Starting phenix.real_space_refine on Sun May 25 19:43:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.map" model { file = "/net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zlu_60233/05_2025/8zlu_60233.cif" } resolution = 2.47 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 573 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 16948 2.51 5 N 4752 2.21 5 O 5176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27053 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1258 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 22, 'rna3p': 36} Chain breaks: 1 Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3495 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 413} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1352 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 156} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2802 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2833 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2787 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2804 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2711 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1919 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2955 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 348} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2135 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 247} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2378 SG CYS C 215 64.504 48.527 169.234 1.00 50.32 S ATOM 2398 SG CYS C 218 64.554 51.595 166.827 1.00 46.18 S ATOM 3117 SG CYS C 311 61.592 49.375 166.675 1.00 44.01 S ATOM 3135 SG CYS C 314 64.737 48.535 165.174 1.00 46.52 S ATOM 24252 SG CYS B 298 40.628 47.547 73.320 1.00 53.16 S ATOM 24273 SG CYS B 301 39.198 49.154 70.411 1.00 52.20 S ATOM 24486 SG CYS B 329 42.689 50.257 71.175 1.00 52.10 S ATOM 24511 SG CYS B 332 40.068 51.316 73.664 1.00 55.86 S Time building chain proxies: 16.50, per 1000 atoms: 0.61 Number of scatterers: 27053 At special positions: 0 Unit cell: (112.05, 142.76, 198.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 58 15.00 Mg 2 11.99 O 5176 8.00 N 4752 7.00 C 16948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 3.6 seconds 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6214 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 33 sheets defined 38.5% alpha, 19.0% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 8.42 Creating SS restraints... Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.836A pdb=" N PHE C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.784A pdb=" N TRP C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.994A pdb=" N LEU C 375 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE C 376 " --> pdb=" O SER C 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 376' Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 428 through 438 removed outlier: 3.570A pdb=" N LYS C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 465 removed outlier: 4.212A pdb=" N ALA C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 456 " --> pdb=" O GLN C 452 " (cutoff:3.500A) Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.510A pdb=" N TYR C 495 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 514 removed outlier: 3.858A pdb=" N SER C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.584A pdb=" N PHE E 8 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 34 through 52 Proline residue: E 47 - end of helix Processing helix chain 'E' and resid 57 through 72 Processing helix chain 'E' and resid 80 through 88 removed outlier: 4.554A pdb=" N GLY E 86 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 96 through 107 removed outlier: 3.651A pdb=" N ARG E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 removed outlier: 3.681A pdb=" N LEU E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.967A pdb=" N MET E 116 " --> pdb=" O ILE E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 removed outlier: 3.559A pdb=" N HIS E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.643A pdb=" N PHE E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 165 removed outlier: 3.510A pdb=" N LYS E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.684A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 89 Processing helix chain 'F' and resid 105 through 117 Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 250 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.555A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.542A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.503A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.637A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 362 removed outlier: 3.868A pdb=" N GLY H 362 " --> pdb=" O LEU H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.634A pdb=" N LEU I 56 " --> pdb=" O LYS I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 69 removed outlier: 4.101A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 89 removed outlier: 4.905A pdb=" N ASN I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY I 89 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 116 removed outlier: 3.828A pdb=" N LYS I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 136 removed outlier: 3.597A pdb=" N GLN I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.732A pdb=" N ASP I 155 " --> pdb=" O ASN I 152 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS I 156 " --> pdb=" O ASP I 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 152 through 156' Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 234 through 251 removed outlier: 3.534A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.587A pdb=" N PHE I 284 " --> pdb=" O ALA I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 316 removed outlier: 3.760A pdb=" N TYR I 316 " --> pdb=" O ARG I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 361 Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.976A pdb=" N GLN I 370 " --> pdb=" O TRP I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 373 No H-bonds generated for 'chain 'I' and resid 371 through 373' Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.651A pdb=" N LYS J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA J 54 " --> pdb=" O ASP J 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 50 through 54' Processing helix chain 'J' and resid 63 through 73 removed outlier: 4.366A pdb=" N LEU J 67 " --> pdb=" O ARG J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.574A pdb=" N GLY J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.584A pdb=" N ASP J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 96' Processing helix chain 'J' and resid 108 through 116 Processing helix chain 'J' and resid 123 through 134 removed outlier: 3.525A pdb=" N ALA J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 280 through 285 removed outlier: 3.589A pdb=" N VAL J 285 " --> pdb=" O ASN J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 315 Processing helix chain 'J' and resid 329 through 332 Processing helix chain 'J' and resid 349 through 363 Processing helix chain 'J' and resid 367 through 372 Processing helix chain 'K' and resid 12 through 16 removed outlier: 4.024A pdb=" N LEU K 16 " --> pdb=" O PRO K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 48 removed outlier: 3.579A pdb=" N ILE K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.852A pdb=" N LEU K 56 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 78 through 89 Processing helix chain 'K' and resid 107 through 116 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 139 through 146 removed outlier: 3.513A pdb=" N LEU K 144 " --> pdb=" O PRO K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'K' and resid 234 through 250 Processing helix chain 'K' and resid 280 through 285 removed outlier: 3.633A pdb=" N PHE K 284 " --> pdb=" O ALA K 281 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL K 285 " --> pdb=" O ASN K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 294 No H-bonds generated for 'chain 'K' and resid 292 through 294' Processing helix chain 'K' and resid 295 through 315 Processing helix chain 'K' and resid 329 through 332 Processing helix chain 'K' and resid 349 through 361 removed outlier: 3.631A pdb=" N ILE K 361 " --> pdb=" O VAL K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 370 removed outlier: 3.788A pdb=" N GLN K 370 " --> pdb=" O TRP K 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 234 through 250 Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.677A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.529A pdb=" N TYR G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 349 through 361 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.311A pdb=" N ALA B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.533A pdb=" N LEU B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.691A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.891A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.919A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.682A pdb=" N ARG B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.843A pdb=" N GLU D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.575A pdb=" N CYS D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 4.017A pdb=" N LYS D 178 " --> pdb=" O TRP D 174 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.901A pdb=" N LEU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.011A pdb=" N GLY D 259 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 248 through 251 removed outlier: 3.903A pdb=" N ASP C 404 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP C 398 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 74 through 75 removed outlier: 5.280A pdb=" N GLU E 74 " --> pdb=" O LEU E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.716A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.716A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'F' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AB1, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.775A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.775A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG H 345 " --> pdb=" O GLY H 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AB4, first strand: chain 'H' and resid 185 through 189 removed outlier: 3.519A pdb=" N PHE H 189 " --> pdb=" O GLY H 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 26 through 29 removed outlier: 6.248A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 26 through 29 removed outlier: 6.248A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY I 268 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG I 345 " --> pdb=" O GLY I 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.768A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.768A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE J 323 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY J 324 " --> pdb=" O ARG J 345 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE J 347 " --> pdb=" O GLY J 324 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP J 326 " --> pdb=" O ILE J 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'K' and resid 26 through 29 removed outlier: 5.304A pdb=" N SER K 35 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE K 177 " --> pdb=" O TYR K 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 26 through 29 removed outlier: 5.304A pdb=" N SER K 35 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE K 177 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY K 268 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE K 273 " --> pdb=" O ILE K 323 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE K 323 " --> pdb=" O PHE K 273 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG K 345 " --> pdb=" O GLY K 324 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 58 through 61 Processing sheet with id=AC5, first strand: chain 'K' and resid 147 through 148 Processing sheet with id=AC6, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.958A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.958A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 268 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG G 345 " --> pdb=" O GLY G 324 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 185 through 189 Processing sheet with id=AC9, first strand: chain 'B' and resid 7 through 17 removed outlier: 6.759A pdb=" N THR B 7 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN B 142 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 9 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 140 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG B 11 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 138 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU B 13 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER B 136 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA B 15 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 28 through 29 removed outlier: 7.561A pdb=" N ARG B 29 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU B 132 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 74 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 138 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 72 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA B 140 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 70 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN B 142 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET B 68 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET B 68 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG B 74 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 207 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ARG B 241 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 243 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AD3, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AD4, first strand: chain 'D' and resid 66 through 70 Processing sheet with id=AD5, first strand: chain 'D' and resid 184 through 205 removed outlier: 7.416A pdb=" N GLN D 187 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLU D 237 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 235 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU D 191 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU D 233 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN D 193 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 131 through 141 removed outlier: 3.618A pdb=" N GLU D 138 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS D 151 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 140 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 10.24 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7338 1.33 - 1.45: 5162 1.45 - 1.57: 14981 1.57 - 1.69: 115 1.69 - 1.81: 175 Bond restraints: 27771 Sorted by residual: bond pdb=" CB ASP C 407 " pdb=" CG ASP C 407 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" C PHE I 102 " pdb=" N MET I 103 " ideal model delta sigma weight residual 1.325 1.343 -0.018 1.41e-02 5.03e+03 1.63e+00 bond pdb=" CB PRO D 180 " pdb=" CG PRO D 180 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.50e+00 bond pdb=" CB GLU I 293 " pdb=" CG GLU I 293 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CA ASP C 407 " pdb=" CB ASP C 407 " ideal model delta sigma weight residual 1.534 1.553 -0.020 1.76e-02 3.23e+03 1.23e+00 ... (remaining 27766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 37459 2.10 - 4.19: 433 4.19 - 6.29: 49 6.29 - 8.38: 9 8.38 - 10.48: 2 Bond angle restraints: 37952 Sorted by residual: angle pdb=" CA ARG J 147 " pdb=" CB ARG J 147 " pdb=" CG ARG J 147 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" N HIS G 339 " pdb=" CA HIS G 339 " pdb=" C HIS G 339 " ideal model delta sigma weight residual 112.57 108.56 4.01 1.13e+00 7.83e-01 1.26e+01 angle pdb=" N ARG J 147 " pdb=" CA ARG J 147 " pdb=" C ARG J 147 " ideal model delta sigma weight residual 109.56 103.76 5.80 1.84e+00 2.95e-01 9.94e+00 angle pdb=" CA PRO D 180 " pdb=" N PRO D 180 " pdb=" CD PRO D 180 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.64e+00 angle pdb=" N MET I 103 " pdb=" CA MET I 103 " pdb=" C MET I 103 " ideal model delta sigma weight residual 107.73 111.70 -3.97 1.34e+00 5.57e-01 8.77e+00 ... (remaining 37947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 15763 34.96 - 69.92: 903 69.92 - 104.88: 65 104.88 - 139.84: 2 139.84 - 174.80: 5 Dihedral angle restraints: 16738 sinusoidal: 7122 harmonic: 9616 Sorted by residual: dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual 200.00 47.52 152.48 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U A 9 " pdb=" C1' U A 9 " pdb=" N1 U A 9 " pdb=" C2 U A 9 " ideal model delta sinusoidal sigma weight residual 200.00 50.13 149.87 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' C A 6 " pdb=" C1' C A 6 " pdb=" N1 C A 6 " pdb=" C2 C A 6 " ideal model delta sinusoidal sigma weight residual 200.00 50.28 149.72 1 1.50e+01 4.44e-03 7.95e+01 ... (remaining 16735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3071 0.038 - 0.076: 863 0.076 - 0.114: 233 0.114 - 0.152: 58 0.152 - 0.190: 6 Chirality restraints: 4231 Sorted by residual: chirality pdb=" CB ILE D 252 " pdb=" CA ILE D 252 " pdb=" CG1 ILE D 252 " pdb=" CG2 ILE D 252 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA TYR I 315 " pdb=" N TYR I 315 " pdb=" C TYR I 315 " pdb=" CB TYR I 315 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CB THR C 126 " pdb=" CA THR C 126 " pdb=" OG1 THR C 126 " pdb=" CG2 THR C 126 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 4228 not shown) Planarity restraints: 4719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 179 " -0.061 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO D 180 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 265 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO K 266 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO K 266 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 266 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 303 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 304 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.028 5.00e-02 4.00e+02 ... (remaining 4716 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 548 2.68 - 3.24: 23896 3.24 - 3.79: 40065 3.79 - 4.35: 54284 4.35 - 4.90: 91738 Nonbonded interactions: 210531 Sorted by model distance: nonbonded pdb=" O ALA K 247 " pdb=" OG1 THR K 251 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASN K 306 " pdb=" OH TYR K 337 " model vdw 2.166 3.040 nonbonded pdb=" O ALA G 247 " pdb=" OG1 THR G 251 " model vdw 2.189 3.040 nonbonded pdb=" O SER I 254 " pdb=" OG SER I 254 " model vdw 2.233 3.040 nonbonded pdb=" N GLU I 293 " pdb=" OE1 GLU I 293 " model vdw 2.236 3.120 ... (remaining 210526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 78 or (resid 79 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 through 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (name \ N or name CA or name C or name O or name CB )) or resid 106 through 117 or (res \ id 118 and (name N or name CA or name C or name O or name CB )) or resid 119 or \ (resid 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ or (resid 122 through 126 and (name N or name CA or name C or name O or name CB \ )) or resid 127 through 155 or (resid 156 and (name N or name CA or name C or n \ ame O or name CB )) or resid 157 through 159 or (resid 160 through 161 and (name \ N or name CA or name C or name O or name CB )) or resid 162 through 192 or resi \ d 208 through 225 or (resid 226 and (name N or name CA or name C or name O or na \ me CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O o \ r name CB )) or resid 229 through 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 through 256 or resid 263 through 291 o \ r (resid 292 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 93 through 315 or (resid 316 through 319 and (name N or name CA or name C or nam \ e O or name CB )) or resid 320 through 338 or (resid 339 and (name N or name CA \ or name C or name O or name CB )) or resid 340 or (resid 341 and (name N or name \ CA or name C or name O or name CB )) or resid 342 through 351 or (resid 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 368 o \ r (resid 369 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 70 through 372)) selection = (chain 'H' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or (r \ esid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 t \ hrough 121 or (resid 122 through 126 and (name N or name CA or name C or name O \ or name CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or \ name CA or name C or name O or name CB )) or resid 155 or (resid 156 and (name N \ or name CA or name C or name O or name CB )) or resid 157 through 159 or (resid \ 160 through 161 and (name N or name CA or name C or name O or name CB )) or res \ id 162 through 192 or resid 208 through 225 or (resid 226 and (name N or name CA \ or name C or name O or name CB )) or resid 227 or (resid 228 and (name N or nam \ e CA or name C or name O or name CB )) or resid 229 through 230 or (resid 231 an \ d (name N or name CA or name C or name O or name CB )) or resid 232 through 256 \ or resid 263 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 311 or (resid 312 and (name N or name CA or \ name C or name O or name CB )) or resid 313 through 316 or (resid 317 through 3 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 320 through \ 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 351 or (resid 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 364 or (resid 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 367 or (resid 368 through 3 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 372)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (nam \ e N or name CA or name C or name O or name CB )) or resid 76 through 82 or (resi \ d 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 97 or (resid 98 through 99 and (name N or name CA or name C or name O or nam \ e CB )) or resid 100 through 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 or (resid 1 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 121 through \ 159 or (resid 160 through 161 and (name N or name CA or name C or name O or nam \ e CB )) or resid 162 through 192 or resid 208 through 225 or (resid 226 and (nam \ e N or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 256 or \ resid 263 through 311 or (resid 312 and (name N or name CA or name C or name O \ or name CB )) or resid 313 through 315 or (resid 316 through 319 and (name N or \ name CA or name C or name O or name CB )) or resid 320 through 338 or (resid 339 \ and (name N or name CA or name C or name O or name CB )) or resid 340 through 3 \ 51 or (resid 352 and (name N or name CA or name C or name O or name CB )) or res \ id 353 through 364 or (resid 365 and (name N or name CA or name C or name O or n \ ame CB )) or resid 366 through 367 or (resid 368 through 369 and (name N or name \ CA or name C or name O or name CB )) or resid 370 or (resid 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372)) selection = (chain 'J' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 or (resid 98 through 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (res \ id 122 through 126 and (name N or name CA or name C or name O or name CB )) or r \ esid 127 through 152 or (resid 153 through 154 and (name N or name CA or name C \ or name O or name CB )) or resid 155 or (resid 156 and (name N or name CA or nam \ e C or name O or name CB )) or resid 157 or (resid 158 through 161 and (name N o \ r name CA or name C or name O or name CB )) or resid 162 through 192 or resid 20 \ 8 through 225 or (resid 226 and (name N or name CA or name C or name O or name C \ B )) or resid 227 through 230 or (resid 231 and (name N or name CA or name C or \ name O or name CB )) or resid 232 through 256 or resid 263 through 311 or (resid \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 315 or (resid 316 through 319 and (name N or name CA or name C or name O or n \ ame CB )) or resid 320 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 367 or (resid 368 through 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 \ and (name N or name CA or name C or name O or name CB )) or resid 372)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 97 or (resid 98 through 99 and (name N or name CA or name C o \ r name O or name CB )) or resid 100 through 104 or (resid 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 117 \ or (resid 118 and (name N or name CA or name C or name O or name CB )) or resid \ 119 or (resid 120 and (name N or name CA or name C or name O or name CB )) or re \ sid 121 or (resid 122 through 126 and (name N or name CA or name C or name O or \ name CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or nam \ e CA or name C or name O or name CB )) or resid 155 or (resid 156 and (name N or \ name CA or name C or name O or name CB )) or resid 157 through 159 or (resid 16 \ 0 through 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 227 or (resid 228 and (name N or name CA or name C or name O or name \ CB )) or resid 229 through 291 or (resid 292 and (name N or name CA or name C o \ r name O or name CB )) or resid 293 through 311 or (resid 312 and (name N or nam \ e CA or name C or name O or name CB )) or resid 313 through 316 or (resid 317 th \ rough 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 338 or (resid 339 and (name N or name CA or name C or name O or name CB \ )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or name \ CB )) or resid 342 through 367 or (resid 368 through 369 and (name N or name CA \ or name C or name O or name CB )) or resid 370 through 372)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 66.350 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.061 27771 Z= 0.101 Angle : 0.536 10.479 37952 Z= 0.279 Chirality : 0.040 0.190 4231 Planarity : 0.004 0.091 4719 Dihedral : 19.715 174.799 10524 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 4.41 % Allowed : 28.17 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.05 (0.15), residues: 3280 helix: 1.18 (0.17), residues: 1137 sheet: 1.43 (0.21), residues: 532 loop : -1.51 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 156 HIS 0.007 0.001 HIS G 339 PHE 0.011 0.001 PHE E 71 TYR 0.015 0.001 TYR F 360 ARG 0.008 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.14552 ( 1062) hydrogen bonds : angle 5.22224 ( 3045) covalent geometry : bond 0.00213 (27771) covalent geometry : angle 0.53575 (37952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 644 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 113 ARG cc_start: 0.6925 (mtp180) cc_final: 0.5876 (mtp180) REVERT: B 345 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7509 (mtt) outliers start: 119 outliers final: 102 residues processed: 748 average time/residue: 1.5267 time to fit residues: 1305.4300 Evaluate side-chains 735 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 632 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 340 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 93 LYS Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 341 LYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 220 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 0.0170 chunk 260 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN C 163 ASN C 353 GLN C 480 GLN F 164 ASN F 225 GLN F 299 GLN F 351 ASN H 252 ASN H 257 GLN H 275 ASN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 ASN I 82 GLN J 17 ASN J 70 GLN J 164 ASN K 9 GLN K 225 GLN D 61 GLN D 85 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108165 restraints weight = 37773.774| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.73 r_work: 0.3419 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27771 Z= 0.160 Angle : 0.582 10.697 37952 Z= 0.301 Chirality : 0.042 0.199 4231 Planarity : 0.004 0.053 4719 Dihedral : 14.782 175.316 4714 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.41 % Rotamer: Outliers : 5.59 % Allowed : 24.66 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.00 (0.15), residues: 3280 helix: 1.28 (0.16), residues: 1149 sheet: 1.37 (0.21), residues: 542 loop : -1.53 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 156 HIS 0.005 0.001 HIS B 83 PHE 0.017 0.002 PHE C 247 TYR 0.014 0.001 TYR F 360 ARG 0.007 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 1062) hydrogen bonds : angle 4.22887 ( 3045) covalent geometry : bond 0.00380 (27771) covalent geometry : angle 0.58156 (37952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 659 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 392 LEU cc_start: 0.8469 (mp) cc_final: 0.8150 (mt) REVERT: F 370 GLN cc_start: 0.7879 (mt0) cc_final: 0.7642 (mt0) REVERT: H 113 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7825 (ttp80) REVERT: H 224 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: J 62 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8079 (ttm170) REVERT: K 338 LYS cc_start: 0.4764 (OUTLIER) cc_final: 0.4411 (mttp) REVERT: B 155 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 272 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7385 (mptm) REVERT: B 309 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7855 (tp40) REVERT: B 314 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6870 (mtm-85) outliers start: 151 outliers final: 87 residues processed: 745 average time/residue: 1.5223 time to fit residues: 1293.7864 Evaluate side-chains 741 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 646 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 269 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 329 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN H 275 ASN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN I 82 GLN I 172 GLN J 17 ASN J 70 GLN J 164 ASN K 70 GLN K 225 GLN D 61 GLN D 85 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108453 restraints weight = 37741.785| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.73 r_work: 0.3423 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27771 Z= 0.138 Angle : 0.564 10.302 37952 Z= 0.291 Chirality : 0.042 0.192 4231 Planarity : 0.004 0.053 4719 Dihedral : 14.356 174.741 4609 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 5.66 % Allowed : 24.25 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.05 (0.15), residues: 3280 helix: 1.36 (0.16), residues: 1152 sheet: 1.33 (0.21), residues: 542 loop : -1.52 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 156 HIS 0.005 0.001 HIS B 83 PHE 0.015 0.001 PHE E 71 TYR 0.014 0.001 TYR F 360 ARG 0.005 0.000 ARG K 113 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 1062) hydrogen bonds : angle 4.12769 ( 3045) covalent geometry : bond 0.00324 (27771) covalent geometry : angle 0.56438 (37952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 638 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7186 (p0) REVERT: C 392 LEU cc_start: 0.8469 (mp) cc_final: 0.8165 (mt) REVERT: F 62 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6934 (ptp-170) REVERT: H 265 TYR cc_start: 0.8470 (m-10) cc_final: 0.8208 (m-10) REVERT: J 62 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8053 (ttm170) REVERT: K 4 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 128 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8667 (ttt-90) REVERT: B 309 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7865 (tp40) REVERT: B 314 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6908 (mtm-85) outliers start: 153 outliers final: 77 residues processed: 725 average time/residue: 1.5748 time to fit residues: 1299.7142 Evaluate side-chains 708 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 624 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 217 optimal weight: 4.9990 chunk 79 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN I 82 GLN I 172 GLN J 70 GLN J 164 ASN K 70 GLN K 225 GLN D 61 GLN D 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108254 restraints weight = 37889.539| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.73 r_work: 0.3420 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27771 Z= 0.137 Angle : 0.563 10.294 37952 Z= 0.290 Chirality : 0.042 0.194 4231 Planarity : 0.004 0.054 4719 Dihedral : 14.104 174.551 4572 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 5.55 % Allowed : 24.58 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.08 (0.15), residues: 3280 helix: 1.39 (0.16), residues: 1155 sheet: 1.33 (0.21), residues: 542 loop : -1.50 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 156 HIS 0.005 0.001 HIS B 83 PHE 0.016 0.001 PHE E 71 TYR 0.014 0.001 TYR F 360 ARG 0.007 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1062) hydrogen bonds : angle 4.08008 ( 3045) covalent geometry : bond 0.00324 (27771) covalent geometry : angle 0.56316 (37952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 639 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8488 (mp) cc_final: 0.8191 (mt) REVERT: F 4 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: F 62 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6901 (ptp-170) REVERT: F 332 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7569 (ttm170) REVERT: H 265 TYR cc_start: 0.8505 (m-10) cc_final: 0.8219 (m-10) REVERT: H 346 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8341 (m-40) REVERT: J 62 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8059 (ttm170) REVERT: J 86 ASN cc_start: 0.8368 (m-40) cc_final: 0.8131 (m-40) REVERT: K 4 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: B 128 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8634 (ttt-90) REVERT: B 155 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7932 (mp) REVERT: B 232 ASP cc_start: 0.7923 (p0) cc_final: 0.7718 (p0) REVERT: B 309 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: D 53 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7427 (mptt) outliers start: 150 outliers final: 84 residues processed: 719 average time/residue: 1.6001 time to fit residues: 1311.7595 Evaluate side-chains 728 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 634 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 276 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 168 optimal weight: 0.0980 chunk 271 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN E 50 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN I 172 GLN I 370 GLN J 17 ASN J 70 GLN J 164 ASN K 70 GLN K 225 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108743 restraints weight = 37729.469| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.72 r_work: 0.3429 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27771 Z= 0.125 Angle : 0.554 10.167 37952 Z= 0.285 Chirality : 0.041 0.190 4231 Planarity : 0.004 0.053 4719 Dihedral : 14.019 174.176 4565 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 5.29 % Allowed : 25.10 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.15 (0.15), residues: 3280 helix: 1.50 (0.16), residues: 1149 sheet: 1.35 (0.21), residues: 541 loop : -1.49 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.015 0.001 PHE E 71 TYR 0.015 0.001 TYR F 360 ARG 0.008 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 1062) hydrogen bonds : angle 4.03638 ( 3045) covalent geometry : bond 0.00291 (27771) covalent geometry : angle 0.55446 (37952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 638 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8466 (mp) cc_final: 0.8171 (mt) REVERT: F 4 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: F 62 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6869 (ptp-170) REVERT: F 103 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.5962 (ppp) REVERT: F 332 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7472 (ttm170) REVERT: H 245 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8407 (tt) REVERT: H 346 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8331 (m-40) REVERT: I 365 LYS cc_start: 0.8194 (mptt) cc_final: 0.7973 (ttmm) REVERT: J 62 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8037 (ttm170) REVERT: J 82 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7774 (tp-100) REVERT: J 86 ASN cc_start: 0.8331 (m-40) cc_final: 0.8067 (m110) REVERT: K 183 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7724 (mtt90) REVERT: B 128 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8633 (ttt-90) REVERT: B 155 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 232 ASP cc_start: 0.7888 (p0) cc_final: 0.7687 (p0) REVERT: B 309 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7848 (tp40) REVERT: D 53 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7451 (mptt) REVERT: D 89 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6950 (tm-30) outliers start: 143 outliers final: 84 residues processed: 714 average time/residue: 1.5664 time to fit residues: 1272.6731 Evaluate side-chains 731 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 634 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 306 ASN Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 201 optimal weight: 0.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN E 50 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 164 ASN I 172 GLN J 17 ASN J 70 GLN J 164 ASN K 225 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109224 restraints weight = 37779.439| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.73 r_work: 0.3436 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27771 Z= 0.114 Angle : 0.547 10.181 37952 Z= 0.281 Chirality : 0.041 0.186 4231 Planarity : 0.004 0.052 4719 Dihedral : 13.852 173.931 4553 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.44 % Favored : 92.50 % Rotamer: Outliers : 4.92 % Allowed : 25.25 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3280 helix: 1.58 (0.16), residues: 1149 sheet: 1.37 (0.21), residues: 541 loop : -1.44 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.014 0.001 PHE E 71 TYR 0.014 0.001 TYR F 360 ARG 0.008 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1062) hydrogen bonds : angle 3.99750 ( 3045) covalent geometry : bond 0.00261 (27771) covalent geometry : angle 0.54730 (37952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 650 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8429 (mp) cc_final: 0.8133 (mt) REVERT: F 4 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: F 62 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.6866 (ptp-170) REVERT: F 318 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: F 332 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7462 (ttm170) REVERT: H 346 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (m-40) REVERT: J 62 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8024 (ttm170) REVERT: J 82 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7802 (tp-100) REVERT: J 86 ASN cc_start: 0.8322 (m-40) cc_final: 0.8068 (m110) REVERT: G 245 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8138 (tt) REVERT: B 128 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8646 (ttt-90) REVERT: B 309 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7825 (tp40) REVERT: D 53 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7425 (mptt) REVERT: D 89 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6974 (tm-30) outliers start: 133 outliers final: 84 residues processed: 720 average time/residue: 1.5738 time to fit residues: 1286.9319 Evaluate side-chains 723 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 628 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 205 optimal weight: 0.8980 chunk 297 optimal weight: 0.5980 chunk 84 optimal weight: 0.0570 chunk 133 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN E 53 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 164 ASN I 172 GLN J 17 ASN J 70 GLN J 164 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108536 restraints weight = 37946.443| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.74 r_work: 0.3425 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27771 Z= 0.132 Angle : 0.564 10.118 37952 Z= 0.290 Chirality : 0.041 0.192 4231 Planarity : 0.004 0.054 4719 Dihedral : 13.841 174.208 4553 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer: Outliers : 4.55 % Allowed : 25.92 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.22 (0.15), residues: 3280 helix: 1.58 (0.16), residues: 1149 sheet: 1.33 (0.21), residues: 542 loop : -1.45 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.015 0.001 PHE E 71 TYR 0.016 0.001 TYR F 360 ARG 0.009 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1062) hydrogen bonds : angle 4.02404 ( 3045) covalent geometry : bond 0.00311 (27771) covalent geometry : angle 0.56416 (37952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 646 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8472 (mp) cc_final: 0.8183 (mt) REVERT: F 4 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: F 62 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6882 (ptp-170) REVERT: F 103 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.5944 (ppp) REVERT: F 318 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: F 332 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7507 (ttm170) REVERT: H 4 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: H 113 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7673 (ttp80) REVERT: H 346 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8321 (m-40) REVERT: J 62 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8036 (ttm170) REVERT: J 82 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7817 (tp-100) REVERT: J 86 ASN cc_start: 0.8313 (m-40) cc_final: 0.8050 (m110) REVERT: G 245 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 128 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8647 (ttt-90) REVERT: B 309 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7888 (tp40) REVERT: B 314 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7123 (mtm-85) REVERT: D 53 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7435 (mptt) REVERT: D 89 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6987 (tm-30) outliers start: 123 outliers final: 88 residues processed: 707 average time/residue: 1.5928 time to fit residues: 1278.2551 Evaluate side-chains 735 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 633 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 233 ASP Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 274 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 164 ASN I 172 GLN J 17 ASN J 70 GLN J 164 ASN K 225 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108484 restraints weight = 37749.781| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.73 r_work: 0.3424 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27771 Z= 0.134 Angle : 0.568 10.069 37952 Z= 0.292 Chirality : 0.042 0.192 4231 Planarity : 0.004 0.054 4719 Dihedral : 13.826 174.208 4552 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 4.59 % Allowed : 25.77 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.22 (0.15), residues: 3280 helix: 1.57 (0.16), residues: 1153 sheet: 1.33 (0.21), residues: 542 loop : -1.44 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.016 0.001 PHE C 444 TYR 0.017 0.001 TYR F 360 ARG 0.008 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1062) hydrogen bonds : angle 4.02359 ( 3045) covalent geometry : bond 0.00316 (27771) covalent geometry : angle 0.56812 (37952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 645 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8480 (mp) cc_final: 0.8275 (mp) REVERT: F 4 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: F 62 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.6871 (ptp-170) REVERT: F 103 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.5969 (ppp) REVERT: F 318 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: F 332 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7523 (ttm170) REVERT: H 4 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: H 346 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: J 62 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8047 (ttm170) REVERT: J 82 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7800 (tp-100) REVERT: J 86 ASN cc_start: 0.8292 (m-40) cc_final: 0.8023 (m-40) REVERT: J 132 VAL cc_start: 0.8740 (p) cc_final: 0.8441 (t) REVERT: G 245 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8090 (tt) REVERT: B 128 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8646 (ttt-90) REVERT: B 309 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7886 (tp40) REVERT: D 53 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7488 (mptt) REVERT: D 89 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.7008 (tm-30) outliers start: 124 outliers final: 83 residues processed: 706 average time/residue: 1.5550 time to fit residues: 1248.0495 Evaluate side-chains 730 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 634 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 92 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 143 optimal weight: 0.0170 chunk 253 optimal weight: 0.0370 chunk 159 optimal weight: 0.6980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 40 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 172 GLN J 70 GLN J 164 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109438 restraints weight = 37906.044| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.74 r_work: 0.3438 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27771 Z= 0.114 Angle : 0.553 10.647 37952 Z= 0.283 Chirality : 0.041 0.186 4231 Planarity : 0.004 0.054 4719 Dihedral : 13.757 173.748 4544 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.50 % Rotamer: Outliers : 3.67 % Allowed : 26.66 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.29 (0.15), residues: 3280 helix: 1.67 (0.16), residues: 1148 sheet: 1.36 (0.21), residues: 538 loop : -1.42 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.014 0.001 PHE C 444 TYR 0.016 0.001 TYR F 360 ARG 0.009 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1062) hydrogen bonds : angle 3.97449 ( 3045) covalent geometry : bond 0.00263 (27771) covalent geometry : angle 0.55255 (37952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 639 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 LEU cc_start: 0.8425 (mp) cc_final: 0.8136 (mt) REVERT: F 4 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: F 62 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6859 (ptp-170) REVERT: F 103 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.5909 (ppp) REVERT: F 318 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: F 332 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7478 (ttm170) REVERT: H 4 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: H 113 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7667 (ttp80) REVERT: H 346 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: J 62 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7980 (ttm170) REVERT: J 82 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7819 (tp-100) REVERT: J 86 ASN cc_start: 0.8241 (m-40) cc_final: 0.7976 (m-40) REVERT: J 132 VAL cc_start: 0.8738 (p) cc_final: 0.8444 (t) REVERT: G 245 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8083 (tt) REVERT: G 341 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6850 (mptp) REVERT: B 22 ASN cc_start: 0.8638 (p0) cc_final: 0.8417 (p0) REVERT: B 128 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8657 (ttt-90) REVERT: B 309 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7864 (tp40) REVERT: D 53 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7474 (mptt) outliers start: 99 outliers final: 72 residues processed: 690 average time/residue: 1.6162 time to fit residues: 1271.8827 Evaluate side-chains 718 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 633 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 331 optimal weight: 0.7980 chunk 206 optimal weight: 0.0020 chunk 106 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 164 ASN I 172 GLN J 70 GLN J 164 ASN K 225 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 GLN D 187 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.122633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108915 restraints weight = 37673.106| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.73 r_work: 0.3430 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27771 Z= 0.129 Angle : 0.571 10.490 37952 Z= 0.292 Chirality : 0.042 0.205 4231 Planarity : 0.004 0.055 4719 Dihedral : 13.758 174.062 4543 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 3.52 % Allowed : 26.77 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.26 (0.15), residues: 3280 helix: 1.61 (0.16), residues: 1153 sheet: 1.34 (0.21), residues: 542 loop : -1.42 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.015 0.001 PHE E 71 TYR 0.017 0.001 TYR F 360 ARG 0.008 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 1062) hydrogen bonds : angle 4.00881 ( 3045) covalent geometry : bond 0.00304 (27771) covalent geometry : angle 0.57125 (37952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 647 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 GLU cc_start: 0.8127 (pm20) cc_final: 0.7905 (mp0) REVERT: C 392 LEU cc_start: 0.8457 (mp) cc_final: 0.8171 (mt) REVERT: F 4 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: F 62 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6860 (ptp-170) REVERT: F 103 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.5906 (ppp) REVERT: F 318 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: F 332 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7514 (ttm170) REVERT: H 4 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: H 113 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7681 (ttp80) REVERT: H 346 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: J 62 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: J 82 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7809 (tp-100) REVERT: J 86 ASN cc_start: 0.8243 (m-40) cc_final: 0.7961 (m-40) REVERT: J 132 VAL cc_start: 0.8760 (p) cc_final: 0.8477 (t) REVERT: G 245 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8078 (tt) REVERT: B 128 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8655 (ttt-90) REVERT: B 309 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: D 53 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7463 (mptt) outliers start: 95 outliers final: 73 residues processed: 695 average time/residue: 1.6540 time to fit residues: 1301.5674 Evaluate side-chains 721 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 636 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 346 ASN Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 60 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain J residue 368 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 93 LYS Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 372 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 228 optimal weight: 0.0670 chunk 243 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN C 480 GLN F 40 GLN F 128 GLN F 164 ASN H 252 ASN H 257 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 172 GLN J 70 GLN J 164 ASN D 61 GLN D 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109577 restraints weight = 37818.840| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.74 r_work: 0.3441 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27771 Z= 0.115 Angle : 0.565 12.305 37952 Z= 0.288 Chirality : 0.041 0.190 4231 Planarity : 0.004 0.054 4719 Dihedral : 13.728 173.789 4539 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 3.22 % Allowed : 27.29 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.30 (0.15), residues: 3280 helix: 1.65 (0.16), residues: 1153 sheet: 1.36 (0.21), residues: 539 loop : -1.39 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 156 HIS 0.004 0.001 HIS B 83 PHE 0.015 0.001 PHE E 71 TYR 0.016 0.001 TYR F 360 ARG 0.010 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1062) hydrogen bonds : angle 3.98241 ( 3045) covalent geometry : bond 0.00265 (27771) covalent geometry : angle 0.56475 (37952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28271.02 seconds wall clock time: 485 minutes 17.28 seconds (29117.28 seconds total)