Starting phenix.real_space_refine on Sun Oct 12 19:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zm3_60235/10_2025/8zm3_60235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zm3_60235/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zm3_60235/10_2025/8zm3_60235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zm3_60235/10_2025/8zm3_60235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zm3_60235/10_2025/8zm3_60235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zm3_60235/10_2025/8zm3_60235.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG: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, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} 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, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} 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, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: {'GLU:plan': 2, 'TYR:plan': 1} 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, 'HIS:plan': 1, 'ASN:plan1': 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: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS: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: 7.07, per 1000 atoms: 0.26 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 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: 3.77 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: 5.24 Time building geometry restraints manager: 3.11 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.850 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- 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 : 9.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG I 62 TYR 0.101 0.002 TYR G 337 PHE 0.036 0.002 PHE C 128 TRP 0.036 0.002 TRP B 59 HIS 0.007 0.001 HIS I 6 Details of bonding type rmsd covalent geometry : bond 0.00563 (27649) covalent geometry : angle 1.02668 (37779) hydrogen bonds : bond 0.19523 ( 945) hydrogen bonds : angle 7.39904 ( 2712) *********************** 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 : 0.984 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: 0.1777 time to fit residues: 111.8589 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 : 0.897 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN E 50 GLN F 239 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN ** 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN K 235 ASN B 242 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS D 135 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.223650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.209666 restraints weight = 59629.964| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 2.39 r_work: 0.4685 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4761 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27649 Z= 0.129 Angle : 0.622 9.786 37779 Z= 0.322 Chirality : 0.041 0.208 4215 Planarity : 0.005 0.076 4692 Dihedral : 14.897 179.015 4606 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.67 % Favored : 92.18 % Rotamer: Outliers : 4.06 % Allowed : 25.37 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.14), residues: 3260 helix: -0.12 (0.16), residues: 1085 sheet: 0.44 (0.22), residues: 520 loop : -2.10 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 147 TYR 0.029 0.001 TYR G 337 PHE 0.028 0.001 PHE C 376 TRP 0.026 0.001 TRP E 156 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00289 (27649) covalent geometry : angle 0.62234 (37779) hydrogen bonds : bond 0.04038 ( 945) hydrogen bonds : angle 5.18566 ( 2712) *********************** 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 446 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 337 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6401 (OUTLIER) cc_final: 0.6025 (p) REVERT: C 424 GLN cc_start: 0.5719 (mm110) cc_final: 0.5203 (mt0) REVERT: C 471 MET cc_start: 0.2557 (mmm) cc_final: 0.2312 (mtp) REVERT: K 42 ILE cc_start: 0.7163 (pt) cc_final: 0.6908 (pt) REVERT: K 43 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.3576 (tptt) REVERT: K 46 ILE cc_start: 0.4772 (OUTLIER) cc_final: 0.4099 (tt) REVERT: K 51 ASP cc_start: 0.5232 (OUTLIER) cc_final: 0.4793 (p0) REVERT: K 78 TRP cc_start: 0.4800 (OUTLIER) cc_final: 0.4423 (t60) REVERT: K 114 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5826 (tp) REVERT: K 256 LYS cc_start: 0.2379 (OUTLIER) cc_final: 0.1009 (tttm) REVERT: B 148 VAL cc_start: 0.5477 (t) cc_final: 0.5229 (p) outliers start: 109 outliers final: 54 residues processed: 415 average time/residue: 0.1754 time to fit residues: 113.3535 Evaluate side-chains 368 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 516 LYS 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 H residue 26 THR Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 205 ILE 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 K residue 5 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 43 LYS 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 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 217 LYS Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS 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 367 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 41 SER 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 172 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 288 optimal weight: 0.0470 chunk 272 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 184 optimal weight: 0.3980 chunk 173 optimal weight: 0.3980 chunk 199 optimal weight: 0.7980 chunk 197 optimal weight: 0.2980 chunk 246 optimal weight: 3.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 501 GLN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 ASN ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.224162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.210195 restraints weight = 59836.897| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 2.40 r_work: 0.4691 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27649 Z= 0.102 Angle : 0.567 10.015 37779 Z= 0.289 Chirality : 0.040 0.191 4215 Planarity : 0.004 0.063 4692 Dihedral : 14.311 179.969 4554 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.45 % Favored : 92.42 % Rotamer: Outliers : 3.73 % Allowed : 25.48 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3260 helix: 0.33 (0.16), residues: 1101 sheet: 0.67 (0.22), residues: 522 loop : -1.97 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.014 0.001 TYR I 28 PHE 0.019 0.001 PHE C 512 TRP 0.021 0.001 TRP E 156 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00222 (27649) covalent geometry : angle 0.56690 (37779) hydrogen bonds : bond 0.03483 ( 945) hydrogen bonds : angle 4.73484 ( 2712) *********************** 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 422 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 322 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6210 (OUTLIER) cc_final: 0.5880 (p) REVERT: C 424 GLN cc_start: 0.5777 (mm110) cc_final: 0.5340 (mt0) REVERT: C 471 MET cc_start: 0.2784 (mmm) cc_final: 0.2341 (mtp) REVERT: C 477 TYR cc_start: 0.5864 (t80) cc_final: 0.5204 (t80) REVERT: C 485 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6832 (tp30) REVERT: I 108 ILE cc_start: 0.1874 (OUTLIER) cc_final: 0.1508 (tt) REVERT: J 209 MET cc_start: 0.2687 (OUTLIER) cc_final: 0.0997 (mmt) REVERT: K 46 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4251 (tt) REVERT: K 114 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5920 (tp) REVERT: K 141 ASP cc_start: 0.4541 (OUTLIER) cc_final: 0.2486 (p0) REVERT: K 299 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5827 (mp-120) outliers start: 100 outliers final: 54 residues processed: 391 average time/residue: 0.1875 time to fit residues: 115.6381 Evaluate side-chains 360 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 127 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 214 CYS Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL 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 100 LEU Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 8 ILE 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 205 ILE Chi-restraints excluded: chain J residue 209 MET 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 142 ILE 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 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 367 GLU Chi-restraints excluded: chain G residue 1 MET 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 29 ARG Chi-restraints excluded: chain B residue 62 LYS 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 B residue 274 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 318 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 299 GLN F 330 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 HIS K 11 HIS K 351 ASN K 370 GLN G 17 ASN G 175 HIS B 22 ASN B 89 GLN B 309 GLN B 376 GLN D 193 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.211432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.196585 restraints weight = 56937.157| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 2.34 r_work: 0.4548 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27649 Z= 0.270 Angle : 0.827 11.778 37779 Z= 0.433 Chirality : 0.049 0.312 4215 Planarity : 0.007 0.102 4692 Dihedral : 14.665 176.576 4537 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.85 % Favored : 89.97 % Rotamer: Outliers : 5.85 % Allowed : 24.93 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.14), residues: 3260 helix: -0.66 (0.15), residues: 1119 sheet: 0.21 (0.22), residues: 501 loop : -2.39 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 379 TYR 0.037 0.003 TYR F 316 PHE 0.032 0.003 PHE C 376 TRP 0.023 0.002 TRP E 156 HIS 0.017 0.002 HIS F 180 Details of bonding type rmsd covalent geometry : bond 0.00593 (27649) covalent geometry : angle 0.82676 (37779) hydrogen bonds : bond 0.05358 ( 945) hydrogen bonds : angle 5.71563 ( 2712) *********************** 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 496 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 339 time to evaluate : 0.922 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: 0.0156 (OUTLIER) cc_final: -0.0145 (tp) REVERT: C 377 SER cc_start: 0.6487 (OUTLIER) cc_final: 0.6074 (p) REVERT: C 424 GLN cc_start: 0.5975 (mm110) cc_final: 0.5237 (mt0) REVERT: C 456 ILE cc_start: 0.4743 (pt) cc_final: 0.4282 (pt) REVERT: C 485 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6961 (tp30) REVERT: C 491 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.6168 (t) REVERT: E 72 ARG cc_start: 0.6659 (mtp85) cc_final: 0.6357 (mtp-110) REVERT: F 80 LYS cc_start: 0.2131 (tttt) cc_final: 0.1131 (ptmt) REVERT: F 226 LEU cc_start: 0.2547 (OUTLIER) cc_final: 0.1729 (tp) REVERT: H 33 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4736 (mp) REVERT: H 162 TRP cc_start: 0.6119 (m100) cc_final: 0.5785 (m100) REVERT: I 330 ASN cc_start: 0.7875 (t0) cc_final: 0.7661 (t0) REVERT: I 335 LEU cc_start: 0.6441 (tp) cc_final: 0.6192 (tp) REVERT: J 1 MET cc_start: 0.3119 (ttt) cc_final: 0.2915 (ttt) REVERT: J 209 MET cc_start: 0.2795 (OUTLIER) cc_final: 0.1179 (mmt) REVERT: J 296 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1894 (tp) REVERT: K 46 ILE cc_start: 0.4655 (OUTLIER) cc_final: 0.4005 (tt) REVERT: K 103 MET cc_start: 0.4264 (ptp) cc_final: 0.3914 (ptp) REVERT: K 141 ASP cc_start: 0.4852 (OUTLIER) cc_final: 0.3656 (m-30) REVERT: K 256 LYS cc_start: 0.3437 (OUTLIER) cc_final: 0.2401 (tptm) REVERT: K 299 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5994 (mp-120) REVERT: G 148 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.4444 (tpt) REVERT: G 265 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: B 95 GLU cc_start: 0.1212 (OUTLIER) cc_final: 0.0909 (tm-30) REVERT: B 148 VAL cc_start: 0.6654 (t) cc_final: 0.6392 (p) REVERT: D 4 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6029 (mp) outliers start: 157 outliers final: 79 residues processed: 461 average time/residue: 0.1768 time to fit residues: 130.1827 Evaluate side-chains 407 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 313 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 THR 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 F residue 290 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 288 VAL 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 100 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 8 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 187 ASP Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 75 THR 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 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 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 299 GLN Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET 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 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 22 ASN 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 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 274 THR 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 88 LEU Chi-restraints excluded: chain D residue 128 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 144 optimal weight: 0.3980 chunk 190 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 197 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 ASN J 92 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 ASN B 22 ASN B 309 GLN B 376 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.213804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.199202 restraints weight = 57141.967| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 2.34 r_work: 0.4579 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.4021 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= 0.126 Angle : 0.624 10.091 37779 Z= 0.319 Chirality : 0.042 0.195 4215 Planarity : 0.005 0.055 4692 Dihedral : 14.214 177.120 4527 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.39 % Rotamer: Outliers : 4.66 % Allowed : 25.89 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 3260 helix: -0.05 (0.16), residues: 1111 sheet: 0.37 (0.22), residues: 510 loop : -2.25 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 18 TYR 0.023 0.001 TYR B 341 PHE 0.022 0.001 PHE J 102 TRP 0.024 0.001 TRP E 156 HIS 0.007 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00285 (27649) covalent geometry : angle 0.62425 (37779) hydrogen bonds : bond 0.03644 ( 945) hydrogen bonds : angle 4.99789 ( 2712) *********************** 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 458 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 333 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6125 (OUTLIER) cc_final: 0.5777 (p) REVERT: C 424 GLN cc_start: 0.5729 (mm110) cc_final: 0.5281 (mt0) REVERT: E 72 ARG cc_start: 0.6584 (mtp85) cc_final: 0.6368 (mtp-110) REVERT: E 85 MET cc_start: 0.2575 (mmt) cc_final: 0.2243 (mmp) REVERT: E 155 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4976 (pm20) REVERT: F 80 LYS cc_start: 0.1993 (tttt) cc_final: 0.0899 (ptmt) REVERT: F 226 LEU cc_start: 0.2291 (OUTLIER) cc_final: 0.1443 (tp) REVERT: H 162 TRP cc_start: 0.6003 (m100) cc_final: 0.5629 (m100) REVERT: I 246 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5998 (tp) REVERT: I 250 LYS cc_start: 0.5685 (OUTLIER) cc_final: 0.5481 (mtmp) REVERT: I 330 ASN cc_start: 0.7738 (t0) cc_final: 0.7504 (t0) REVERT: J 209 MET cc_start: 0.2920 (OUTLIER) cc_final: 0.2442 (mpp) REVERT: J 210 PHE cc_start: 0.2252 (OUTLIER) cc_final: 0.1545 (p90) REVERT: K 33 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5351 (mp) REVERT: K 46 ILE cc_start: 0.4838 (OUTLIER) cc_final: 0.4348 (tt) REVERT: K 141 ASP cc_start: 0.4721 (OUTLIER) cc_final: 0.3627 (m-30) REVERT: K 148 MET cc_start: 0.7013 (ttm) cc_final: 0.6796 (ttm) REVERT: G 148 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.4380 (tpt) REVERT: B 148 VAL cc_start: 0.6654 (t) cc_final: 0.6444 (t) REVERT: B 164 LEU cc_start: 0.7391 (mp) cc_final: 0.7057 (mt) outliers start: 125 outliers final: 67 residues processed: 425 average time/residue: 0.1858 time to fit residues: 125.3131 Evaluate side-chains 396 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 318 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 183 SER 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 E residue 152 VAL Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 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 103 MET Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 250 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 61 THR Chi-restraints excluded: chain J residue 101 VAL 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 15 ASN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 ILE 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 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 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 301 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 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 381 MET 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 280 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 274 optimal weight: 3.9990 chunk 275 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 chunk 208 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 180 HIS ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.212981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.198113 restraints weight = 56609.879| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 2.36 r_work: 0.4569 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5196 moved from start: 0.4396 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= 0.125 Angle : 0.612 9.772 37779 Z= 0.313 Chirality : 0.041 0.182 4215 Planarity : 0.005 0.056 4692 Dihedral : 14.053 179.476 4527 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.22 % Favored : 91.60 % Rotamer: Outliers : 4.47 % Allowed : 25.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.14), residues: 3260 helix: 0.17 (0.16), residues: 1118 sheet: 0.43 (0.22), residues: 499 loop : -2.21 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 36 TYR 0.032 0.001 TYR G 337 PHE 0.023 0.001 PHE I 210 TRP 0.025 0.001 TRP I 162 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00278 (27649) covalent geometry : angle 0.61234 (37779) hydrogen bonds : bond 0.03585 ( 945) hydrogen bonds : angle 4.86287 ( 2712) *********************** 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 452 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 332 time to evaluate : 1.110 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 377 SER cc_start: 0.5848 (OUTLIER) cc_final: 0.5462 (p) REVERT: C 424 GLN cc_start: 0.5657 (mm110) cc_final: 0.5271 (mt0) REVERT: C 485 GLU cc_start: 0.7080 (tp30) cc_final: 0.6597 (tp30) REVERT: E 155 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4873 (pm20) REVERT: F 80 LYS cc_start: 0.1919 (tttt) cc_final: 0.1134 (ptmt) REVERT: F 226 LEU cc_start: 0.2416 (OUTLIER) cc_final: 0.1548 (tp) REVERT: H 338 LYS cc_start: 0.4077 (OUTLIER) cc_final: 0.3163 (pttm) REVERT: I 63 ARG cc_start: 0.3861 (OUTLIER) cc_final: 0.2863 (ptp-170) REVERT: I 330 ASN cc_start: 0.7817 (t0) cc_final: 0.7570 (t0) REVERT: I 345 ARG cc_start: 0.5905 (mtp-110) cc_final: 0.5021 (mtp-110) REVERT: J 167 VAL cc_start: 0.1526 (OUTLIER) cc_final: 0.1252 (p) REVERT: J 209 MET cc_start: 0.2966 (OUTLIER) cc_final: 0.2465 (mpp) REVERT: J 210 PHE cc_start: 0.2152 (OUTLIER) cc_final: 0.1612 (p90) REVERT: K 33 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5374 (mp) REVERT: K 141 ASP cc_start: 0.4542 (OUTLIER) cc_final: 0.3044 (m-30) REVERT: K 256 LYS cc_start: 0.3338 (OUTLIER) cc_final: 0.2611 (tptm) REVERT: K 299 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.6030 (mp-120) REVERT: G 265 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5524 (m-10) REVERT: B 148 VAL cc_start: 0.6760 (t) cc_final: 0.6484 (t) REVERT: D 4 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5900 (mp) outliers start: 120 outliers final: 80 residues processed: 424 average time/residue: 0.1897 time to fit residues: 127.0720 Evaluate side-chains 416 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 322 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 377 SER 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 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 226 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 347 ILE 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 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 246 LEU 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 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 153 ASP 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 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 15 ASN Chi-restraints excluded: chain K residue 33 LEU 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 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 171 LEU 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 299 GLN Chi-restraints excluded: chain K residue 301 ILE 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 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 31 optimal weight: 0.0170 chunk 150 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 283 optimal weight: 0.4980 chunk 275 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 161 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 15 ASN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 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** B 309 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.213609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.198877 restraints weight = 56414.531| |-----------------------------------------------------------------------------| r_work (start): 0.4642 rms_B_bonded: 2.36 r_work: 0.4575 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.4673 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 : 0.590 9.561 37779 Z= 0.299 Chirality : 0.041 0.182 4215 Planarity : 0.004 0.056 4692 Dihedral : 13.892 179.751 4523 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.87 % Favored : 92.94 % Rotamer: Outliers : 3.99 % Allowed : 26.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.14), residues: 3260 helix: 0.36 (0.16), residues: 1129 sheet: 0.55 (0.23), residues: 476 loop : -2.10 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG J 36 TYR 0.016 0.001 TYR B 341 PHE 0.026 0.001 PHE J 102 TRP 0.019 0.001 TRP I 162 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00245 (27649) covalent geometry : angle 0.59034 (37779) hydrogen bonds : bond 0.03272 ( 945) hydrogen bonds : angle 4.64009 ( 2712) *********************** 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 437 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 330 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.2302 (OUTLIER) cc_final: 0.1999 (p0) REVERT: C 288 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0726 (tp) REVERT: C 377 SER cc_start: 0.5245 (OUTLIER) cc_final: 0.4999 (p) REVERT: C 485 GLU cc_start: 0.7031 (tp30) cc_final: 0.6569 (tp30) REVERT: E 155 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4834 (pm20) REVERT: F 80 LYS cc_start: 0.1817 (tttt) cc_final: 0.1152 (ptmt) REVERT: F 226 LEU cc_start: 0.2366 (OUTLIER) cc_final: 0.1517 (tp) REVERT: F 233 ASP cc_start: 0.5736 (t0) cc_final: 0.5530 (t0) REVERT: H 338 LYS cc_start: 0.4019 (OUTLIER) cc_final: 0.3107 (pttm) REVERT: I 63 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.3003 (ptp-170) REVERT: I 330 ASN cc_start: 0.7812 (t0) cc_final: 0.7577 (t0) REVERT: J 167 VAL cc_start: 0.1338 (OUTLIER) cc_final: 0.1066 (p) REVERT: J 209 MET cc_start: 0.3169 (OUTLIER) cc_final: 0.2893 (mpp) REVERT: J 210 PHE cc_start: 0.2103 (OUTLIER) cc_final: 0.1767 (p90) REVERT: K 33 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5346 (mp) REVERT: K 141 ASP cc_start: 0.4379 (OUTLIER) cc_final: 0.2812 (m-30) REVERT: K 370 GLN cc_start: 0.3172 (tp-100) cc_final: 0.2920 (tp40) REVERT: G 148 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.4276 (tpt) REVERT: G 265 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5617 (m-10) REVERT: B 148 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6594 (t) REVERT: D 4 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5810 (mp) outliers start: 107 outliers final: 62 residues processed: 412 average time/residue: 0.1784 time to fit residues: 116.5571 Evaluate side-chains 397 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 209 ASP 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 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 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 104 SER Chi-restraints excluded: chain F residue 195 VAL 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 133 ILE Chi-restraints excluded: chain H residue 166 THR 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 99 MET Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 153 ASP 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 210 PHE Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 33 LEU 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 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 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 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 253 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 161 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 50 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 306 optimal weight: 0.7980 chunk 93 optimal weight: 0.0020 chunk 248 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 HIS H 275 ASN I 239 HIS ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.212087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.197109 restraints weight = 56780.981| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.38 r_work: 0.4558 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5225 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27649 Z= 0.118 Angle : 0.601 11.053 37779 Z= 0.305 Chirality : 0.041 0.171 4215 Planarity : 0.004 0.056 4692 Dihedral : 13.755 178.941 4516 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.88 % Favored : 91.96 % Rotamer: Outliers : 3.61 % Allowed : 26.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 3260 helix: 0.41 (0.16), residues: 1140 sheet: 0.70 (0.24), residues: 445 loop : -2.04 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 36 TYR 0.018 0.001 TYR B 341 PHE 0.019 0.001 PHE J 102 TRP 0.032 0.001 TRP I 326 HIS 0.007 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00266 (27649) covalent geometry : angle 0.60060 (37779) hydrogen bonds : bond 0.03363 ( 945) hydrogen bonds : angle 4.59508 ( 2712) *********************** 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 428 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 331 time to evaluate : 0.919 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: 0.6062 (tp) cc_final: 0.5357 (mp) REVERT: C 141 ASN cc_start: 0.2227 (OUTLIER) cc_final: 0.1840 (p0) REVERT: C 288 LEU cc_start: 0.1304 (OUTLIER) cc_final: 0.1027 (tp) REVERT: C 377 SER cc_start: 0.4270 (OUTLIER) cc_final: 0.4026 (p) REVERT: C 419 ASP cc_start: 0.5002 (OUTLIER) cc_final: 0.4614 (m-30) REVERT: C 485 GLU cc_start: 0.7007 (tp30) cc_final: 0.6558 (tp30) REVERT: E 155 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.4795 (pm20) REVERT: F 80 LYS cc_start: 0.1923 (tttt) cc_final: 0.1327 (ptmt) REVERT: H 338 LYS cc_start: 0.4039 (OUTLIER) cc_final: 0.3134 (pttm) REVERT: I 63 ARG cc_start: 0.3981 (OUTLIER) cc_final: 0.3327 (ptp-170) REVERT: I 330 ASN cc_start: 0.7855 (t0) cc_final: 0.7615 (t0) REVERT: J 209 MET cc_start: 0.3416 (OUTLIER) cc_final: 0.3080 (mpp) REVERT: K 370 GLN cc_start: 0.3063 (tp-100) cc_final: 0.2840 (tp40) REVERT: G 148 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.4227 (tpt) REVERT: G 265 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5747 (m-10) REVERT: B 148 VAL cc_start: 0.6866 (OUTLIER) cc_final: 0.6601 (t) REVERT: D 4 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5891 (mp) outliers start: 97 outliers final: 63 residues processed: 404 average time/residue: 0.1852 time to fit residues: 118.5603 Evaluate side-chains 391 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 141 ASN 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 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 501 GLN 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 104 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR 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 99 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 187 ASP 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 271 VAL Chi-restraints excluded: chain K residue 15 ASN 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 171 LEU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE 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 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 148 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 184 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 308 optimal weight: 0.0370 chunk 101 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.211144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.196250 restraints weight = 56421.913| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 2.36 r_work: 0.4550 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27649 Z= 0.116 Angle : 0.603 12.220 37779 Z= 0.305 Chirality : 0.041 0.182 4215 Planarity : 0.004 0.072 4692 Dihedral : 13.703 179.000 4516 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.09 % Favored : 92.76 % Rotamer: Outliers : 3.32 % Allowed : 27.05 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 3260 helix: 0.54 (0.16), residues: 1126 sheet: 0.62 (0.24), residues: 459 loop : -1.99 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 36 TYR 0.016 0.001 TYR B 341 PHE 0.019 0.001 PHE J 102 TRP 0.033 0.001 TRP I 326 HIS 0.018 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00263 (27649) covalent geometry : angle 0.60305 (37779) hydrogen bonds : bond 0.03352 ( 945) hydrogen bonds : angle 4.56267 ( 2712) *********************** 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 410 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 321 time to evaluate : 1.218 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: 0.5915 (tp) cc_final: 0.5411 (mp) REVERT: C 141 ASN cc_start: 0.2107 (OUTLIER) cc_final: 0.1705 (p0) REVERT: C 288 LEU cc_start: 0.1326 (OUTLIER) cc_final: 0.1078 (tp) REVERT: C 419 ASP cc_start: 0.4697 (OUTLIER) cc_final: 0.4373 (m-30) REVERT: C 485 GLU cc_start: 0.7042 (tp30) cc_final: 0.6607 (tp30) REVERT: E 155 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4752 (pm20) REVERT: F 80 LYS cc_start: 0.1707 (tttt) cc_final: 0.1139 (ptmt) REVERT: F 226 LEU cc_start: 0.2485 (OUTLIER) cc_final: 0.1579 (tp) REVERT: H 338 LYS cc_start: 0.4027 (OUTLIER) cc_final: 0.3134 (pttm) REVERT: I 63 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.3481 (ptp-170) REVERT: I 108 ILE cc_start: 0.3072 (OUTLIER) cc_final: 0.2844 (tt) REVERT: I 330 ASN cc_start: 0.7922 (t0) cc_final: 0.7659 (t0) REVERT: J 209 MET cc_start: 0.3832 (OUTLIER) cc_final: 0.3514 (mpp) REVERT: G 148 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.4112 (tpt) REVERT: G 265 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5919 (m-10) REVERT: G 360 TYR cc_start: 0.6980 (t80) cc_final: 0.6774 (t80) REVERT: B 212 MET cc_start: 0.5412 (ttt) cc_final: 0.5200 (ttt) REVERT: D 4 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5867 (mp) outliers start: 89 outliers final: 66 residues processed: 388 average time/residue: 0.1949 time to fit residues: 119.1444 Evaluate side-chains 393 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 501 GLN 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 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 21 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE 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 108 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 52 PHE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 LEU 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 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 15 ASN 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 171 LEU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE 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 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 321 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 26 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 291 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 144 optimal weight: 0.7980 chunk 174 optimal weight: 0.2980 chunk 169 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 ASN I 239 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN ** K 17 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 = 0.4783 r_free = 0.4783 target = 0.212254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.197277 restraints weight = 56344.345| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 2.39 r_work: 0.4563 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27649 Z= 0.104 Angle : 0.589 10.948 37779 Z= 0.296 Chirality : 0.040 0.174 4215 Planarity : 0.004 0.057 4692 Dihedral : 13.566 178.344 4514 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.93 % Favored : 92.91 % Rotamer: Outliers : 3.02 % Allowed : 27.68 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3260 helix: 0.72 (0.16), residues: 1121 sheet: 0.67 (0.24), residues: 453 loop : -1.94 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 47 TYR 0.013 0.001 TYR K 218 PHE 0.021 0.001 PHE C 229 TRP 0.029 0.001 TRP I 326 HIS 0.009 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00236 (27649) covalent geometry : angle 0.58912 (37779) hydrogen bonds : bond 0.03081 ( 945) hydrogen bonds : angle 4.41001 ( 2712) ********************** 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 415 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 334 time to evaluate : 1.014 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: 0.5871 (tp) cc_final: 0.5275 (mp) REVERT: C 141 ASN cc_start: 0.1992 (OUTLIER) cc_final: 0.1613 (p0) REVERT: C 288 LEU cc_start: 0.1390 (OUTLIER) cc_final: 0.1150 (tp) REVERT: C 372 TYR cc_start: 0.5204 (p90) cc_final: 0.2960 (p90) REVERT: E 155 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.4740 (pm20) REVERT: F 80 LYS cc_start: 0.1549 (tttt) cc_final: 0.1295 (ptmt) REVERT: F 226 LEU cc_start: 0.2436 (OUTLIER) cc_final: 0.1513 (tp) REVERT: H 338 LYS cc_start: 0.3877 (OUTLIER) cc_final: 0.2926 (pttm) REVERT: I 330 ASN cc_start: 0.7940 (t0) cc_final: 0.7675 (t0) REVERT: J 7 MET cc_start: 0.3221 (mmp) cc_final: 0.2909 (mmp) REVERT: J 52 PHE cc_start: 0.1749 (OUTLIER) cc_final: -0.0542 (t80) REVERT: K 256 LYS cc_start: 0.3688 (OUTLIER) cc_final: 0.2901 (mmtt) REVERT: G 265 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5927 (m-10) REVERT: G 360 TYR cc_start: 0.6991 (t80) cc_final: 0.6738 (t80) REVERT: B 148 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6460 (t) REVERT: B 212 MET cc_start: 0.5353 (ttt) cc_final: 0.5126 (ttt) REVERT: D 4 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5847 (mp) outliers start: 81 outliers final: 55 residues processed: 394 average time/residue: 0.1788 time to fit residues: 109.7507 Evaluate side-chains 384 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 319 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 501 GLN 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 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 21 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 288 VAL 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 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 15 ASN 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 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 171 LEU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE 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 181 ILE Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 143 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 309 optimal weight: 0.1980 chunk 181 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 232 optimal weight: 1.9990 chunk 206 optimal weight: 0.0020 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.211282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.194890 restraints weight = 55360.229| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.85 r_work: 0.4521 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27649 Z= 0.105 Angle : 0.588 10.663 37779 Z= 0.295 Chirality : 0.040 0.209 4215 Planarity : 0.004 0.055 4692 Dihedral : 13.483 178.263 4512 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.47 % Rotamer: Outliers : 2.76 % Allowed : 28.13 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 3260 helix: 0.79 (0.16), residues: 1125 sheet: 0.74 (0.24), residues: 463 loop : -1.91 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 36 TYR 0.015 0.001 TYR C 372 PHE 0.022 0.001 PHE C 229 TRP 0.026 0.001 TRP I 326 HIS 0.014 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00238 (27649) covalent geometry : angle 0.58840 (37779) hydrogen bonds : bond 0.03056 ( 945) hydrogen bonds : angle 4.37896 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6787.56 seconds wall clock time: 117 minutes 3.08 seconds (7023.08 seconds total)