Starting phenix.real_space_refine on Sun May 25 16:08:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.map" model { file = "/net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zm3_60235/05_2025/8zm3_60235.cif" } resolution = 3.1 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= 0.004 sd= 0.048 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 16878 2.51 5 N 4735 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26938 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: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3476 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 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: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2799 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 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: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2781 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 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: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2624 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 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 2398 SG CYS C 218 63.786 53.238 166.219 1.00 96.02 S ATOM 3098 SG CYS C 311 60.901 49.853 165.071 1.00 96.16 S ATOM 24137 SG CYS B 298 41.193 48.632 72.333 1.00 28.05 S ATOM 24158 SG CYS B 301 39.361 50.567 69.937 1.00 27.63 S ATOM 24371 SG CYS B 329 43.440 51.007 69.732 1.00 27.44 S ATOM 24396 SG CYS B 332 40.606 52.341 72.967 1.00 26.81 S Time building chain proxies: 15.58, per 1000 atoms: 0.58 Number of scatterers: 26938 At special positions: 0 Unit cell: (113.71, 144.42, 197.54, 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 5148 8.00 N 4735 7.00 C 16878 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: 6.36 Conformation dependent library (CDL) restraints added in 3.3 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6190 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 30 sheets defined 35.1% alpha, 17.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.558A pdb=" N PHE C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.189A pdb=" N TRP C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 167 removed outlier: 3.638A pdb=" N PHE C 167 " --> pdb=" O LYS C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.691A pdb=" N THR C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 4.095A pdb=" N LEU C 375 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.231A 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 418 through 427 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 450 through 465 removed outlier: 3.660A pdb=" N ALA C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.784A pdb=" N GLU C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.564A pdb=" N THR C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.644A pdb=" N TYR C 495 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.629A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) 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: 5.059A pdb=" N GLY E 86 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.665A pdb=" N LEU E 92 " --> pdb=" O CYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 96 through 107 removed outlier: 3.744A pdb=" N ARG E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.558A pdb=" N MET E 116 " --> pdb=" O ILE E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 149 through 155 removed outlier: 3.679A pdb=" N LYS E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.725A pdb=" N ILE E 166 " --> pdb=" O LYS E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 52 through 56 removed outlier: 4.107A pdb=" N LEU F 56 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 78 through 89 removed outlier: 3.509A pdb=" N GLY F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.744A pdb=" N ASP F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) 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 removed outlier: 3.529A pdb=" N ALA F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.818A pdb=" N ALA F 283 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 285' Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.587A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.764A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 96 removed outlier: 3.547A pdb=" N ASP H 95 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 122 through 134 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 286 removed outlier: 4.417A pdb=" N ARG H 286 " --> pdb=" O ALA H 283 " (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: 3.828A 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 49 removed outlier: 3.560A pdb=" N ILE I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 53 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 80 through 88 removed outlier: 4.901A pdb=" N ASN I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 116 removed outlier: 3.720A pdb=" N LYS I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 134 removed outlier: 3.790A 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 223 through 230 Processing helix chain 'I' and resid 235 through 250 removed outlier: 3.782A pdb=" N HIS I 239 " --> pdb=" O ASN I 235 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.687A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 315 removed outlier: 3.642A pdb=" N GLN I 299 " --> pdb=" O ASP I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 363 removed outlier: 3.540A pdb=" N GLY I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.627A 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 63 through 73 removed outlier: 4.589A pdb=" N LEU J 67 " --> pdb=" O ARG J 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.509A pdb=" N ALA J 81 " --> pdb=" O CYS J 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.736A pdb=" N ASP J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.841A 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 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.558A pdb=" N LEU J 230 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 280 through 285 removed outlier: 3.580A pdb=" N PHE J 284 " --> pdb=" O ALA J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 313 Processing helix chain 'J' and resid 349 through 363 Processing helix chain 'J' and resid 365 through 370 removed outlier: 3.669A pdb=" N VAL J 369 " --> pdb=" O LYS J 365 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 370 " --> pdb=" O TRP J 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 365 through 370' Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 42 through 47 removed outlier: 3.958A pdb=" N ARG K 47 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 removed outlier: 3.774A pdb=" N GLY K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 129 removed outlier: 3.753A pdb=" N GLN K 127 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 250 removed outlier: 3.705A pdb=" N ALA K 248 " --> pdb=" O PHE K 244 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 313 Processing helix chain 'K' and resid 349 through 359 Processing helix chain 'K' and resid 365 through 371 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 removed outlier: 3.578A pdb=" N LYS G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.573A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.816A pdb=" N TYR G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 362 Processing helix chain 'B' and resid 36 through 49 removed outlier: 3.547A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.005A pdb=" N LEU B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.862A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.590A 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 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 372 Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.709A pdb=" N ARG B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.818A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.783A pdb=" N ASP D 59 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.523A pdb=" N CYS D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 96' Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.548A pdb=" N LEU D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 255 through 259 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 252 removed outlier: 4.289A pdb=" N LYS C 389 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 388 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP C 404 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP C 398 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 5.504A 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: 5.378A 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: 3.702A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.702A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (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 185 through 187 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.660A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.660A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 345 " --> pdb=" O GLY H 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AB3, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AB4, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.518A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.518A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP I 326 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'J' and resid 25 through 29 removed outlier: 4.161A pdb=" N LYS J 25 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 25 through 29 removed outlier: 4.161A pdb=" N LYS J 25 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU J 2 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE J 273 " --> pdb=" O LEU J 2 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU J 4 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL J 271 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS J 6 " --> pdb=" O ILE J 269 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE J 269 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE J 8 " --> pdb=" O ASP J 267 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE J 323 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY J 324 " --> pdb=" O ARG J 345 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE J 347 " --> pdb=" O GLY J 324 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP J 326 " --> pdb=" O ILE J 347 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'K' and resid 172 through 177 removed outlier: 3.607A pdb=" N TYR K 218 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA K 176 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR K 216 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 217 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU K 4 " --> pdb=" O GLU K 272 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU K 272 " --> pdb=" O GLU K 4 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS K 6 " --> pdb=" O LEU K 270 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU K 270 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP K 326 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 60 through 61 Processing sheet with id=AC3, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.767A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.767A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY G 268 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG G 345 " --> pdb=" O GLY G 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 7 through 17 removed outlier: 6.799A pdb=" N THR B 7 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 142 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 9 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 140 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG B 11 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 138 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 13 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER B 136 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 15 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 134 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 29 removed outlier: 7.701A pdb=" N ARG B 29 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N LEU B 132 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 136 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 69 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG B 74 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N ILE B 207 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 212 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG B 241 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU B 243 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AC9, first strand: chain 'B' and resid 307 through 310 removed outlier: 3.543A pdb=" N LEU B 328 " --> pdb=" O THR B 307 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.613A pdb=" N GLU D 108 " --> pdb=" O ARG D 6 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 184 through 205 removed outlier: 7.728A pdb=" N GLN D 187 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N GLU D 237 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL D 235 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 191 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU D 233 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 193 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 201 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 131 through 140 removed outlier: 6.178A pdb=" N LYS D 151 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL D 140 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2694 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 8.47 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4536 1.32 - 1.45: 7677 1.45 - 1.57: 15142 1.57 - 1.70: 119 1.70 - 1.83: 175 Bond restraints: 27649 Sorted by residual: bond pdb=" CA ASN K 282 " pdb=" C ASN K 282 " ideal model delta sigma weight residual 1.521 1.472 0.048 9.90e-03 1.02e+04 2.37e+01 bond pdb=" CB MET G 209 " pdb=" CG MET G 209 " ideal model delta sigma weight residual 1.520 1.376 0.144 3.00e-02 1.11e+03 2.32e+01 bond pdb=" N TYR K 280 " pdb=" CA TYR K 280 " ideal model delta sigma weight residual 1.457 1.410 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" CA SER K 178 " pdb=" C SER K 178 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" CA PHE K 215 " pdb=" C PHE K 215 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.03e-02 9.43e+03 1.60e+01 ... (remaining 27644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 37198 3.49 - 6.97: 482 6.97 - 10.46: 77 10.46 - 13.94: 20 13.94 - 17.43: 2 Bond angle restraints: 37779 Sorted by residual: angle pdb=" N VAL K 129 " pdb=" CA VAL K 129 " pdb=" C VAL K 129 " ideal model delta sigma weight residual 112.96 97.21 15.75 1.00e+00 1.00e+00 2.48e+02 angle pdb=" N TYR K 280 " pdb=" CA TYR K 280 " pdb=" C TYR K 280 " ideal model delta sigma weight residual 112.57 99.51 13.06 1.13e+00 7.83e-01 1.34e+02 angle pdb=" N SER K 39 " pdb=" CA SER K 39 " pdb=" C SER K 39 " ideal model delta sigma weight residual 113.20 99.60 13.60 1.21e+00 6.83e-01 1.26e+02 angle pdb=" N ASN K 235 " pdb=" CA ASN K 235 " pdb=" C ASN K 235 " ideal model delta sigma weight residual 111.71 99.40 12.31 1.15e+00 7.56e-01 1.15e+02 angle pdb=" N ILE K 181 " pdb=" CA ILE K 181 " pdb=" C ILE K 181 " ideal model delta sigma weight residual 109.58 96.52 13.06 1.29e+00 6.01e-01 1.02e+02 ... (remaining 37774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 15758 35.82 - 71.63: 835 71.63 - 107.45: 61 107.45 - 143.27: 3 143.27 - 179.08: 4 Dihedral angle restraints: 16661 sinusoidal: 7086 harmonic: 9575 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 36.58 163.42 1 1.50e+01 4.44e-03 8.36e+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 49.58 150.42 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' U A 18 " pdb=" C1' U A 18 " pdb=" N1 U A 18 " pdb=" C2 U A 18 " ideal model delta sinusoidal sigma weight residual 200.00 62.30 137.70 1 1.50e+01 4.44e-03 7.42e+01 ... (remaining 16658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3884 0.101 - 0.201: 292 0.201 - 0.302: 29 0.302 - 0.402: 8 0.402 - 0.503: 2 Chirality restraints: 4215 Sorted by residual: chirality pdb=" CA ASP K 20 " pdb=" N ASP K 20 " pdb=" C ASP K 20 " pdb=" CB ASP K 20 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA TRP K 223 " pdb=" N TRP K 223 " pdb=" C TRP K 223 " pdb=" CB TRP K 223 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP K 19 " pdb=" N ASP K 19 " pdb=" C ASP K 19 " pdb=" CB ASP K 19 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 4212 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 337 " 0.035 2.00e-02 2.50e+03 4.42e-02 3.92e+01 pdb=" CG TYR G 337 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TYR G 337 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR G 337 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 337 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 337 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR G 337 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 337 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA I 23 " 0.096 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO I 24 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO I 24 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO I 24 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 252 " 0.083 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO K 253 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " 0.064 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1052 2.71 - 3.25: 24361 3.25 - 3.80: 42740 3.80 - 4.35: 52823 4.35 - 4.90: 87979 Nonbonded interactions: 208955 Sorted by model distance: nonbonded pdb=" O PHE J 29 " pdb=" NH1 ARG J 34 " model vdw 2.157 3.120 nonbonded pdb=" O ALA G 247 " pdb=" OG1 THR G 251 " model vdw 2.199 3.040 nonbonded pdb=" O ASP D 48 " pdb=" OH TYR D 94 " model vdw 2.209 3.040 nonbonded pdb=" O GLU G 185 " pdb=" CG MET G 209 " model vdw 2.230 3.440 nonbonded pdb=" ND2 ASN F 252 " pdb=" O ALA F 262 " model vdw 2.245 3.120 ... (remaining 208950 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 116 or (res \ id 117 through 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 name O or name CB )) or resid 157 through 159 or (resid 160 through 1 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 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 name CA or name C \ or name O or name CB )) or resid 229 through 230 or (resid 231 and (name N or n \ ame CA or name C or name O or name CB )) or resid 232 through 256 or resid 263 t \ hrough 291 or (resid 292 and (name N or name CA or name C or name O or name CB ) \ ) or resid 293 through 315 or (resid 316 and (name N or name CA or name C or nam \ e O or name CB )) or resid 324 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 359 o \ r resid 361 through 368 or (resid 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 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 116 or (r \ esid 117 through 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 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 1 \ 59 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 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 229 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 291 or (resid 292 and (name N or name CA or nam \ e C or name O or name CB )) or resid 293 through 311 or (resid 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 316 or resid 32 \ 4 through 338 or (resid 339 and (name N or name CA or name C or name O or name C \ B )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or na \ me 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 359 or resid 361 through 364 or (r \ esid 365 and (name N or name CA or name C or name O or name CB )) or resid 366 t \ hrough 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)) 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 119 or (resid 120 a \ nd (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 name CB \ )) or resid 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 (nam \ e N or name CA or name C or name O or name CB )) or resid 229 through 256 or res \ id 263 through 311 or (resid 312 and (name N or name CA or name C or name O or n \ ame CB )) or resid 313 through 315 or (resid 316 and (name N or name CA or name \ C or name O or name CB )) or resid 324 through 338 or (resid 339 and (name N or \ name CA or name C or name O or name CB )) or resid 340 through 351 or (resid 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 through 3 \ 59 or resid 361 through 364 or (resid 365 and (name N or name CA or name C or na \ me O or name 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 (n \ ame 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 116 or (res \ id 117 through 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 119 through 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 a \ nd (name N or name CA or name C or name O or name CB )) or resid 157 or (resid 1 \ 58 through 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 192 or resid 208 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 256 or res \ id 263 through 311 or (resid 312 and (name N or name CA or name C or name O or n \ ame CB )) or resid 313 through 315 or (resid 316 and (name N or name CA or name \ C or name O or name CB )) or resid 324 through 351 or (resid 352 and (name N or \ name CA or name C or name O or name CB )) or resid 353 through 359 or resid 361 \ 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 na \ me 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 116 \ or (resid 117 through 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 o \ r name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and (n \ ame N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 an \ d (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 resid 162 through 227 or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 313 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 na \ me 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 60.660 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 27649 Z= 0.301 Angle : 1.027 17.429 37779 Z= 0.585 Chirality : 0.058 0.503 4215 Planarity : 0.008 0.143 4692 Dihedral : 19.992 179.084 10471 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.03 % Favored : 89.39 % Rotamer: Outliers : 4.62 % Allowed : 26.01 % Favored : 69.37 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.63 % 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: -2.24 (0.13), residues: 3260 helix: -1.17 (0.14), residues: 1094 sheet: 0.34 (0.22), residues: 511 loop : -2.36 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 59 HIS 0.007 0.001 HIS I 6 PHE 0.036 0.002 PHE C 128 TYR 0.101 0.002 TYR G 337 ARG 0.017 0.001 ARG I 62 Details of bonding type rmsd hydrogen bonds : bond 0.19523 ( 945) hydrogen bonds : angle 7.39904 ( 2712) covalent geometry : bond 0.00563 (27649) covalent geometry : angle 1.02668 (37779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 313 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.3753 (m-70) REVERT: K 21 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3469 (mp) REVERT: K 33 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.3992 (tp) REVERT: K 44 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5999 (ttt-90) REVERT: K 78 TRP cc_start: 0.4807 (OUTLIER) cc_final: 0.4522 (t60) REVERT: K 280 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.4254 (m-80) REVERT: K 295 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6778 (t0) REVERT: K 298 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5918 (mt-10) REVERT: K 299 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6406 (mp-120) outliers start: 124 outliers final: 49 residues processed: 401 average time/residue: 0.3888 time to fit residues: 242.7367 Evaluate side-chains 361 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 10 ASN Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 78 TRP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 172 GLN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain D residue 41 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 0.0870 chunk 259 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 HIS C 501 GLN F 239 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 ASN J 172 GLN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 ASN K 17 ASN K 86 ASN K 131 ASN K 135 GLN K 152 ASN ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN K 235 ASN K 263 HIS B 22 ASN B 242 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS D 135 HIS D 193 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.219906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.205615 restraints weight = 58681.805| |-----------------------------------------------------------------------------| r_work (start): 0.4709 rms_B_bonded: 2.38 r_work: 0.4644 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4924 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27649 Z= 0.175 Angle : 0.687 10.233 37779 Z= 0.356 Chirality : 0.044 0.215 4215 Planarity : 0.006 0.079 4692 Dihedral : 14.967 177.415 4606 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 5.10 % Allowed : 25.30 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3260 helix: -0.44 (0.15), residues: 1106 sheet: 0.29 (0.21), residues: 519 loop : -2.24 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 156 HIS 0.009 0.001 HIS F 180 PHE 0.033 0.002 PHE C 376 TYR 0.030 0.002 TYR G 337 ARG 0.007 0.001 ARG I 62 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 945) hydrogen bonds : angle 5.36033 ( 2712) covalent geometry : bond 0.00395 (27649) covalent geometry : angle 0.68665 (37779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 357 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6316 (OUTLIER) cc_final: 0.5974 (p) REVERT: C 424 GLN cc_start: 0.5845 (mm110) cc_final: 0.5246 (mt0) REVERT: C 471 MET cc_start: 0.2662 (mmm) cc_final: 0.2326 (mtp) REVERT: C 485 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6929 (mm-30) REVERT: I 209 MET cc_start: 0.6188 (mtt) cc_final: 0.5920 (mtt) REVERT: J 103 MET cc_start: 0.3215 (ptt) cc_final: 0.2812 (ptt) REVERT: J 209 MET cc_start: 0.2701 (OUTLIER) cc_final: 0.0965 (mmt) REVERT: K 42 ILE cc_start: 0.7451 (pt) cc_final: 0.7165 (pt) REVERT: K 46 ILE cc_start: 0.4819 (OUTLIER) cc_final: 0.4139 (tt) REVERT: K 51 ASP cc_start: 0.5091 (OUTLIER) cc_final: 0.4814 (p0) REVERT: K 141 ASP cc_start: 0.4630 (OUTLIER) cc_final: 0.2966 (p0) REVERT: K 256 LYS cc_start: 0.2755 (OUTLIER) cc_final: 0.1298 (tttm) REVERT: K 298 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6142 (mt-10) REVERT: K 299 GLN cc_start: 0.6194 (OUTLIER) cc_final: 0.5737 (mp-120) REVERT: B 95 GLU cc_start: 0.1077 (OUTLIER) cc_final: -0.2062 (tm-30) REVERT: B 148 VAL cc_start: 0.5918 (t) cc_final: 0.5629 (p) REVERT: D 139 MET cc_start: 0.5997 (mpp) cc_final: 0.5602 (mmp) outliers start: 137 outliers final: 69 residues processed: 457 average time/residue: 0.3830 time to fit residues: 275.0106 Evaluate side-chains 395 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 214 CYS Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 110 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 315 optimal weight: 0.0170 chunk 284 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 ASN G 17 ASN B 22 ASN B 309 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.220708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.206179 restraints weight = 58100.796| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 2.38 r_work: 0.4652 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4900 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27649 Z= 0.115 Angle : 0.601 13.624 37779 Z= 0.306 Chirality : 0.041 0.195 4215 Planarity : 0.005 0.059 4692 Dihedral : 14.503 178.270 4553 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.01 % Favored : 91.87 % Rotamer: Outliers : 4.17 % Allowed : 25.56 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3260 helix: -0.04 (0.16), residues: 1118 sheet: 0.63 (0.22), residues: 503 loop : -2.10 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 156 HIS 0.005 0.001 HIS C 112 PHE 0.020 0.001 PHE J 102 TYR 0.014 0.001 TYR G 337 ARG 0.006 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 945) hydrogen bonds : angle 4.95518 ( 2712) covalent geometry : bond 0.00254 (27649) covalent geometry : angle 0.60091 (37779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 317 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.3639 (tmm) cc_final: 0.3430 (mtm) REVERT: C 377 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.5890 (p) REVERT: C 424 GLN cc_start: 0.5816 (mm110) cc_final: 0.5307 (mt0) REVERT: C 471 MET cc_start: 0.2742 (mmm) cc_final: 0.2375 (mtp) REVERT: C 485 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6726 (tp30) REVERT: H 167 VAL cc_start: 0.2239 (OUTLIER) cc_final: 0.0097 (t) REVERT: H 338 LYS cc_start: 0.3820 (OUTLIER) cc_final: 0.3024 (pttm) REVERT: J 103 MET cc_start: 0.3274 (ptt) cc_final: 0.3015 (ptt) REVERT: J 209 MET cc_start: 0.2689 (OUTLIER) cc_final: 0.2090 (mpp) REVERT: K 42 ILE cc_start: 0.7277 (pt) cc_final: 0.7039 (pt) REVERT: K 46 ILE cc_start: 0.4680 (OUTLIER) cc_final: 0.4109 (tt) REVERT: K 141 ASP cc_start: 0.4617 (OUTLIER) cc_final: 0.2624 (p0) REVERT: K 299 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5869 (mp-120) REVERT: G 148 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.4108 (tpt) REVERT: B 91 MET cc_start: 0.5212 (mmm) cc_final: 0.4822 (mmm) REVERT: B 148 VAL cc_start: 0.5857 (t) cc_final: 0.5580 (p) REVERT: D 139 MET cc_start: 0.5981 (mpp) cc_final: 0.5733 (mmp) outliers start: 112 outliers final: 50 residues processed: 400 average time/residue: 0.3783 time to fit residues: 238.7720 Evaluate side-chains 358 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 214 CYS Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 51 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 144 optimal weight: 0.0070 chunk 93 optimal weight: 0.0020 overall best weight: 0.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 ASN B 309 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.217891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.203152 restraints weight = 56730.315| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 2.35 r_work: 0.4621 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5018 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27649 Z= 0.134 Angle : 0.614 10.520 37779 Z= 0.313 Chirality : 0.042 0.435 4215 Planarity : 0.005 0.067 4692 Dihedral : 14.325 179.063 4538 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.07 % Favored : 91.75 % Rotamer: Outliers : 4.92 % Allowed : 25.00 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3260 helix: 0.02 (0.16), residues: 1132 sheet: 0.59 (0.22), residues: 498 loop : -2.08 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 156 HIS 0.007 0.001 HIS D 135 PHE 0.020 0.002 PHE J 284 TYR 0.030 0.001 TYR G 337 ARG 0.008 0.000 ARG J 34 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 945) hydrogen bonds : angle 4.88199 ( 2712) covalent geometry : bond 0.00303 (27649) covalent geometry : angle 0.61408 (37779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 327 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6250 (OUTLIER) cc_final: 0.5906 (p) REVERT: C 424 GLN cc_start: 0.5747 (mm110) cc_final: 0.5175 (mt0) REVERT: C 485 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6876 (tp30) REVERT: E 85 MET cc_start: 0.2780 (mmt) cc_final: 0.2407 (mmp) REVERT: H 338 LYS cc_start: 0.3915 (OUTLIER) cc_final: 0.3118 (pttm) REVERT: J 61 THR cc_start: 0.2607 (OUTLIER) cc_final: 0.2293 (p) REVERT: J 209 MET cc_start: 0.2681 (OUTLIER) cc_final: 0.2051 (mpp) REVERT: J 296 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.0365 (tt) REVERT: K 28 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: K 42 ILE cc_start: 0.7373 (pt) cc_final: 0.7143 (pt) REVERT: K 46 ILE cc_start: 0.4904 (OUTLIER) cc_final: 0.4371 (tt) REVERT: K 141 ASP cc_start: 0.4671 (OUTLIER) cc_final: 0.3048 (m-30) REVERT: K 256 LYS cc_start: 0.3016 (OUTLIER) cc_final: 0.2647 (tptm) REVERT: K 299 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5735 (mp-120) REVERT: G 148 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.4193 (tpt) REVERT: B 95 GLU cc_start: 0.0826 (OUTLIER) cc_final: -0.2088 (tm-30) REVERT: B 148 VAL cc_start: 0.6290 (t) cc_final: 0.5985 (p) outliers start: 132 outliers final: 78 residues processed: 424 average time/residue: 0.3583 time to fit residues: 243.7946 Evaluate side-chains 394 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 304 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 214 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN J 40 GLN J 92 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 309 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.214603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.199238 restraints weight = 55665.496| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 2.45 r_work: 0.4580 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5173 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27649 Z= 0.150 Angle : 0.642 11.936 37779 Z= 0.325 Chirality : 0.042 0.350 4215 Planarity : 0.005 0.063 4692 Dihedral : 14.183 179.601 4533 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.04 % Favored : 91.78 % Rotamer: Outliers : 5.22 % Allowed : 24.81 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3260 helix: 0.07 (0.16), residues: 1131 sheet: 0.60 (0.22), residues: 494 loop : -2.12 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 156 HIS 0.007 0.001 HIS D 135 PHE 0.019 0.002 PHE K 102 TYR 0.019 0.002 TYR F 316 ARG 0.007 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 945) hydrogen bonds : angle 4.83338 ( 2712) covalent geometry : bond 0.00322 (27649) covalent geometry : angle 0.64237 (37779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 330 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.4452 (tmm) cc_final: 0.3828 (mtm) REVERT: C 288 LEU cc_start: 0.0474 (OUTLIER) cc_final: 0.0232 (tp) REVERT: C 377 SER cc_start: 0.5820 (OUTLIER) cc_final: 0.5513 (p) REVERT: C 395 PHE cc_start: 0.4772 (OUTLIER) cc_final: 0.4488 (t80) REVERT: C 424 GLN cc_start: 0.5738 (mm110) cc_final: 0.5382 (mt0) REVERT: E 155 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5334 (pm20) REVERT: F 80 LYS cc_start: 0.1722 (tttt) cc_final: 0.0834 (ptmt) REVERT: H 33 LEU cc_start: 0.4664 (OUTLIER) cc_final: 0.4226 (mp) REVERT: H 162 TRP cc_start: 0.6023 (m100) cc_final: 0.5582 (m100) REVERT: I 162 TRP cc_start: 0.6508 (m-90) cc_final: 0.6174 (m-10) REVERT: J 181 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (tt) REVERT: J 209 MET cc_start: 0.2752 (OUTLIER) cc_final: 0.2278 (mpp) REVERT: J 210 PHE cc_start: 0.2063 (OUTLIER) cc_final: 0.1502 (p90) REVERT: J 315 TYR cc_start: 0.5078 (m-10) cc_final: 0.4871 (m-10) REVERT: K 46 ILE cc_start: 0.4868 (OUTLIER) cc_final: 0.4345 (tt) REVERT: K 141 ASP cc_start: 0.4450 (OUTLIER) cc_final: 0.2802 (p0) REVERT: K 299 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5761 (mp-120) REVERT: G 148 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.4239 (tpt) REVERT: B 71 ARG cc_start: 0.7081 (tmm-80) cc_final: 0.6432 (ttt180) REVERT: B 95 GLU cc_start: 0.0951 (OUTLIER) cc_final: -0.1838 (tm-30) REVERT: D 4 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5887 (mp) outliers start: 140 outliers final: 80 residues processed: 438 average time/residue: 0.3681 time to fit residues: 254.1352 Evaluate side-chains 401 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 307 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 209 MET Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 GLN G 258 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 376 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.212696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.197747 restraints weight = 56574.209| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 2.36 r_work: 0.4564 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5219 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27649 Z= 0.141 Angle : 0.620 12.480 37779 Z= 0.316 Chirality : 0.042 0.357 4215 Planarity : 0.005 0.061 4692 Dihedral : 14.107 179.914 4530 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.16 % Favored : 91.66 % Rotamer: Outliers : 4.99 % Allowed : 24.74 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3260 helix: 0.09 (0.16), residues: 1149 sheet: 0.50 (0.22), residues: 489 loop : -2.12 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 156 HIS 0.008 0.001 HIS D 135 PHE 0.026 0.002 PHE J 102 TYR 0.034 0.002 TYR I 360 ARG 0.012 0.001 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 945) hydrogen bonds : angle 4.82553 ( 2712) covalent geometry : bond 0.00318 (27649) covalent geometry : angle 0.61963 (37779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 327 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LEU cc_start: 0.0712 (OUTLIER) cc_final: 0.0475 (tp) REVERT: C 377 SER cc_start: 0.5813 (OUTLIER) cc_final: 0.5427 (p) REVERT: C 424 GLN cc_start: 0.5697 (mm110) cc_final: 0.5296 (mt0) REVERT: E 155 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5441 (pm20) REVERT: F 80 LYS cc_start: 0.1977 (tttt) cc_final: 0.1204 (ptmt) REVERT: F 226 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.1715 (tp) REVERT: H 33 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4316 (mp) REVERT: H 70 GLN cc_start: 0.6134 (mp10) cc_final: 0.5881 (mp10) REVERT: I 162 TRP cc_start: 0.6397 (m-90) cc_final: 0.6011 (m-10) REVERT: I 246 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6262 (tp) REVERT: J 96 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4906 (p0) REVERT: J 167 VAL cc_start: 0.1695 (OUTLIER) cc_final: 0.1398 (p) REVERT: J 181 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8016 (tt) REVERT: J 209 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.2545 (mpp) REVERT: J 210 PHE cc_start: 0.2179 (OUTLIER) cc_final: 0.1722 (p90) REVERT: K 91 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6832 (tmtt) REVERT: K 256 LYS cc_start: 0.3586 (OUTLIER) cc_final: 0.3124 (tptp) REVERT: G 148 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.4178 (tpt) REVERT: G 265 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5638 (m-10) REVERT: B 95 GLU cc_start: 0.0869 (OUTLIER) cc_final: -0.1886 (tm-30) REVERT: B 121 ARG cc_start: 0.3010 (OUTLIER) cc_final: 0.2614 (ttt180) REVERT: B 164 LEU cc_start: 0.7272 (mp) cc_final: 0.7005 (mt) REVERT: D 4 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5937 (mp) outliers start: 134 outliers final: 77 residues processed: 434 average time/residue: 0.3757 time to fit residues: 257.8114 Evaluate side-chains 407 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 312 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 209 MET Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 231 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS I 330 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.210294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.195172 restraints weight = 56183.294| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.35 r_work: 0.4532 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27649 Z= 0.148 Angle : 0.644 14.182 37779 Z= 0.327 Chirality : 0.043 0.397 4215 Planarity : 0.005 0.056 4692 Dihedral : 13.981 179.745 4518 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.37 % Favored : 91.44 % Rotamer: Outliers : 4.84 % Allowed : 25.41 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3260 helix: 0.07 (0.16), residues: 1151 sheet: 0.44 (0.23), residues: 484 loop : -2.10 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 156 HIS 0.009 0.001 HIS D 135 PHE 0.018 0.002 PHE E 71 TYR 0.038 0.002 TYR I 360 ARG 0.009 0.001 ARG I 36 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 945) hydrogen bonds : angle 4.82403 ( 2712) covalent geometry : bond 0.00341 (27649) covalent geometry : angle 0.64378 (37779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 338 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ARG cc_start: 0.3052 (ttm170) cc_final: 0.0725 (ttm170) REVERT: C 288 LEU cc_start: 0.1355 (OUTLIER) cc_final: 0.1098 (tp) REVERT: C 377 SER cc_start: 0.5503 (OUTLIER) cc_final: 0.5260 (p) REVERT: C 424 GLN cc_start: 0.5257 (mm110) cc_final: 0.5049 (mt0) REVERT: F 80 LYS cc_start: 0.1830 (tttt) cc_final: 0.1087 (ptmt) REVERT: F 226 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.1624 (tp) REVERT: H 33 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4357 (mp) REVERT: I 63 ARG cc_start: 0.4298 (OUTLIER) cc_final: 0.3299 (ptp-170) REVERT: I 162 TRP cc_start: 0.6380 (m-90) cc_final: 0.6061 (m-10) REVERT: I 335 LEU cc_start: 0.6123 (tp) cc_final: 0.5764 (tp) REVERT: I 344 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7962 (t) REVERT: J 181 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7904 (tt) REVERT: J 209 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.2996 (mpp) REVERT: J 210 PHE cc_start: 0.2409 (OUTLIER) cc_final: 0.2125 (p90) REVERT: K 91 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6910 (tmtt) REVERT: K 148 MET cc_start: 0.8113 (tmm) cc_final: 0.7853 (ppp) REVERT: K 256 LYS cc_start: 0.3823 (OUTLIER) cc_final: 0.3274 (tptp) REVERT: G 148 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.4232 (tpt) REVERT: G 360 TYR cc_start: 0.7142 (t80) cc_final: 0.6864 (t80) REVERT: B 95 GLU cc_start: 0.0814 (OUTLIER) cc_final: 0.0521 (tm-30) REVERT: B 121 ARG cc_start: 0.3144 (OUTLIER) cc_final: 0.2653 (ttt180) REVERT: D 4 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5934 (mp) REVERT: D 89 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.4311 (mt-10) REVERT: D 112 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.3857 (t80) outliers start: 130 outliers final: 77 residues processed: 443 average time/residue: 0.3943 time to fit residues: 271.4891 Evaluate side-chains 415 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 321 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 159 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 187 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN J 96 ASN K 10 ASN ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.209828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.194613 restraints weight = 56124.998| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.37 r_work: 0.4532 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27649 Z= 0.129 Angle : 0.624 13.517 37779 Z= 0.315 Chirality : 0.042 0.359 4215 Planarity : 0.005 0.068 4692 Dihedral : 13.874 179.537 4516 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.98 % Favored : 91.84 % Rotamer: Outliers : 4.21 % Allowed : 26.86 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3260 helix: 0.24 (0.16), residues: 1148 sheet: 0.52 (0.23), residues: 476 loop : -2.07 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 156 HIS 0.008 0.001 HIS D 135 PHE 0.024 0.002 PHE J 102 TYR 0.037 0.002 TYR I 28 ARG 0.010 0.000 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 945) hydrogen bonds : angle 4.74826 ( 2712) covalent geometry : bond 0.00294 (27649) covalent geometry : angle 0.62362 (37779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 337 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ARG cc_start: 0.3192 (ttm170) cc_final: 0.2742 (ttm170) REVERT: C 131 LEU cc_start: 0.5986 (tp) cc_final: 0.5310 (mp) REVERT: C 288 LEU cc_start: 0.1312 (OUTLIER) cc_final: 0.1039 (tp) REVERT: C 372 TYR cc_start: 0.5625 (p90) cc_final: 0.2963 (p90) REVERT: C 377 SER cc_start: 0.4676 (OUTLIER) cc_final: 0.4417 (p) REVERT: C 498 GLU cc_start: 0.6621 (tp30) cc_final: 0.6395 (tp30) REVERT: F 80 LYS cc_start: 0.1575 (tttt) cc_final: 0.1199 (ptmt) REVERT: F 209 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.4769 (mmt) REVERT: F 226 LEU cc_start: 0.2645 (OUTLIER) cc_final: 0.1826 (mt) REVERT: F 233 ASP cc_start: 0.5824 (t0) cc_final: 0.5566 (t0) REVERT: F 341 LYS cc_start: 0.5560 (mmmt) cc_final: 0.5252 (mmmt) REVERT: H 338 LYS cc_start: 0.4026 (OUTLIER) cc_final: 0.3094 (pttm) REVERT: H 347 ILE cc_start: 0.7870 (tp) cc_final: 0.7652 (tt) REVERT: I 63 ARG cc_start: 0.4332 (OUTLIER) cc_final: 0.3657 (ptp-170) REVERT: I 335 LEU cc_start: 0.6080 (tp) cc_final: 0.5748 (tp) REVERT: J 156 LYS cc_start: -0.1396 (OUTLIER) cc_final: -0.2818 (ptmm) REVERT: J 181 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7775 (tt) REVERT: J 209 MET cc_start: 0.3829 (OUTLIER) cc_final: 0.3472 (mpp) REVERT: K 141 ASP cc_start: 0.4357 (OUTLIER) cc_final: 0.2456 (p0) REVERT: K 256 LYS cc_start: 0.3765 (OUTLIER) cc_final: 0.3218 (tptp) REVERT: G 148 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.4131 (tpt) REVERT: G 209 MET cc_start: 0.5826 (ttt) cc_final: 0.5623 (ptt) REVERT: G 265 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: G 360 TYR cc_start: 0.7326 (t80) cc_final: 0.7079 (t80) REVERT: B 95 GLU cc_start: 0.0739 (OUTLIER) cc_final: 0.0418 (tm-30) REVERT: B 121 ARG cc_start: 0.3156 (OUTLIER) cc_final: 0.2881 (ttt180) REVERT: D 4 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5893 (mp) REVERT: D 89 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.4239 (mt-10) outliers start: 113 outliers final: 75 residues processed: 420 average time/residue: 0.3915 time to fit residues: 257.3451 Evaluate side-chains 420 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 209 MET Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 148 MET Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 265 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.0010 chunk 165 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 214 optimal weight: 3.9990 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 HIS C 467 ASN F 282 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 GLN G 175 HIS ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.210990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.196105 restraints weight = 56870.162| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.31 r_work: 0.4549 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5260 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27649 Z= 0.109 Angle : 0.598 12.277 37779 Z= 0.303 Chirality : 0.041 0.374 4215 Planarity : 0.004 0.056 4692 Dihedral : 13.736 178.943 4514 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.33 % Favored : 92.52 % Rotamer: Outliers : 3.17 % Allowed : 27.68 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3260 helix: 0.48 (0.16), residues: 1138 sheet: 0.55 (0.23), residues: 473 loop : -1.98 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 162 HIS 0.006 0.001 HIS D 135 PHE 0.040 0.001 PHE J 102 TYR 0.039 0.001 TYR I 360 ARG 0.010 0.000 ARG I 36 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 945) hydrogen bonds : angle 4.62094 ( 2712) covalent geometry : bond 0.00248 (27649) covalent geometry : angle 0.59829 (37779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 334 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 LEU cc_start: 0.5832 (tp) cc_final: 0.5301 (mp) REVERT: C 288 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.1104 (tp) REVERT: C 419 ASP cc_start: 0.4616 (OUTLIER) cc_final: 0.4257 (m-30) REVERT: F 80 LYS cc_start: 0.1558 (tttt) cc_final: 0.1150 (ptmt) REVERT: F 209 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4755 (mmt) REVERT: F 226 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.1716 (mt) REVERT: F 233 ASP cc_start: 0.5700 (t0) cc_final: 0.5495 (t0) REVERT: F 341 LYS cc_start: 0.5574 (mmmt) cc_final: 0.5285 (mmmt) REVERT: I 63 ARG cc_start: 0.4161 (OUTLIER) cc_final: 0.3959 (ptp-170) REVERT: I 335 LEU cc_start: 0.5951 (tp) cc_final: 0.5544 (tp) REVERT: I 344 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7907 (t) REVERT: J 181 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7737 (tt) REVERT: K 141 ASP cc_start: 0.4264 (OUTLIER) cc_final: 0.2633 (p0) REVERT: K 370 GLN cc_start: 0.2567 (OUTLIER) cc_final: 0.2080 (tp40) REVERT: G 265 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: G 360 TYR cc_start: 0.7359 (t80) cc_final: 0.7097 (t80) REVERT: B 95 GLU cc_start: 0.0549 (OUTLIER) cc_final: 0.0340 (tm-30) REVERT: D 4 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5846 (mp) REVERT: D 89 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.4188 (mt-10) REVERT: D 201 LYS cc_start: 0.6332 (ttmm) cc_final: 0.6027 (ptmt) outliers start: 85 outliers final: 50 residues processed: 397 average time/residue: 0.3986 time to fit residues: 245.2141 Evaluate side-chains 383 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 320 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 0.0000 chunk 136 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 467 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.208641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.192349 restraints weight = 54846.798| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.66 r_work: 0.4496 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27649 Z= 0.127 Angle : 0.630 12.793 37779 Z= 0.317 Chirality : 0.041 0.377 4215 Planarity : 0.005 0.060 4692 Dihedral : 13.724 178.717 4514 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.10 % Favored : 91.75 % Rotamer: Outliers : 3.02 % Allowed : 27.83 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3260 helix: 0.52 (0.16), residues: 1138 sheet: 0.58 (0.23), residues: 472 loop : -1.99 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 162 HIS 0.009 0.001 HIS K 6 PHE 0.038 0.002 PHE J 102 TYR 0.030 0.001 TYR I 360 ARG 0.007 0.000 ARG C 463 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 945) hydrogen bonds : angle 4.64818 ( 2712) covalent geometry : bond 0.00289 (27649) covalent geometry : angle 0.62958 (37779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 329 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 LEU cc_start: 0.5683 (tp) cc_final: 0.5130 (mp) REVERT: C 288 LEU cc_start: 0.1833 (OUTLIER) cc_final: 0.1503 (tp) REVERT: C 498 GLU cc_start: 0.7087 (tp30) cc_final: 0.6856 (tp30) REVERT: F 7 MET cc_start: 0.8047 (tpp) cc_final: 0.7419 (ttp) REVERT: F 80 LYS cc_start: 0.1116 (tttt) cc_final: 0.0913 (ptmt) REVERT: F 209 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5285 (mmt) REVERT: F 226 LEU cc_start: 0.2199 (OUTLIER) cc_final: 0.1133 (tp) REVERT: F 341 LYS cc_start: 0.5745 (mmmt) cc_final: 0.5543 (mmmt) REVERT: H 338 LYS cc_start: 0.4221 (OUTLIER) cc_final: 0.3212 (pttm) REVERT: H 347 ILE cc_start: 0.7648 (tt) cc_final: 0.7304 (tt) REVERT: I 63 ARG cc_start: 0.4027 (OUTLIER) cc_final: 0.3709 (ptp-170) REVERT: I 335 LEU cc_start: 0.6176 (tp) cc_final: 0.5725 (tp) REVERT: J 52 PHE cc_start: 0.1844 (OUTLIER) cc_final: -0.0474 (t80) REVERT: J 153 ASP cc_start: 0.4831 (OUTLIER) cc_final: 0.4628 (t70) REVERT: J 156 LYS cc_start: -0.1852 (OUTLIER) cc_final: -0.2958 (ptmm) REVERT: J 181 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7802 (tt) REVERT: J 209 MET cc_start: 0.4144 (mpp) cc_final: 0.3032 (mtt) REVERT: K 141 ASP cc_start: 0.4376 (OUTLIER) cc_final: 0.2477 (p0) REVERT: G 265 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6267 (m-10) REVERT: B 48 MET cc_start: 0.3542 (mtt) cc_final: 0.2938 (mtt) REVERT: B 95 GLU cc_start: 0.0196 (OUTLIER) cc_final: -0.2216 (tm-30) REVERT: B 121 ARG cc_start: 0.3273 (OUTLIER) cc_final: 0.3059 (ttt180) REVERT: D 4 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5777 (mp) REVERT: D 89 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.4253 (mt-10) REVERT: D 201 LYS cc_start: 0.6496 (ttmm) cc_final: 0.6091 (ptmt) outliers start: 81 outliers final: 55 residues processed: 393 average time/residue: 0.3880 time to fit residues: 237.7435 Evaluate side-chains 393 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 323 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 209 MET Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 161 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 303 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 175 optimal weight: 0.0030 chunk 272 optimal weight: 0.0980 chunk 236 optimal weight: 3.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.208693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.192507 restraints weight = 54884.944| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.64 r_work: 0.4497 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.187 27649 Z= 0.156 Angle : 0.745 59.199 37779 Z= 0.410 Chirality : 0.043 0.796 4215 Planarity : 0.005 0.062 4692 Dihedral : 13.729 178.726 4514 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.13 % Favored : 91.69 % Rotamer: Outliers : 3.02 % Allowed : 28.13 % Favored : 68.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3260 helix: 0.52 (0.16), residues: 1138 sheet: 0.58 (0.23), residues: 472 loop : -1.99 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 162 HIS 0.010 0.001 HIS F 180 PHE 0.036 0.002 PHE J 102 TYR 0.027 0.001 TYR I 360 ARG 0.010 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 945) hydrogen bonds : angle 4.65020 ( 2712) covalent geometry : bond 0.00339 (27649) covalent geometry : angle 0.74495 (37779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13317.66 seconds wall clock time: 231 minutes 18.67 seconds (13878.67 seconds total)