cc_final: 0.7836 (t) REVERT: B 1021 LEU cc_start: 0.9237 (mt) cc_final: 0.9030 (mm) REVERT: B 1062 ILE cc_start: 0.8186 (tt) cc_final: 0.7902 (tp) REVERT: B 1085 TYR cc_start: 0.8543 (m-80) cc_final: 0.7667 (m-10) REVERT: B 1141 ASP cc_start: 0.8106 (m-30) cc_final: 0.7815 (m-30) REVERT: E 51 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8337 (tmt-80) REVERT: E 80 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: F 81 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: F 94 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8542 (mt0) REVERT: G 83 ASP cc_start: 0.7368 (m-30) cc_final: 0.6794 (m-30) REVERT: G 103 ASP cc_start: 0.7753 (p0) cc_final: 0.6404 (m-30) REVERT: G 104 LEU cc_start: 0.8960 (tp) cc_final: 0.8571 (tp) REVERT: G 111 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8405 (p0) REVERT: I 168 MET cc_start: 0.8334 (mtp) cc_final: 0.7978 (mmm) REVERT: I 169 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8558 (tppt) REVERT: I 205 LYS cc_start: 0.8552 (mtmt) cc_final: 0.7978 (tttt) REVERT: I 255 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.7876 (t) REVERT: I 259 TRP cc_start: 0.8751 (m-10) cc_final: 0.8479 (m-10) REVERT: I 376 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7579 (t70) REVERT: I 487 MET cc_start: 0.7377 (mmp) cc_final: 0.6805 (tpt) REVERT: I 560 MET cc_start: 0.6884 (ttp) cc_final: 0.6484 (tmm) REVERT: I 593 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: I 595 ARG cc_start: 0.7812 (mmt-90) cc_final: 0.7454 (mmt180) REVERT: I 695 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7279 (p0) REVERT: I 715 MET cc_start: 0.8442 (mmm) cc_final: 0.8124 (tpt) REVERT: R 50 TYR cc_start: 0.6383 (m-10) cc_final: 0.6010 (m-10) REVERT: A 105 ASP cc_start: 0.8421 (m-30) cc_final: 0.7727 (p0) REVERT: A 282 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8697 (mmmm) REVERT: A 287 ARG cc_start: 0.8845 (ttp-170) cc_final: 0.8292 (ttm-80) REVERT: A 664 MET cc_start: 0.8240 (tpp) cc_final: 0.7970 (ttt) REVERT: A 675 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 1024 ARG cc_start: 0.9366 (ptp-110) cc_final: 0.8965 (ttm110) REVERT: A 1026 TYR cc_start: 0.8021 (m-10) cc_final: 0.7630 (m-80) REVERT: A 1031 GLU cc_start: 0.8236 (mp0) cc_final: 0.7998 (tp30) REVERT: A 1242 SER cc_start: 0.8978 (m) cc_final: 0.8502 (p) REVERT: Q 16 LYS cc_start: 0.4988 (ptmt) cc_final: 0.4675 (ptmt) REVERT: Y 24 MET cc_start: 0.5996 (tpp) cc_final: 0.5492 (tpt) REVERT: Y 69 LEU cc_start: 0.8540 (mt) cc_final: 0.8315 (mt) REVERT: Y 108 ASP cc_start: 0.6008 (m-30) cc_final: 0.5710 (m-30) REVERT: Y 192 GLN cc_start: 0.8495 (pt0) cc_final: 0.8170 (pt0) REVERT: Y 258 MET cc_start: 0.3070 (mtt) cc_final: 0.2797 (mmt) REVERT: Y 531 PHE cc_start: 0.8392 (m-80) cc_final: 0.7954 (m-80) REVERT: C 98 ASP cc_start: 0.7931 (m-30) cc_final: 0.7592 (t0) REVERT: C 142 ILE cc_start: 0.8589 (tt) cc_final: 0.8337 (tp) REVERT: C 279 MET cc_start: 0.8317 (mmm) cc_final: 0.8111 (mmt) REVERT: S 39 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.7987 (p0) REVERT: S 105 ASP cc_start: 0.5189 (m-30) cc_final: 0.4025 (t0) outliers start: 180 outliers final: 125 residues processed: 627 average time/residue: 0.5121 time to fit residues: 539.8668 Evaluate side-chains 594 residues out of total 4517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 458 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 LYS Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1068 ASN Chi-restraints excluded: chain B residue 1071 THR Chi-restraints excluded: chain B residue 1083 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 386 ILE Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain A residue 1235 ASN Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 45 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 33 ASP Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 63 MET Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 117 PHE Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.463 > 50: distance: 32 - 37: 34.825 distance: 38 - 39: 32.986 distance: 38 - 41: 5.740 distance: 39 - 40: 25.143 distance: 39 - 45: 18.673 distance: 41 - 42: 4.374 distance: 42 - 43: 4.682 distance: 42 - 44: 5.065 distance: 45 - 46: 46.575 distance: 46 - 47: 11.120 distance: 46 - 49: 21.363 distance: 47 - 48: 13.275 distance: 47 - 51: 13.659 distance: 49 - 50: 16.652 distance: 53 - 54: 32.031 distance: 53 - 55: 21.288 distance: 55 - 56: 39.186 distance: 56 - 57: 33.259 distance: 56 - 59: 12.387 distance: 57 - 58: 11.562 distance: 57 - 65: 20.522 distance: 58 - 89: 6.524 distance: 59 - 60: 24.575 distance: 60 - 61: 9.528 distance: 60 - 62: 26.894 distance: 61 - 63: 19.785 distance: 62 - 64: 8.995 distance: 63 - 64: 23.029 distance: 65 - 66: 9.974 distance: 66 - 67: 24.670 distance: 66 - 69: 38.251 distance: 67 - 68: 14.041 distance: 67 - 70: 35.929 distance: 68 - 100: 10.280 distance: 70 - 71: 21.326 distance: 71 - 72: 10.517 distance: 71 - 74: 28.875 distance: 72 - 73: 35.557 distance: 72 - 78: 30.470 distance: 73 - 108: 32.595 distance: 74 - 75: 11.135 distance: 75 - 76: 17.280 distance: 75 - 77: 42.499 distance: 78 - 79: 12.973 distance: 79 - 80: 20.717 distance: 79 - 82: 12.762 distance: 80 - 81: 25.281 distance: 80 - 89: 42.325 distance: 81 - 117: 30.464 distance: 82 - 83: 16.889 distance: 83 - 84: 3.579 distance: 84 - 85: 4.131 distance: 85 - 86: 14.591 distance: 86 - 87: 4.460 distance: 86 - 88: 8.339 distance: 89 - 90: 15.328 distance: 90 - 91: 13.272 distance: 90 - 93: 15.160 distance: 91 - 92: 26.866 distance: 91 - 100: 31.191 distance: 92 - 125: 31.225 distance: 93 - 94: 12.697 distance: 94 - 95: 24.635 distance: 95 - 96: 4.210 distance: 96 - 97: 6.410 distance: 97 - 98: 11.765 distance: 97 - 99: 8.047 distance: 100 - 101: 24.592 distance: 101 - 102: 28.293 distance: 101 - 104: 12.061 distance: 102 - 103: 21.621 distance: 102 - 108: 36.687 distance: 103 - 134: 24.450 distance: 104 - 105: 28.753 distance: 105 - 106: 19.022 distance: 105 - 107: 11.198 distance: 108 - 109: 25.953 distance: 109 - 110: 23.977 distance: 109 - 112: 9.799 distance: 110 - 111: 19.998 distance: 110 - 117: 10.574 distance: 111 - 142: 22.659 distance: 115 - 116: 40.065