Starting phenix.real_space_refine on Sat Jun 28 23:05:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcu_28993/06_2025/8fcu_28993.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 sd= 0.876 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 859 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 159 5.49 5 Mg 1 5.21 5 S 121 5.16 5 C 20442 2.51 5 N 5567 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32692 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "O" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.76, per 1000 atoms: 0.54 Number of scatterers: 32692 At special positions: 0 Unit cell: (105.4, 168.64, 254.014, 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 121 16.00 P 159 15.00 Mg 1 11.99 O 6402 8.00 N 5567 7.00 C 20442 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: 7.86 Conformation dependent library (CDL) restraints added in 3.7 seconds 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6750 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 49 sheets defined 42.9% alpha, 18.0% beta 56 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 11.35 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.634A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.617A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.897A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 285 removed outlier: 3.610A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.751A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.019A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 285 removed outlier: 3.910A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 removed outlier: 3.644A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.932A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.670A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.517A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.949A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.526A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.671A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.595A pdb=" N ARG I 46 " --> pdb=" O SER I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.641A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.957A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.544A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.756A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.502A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.549A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 Processing helix chain 'L' and resid 93 through 107 Processing helix chain 'P' and resid 36 through 48 Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 69 through 74 Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 78 through 83 Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 113 through 118 removed outlier: 3.603A pdb=" N THR P 118 " --> pdb=" O ARG P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 139 through 149 Processing helix chain 'P' and resid 156 through 161 Processing helix chain 'P' and resid 214 through 235 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix removed outlier: 4.452A pdb=" N GLY P 235 " --> pdb=" O THR P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 263 through 281 removed outlier: 3.831A pdb=" N ASP P 267 " --> pdb=" O LYS P 263 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY P 270 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE P 271 " --> pdb=" O ASP P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 300 Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'P' and resid 311 through 323 Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 25 Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 83 Proline residue: Q 80 - end of helix removed outlier: 4.384A pdb=" N GLU Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.787A pdb=" N TYR Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 3.534A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 198 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 214 Processing helix chain 'Q' and resid 217 through 224 removed outlier: 3.904A pdb=" N LEU Q 221 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.575A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 295 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.868A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 163 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.280A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.280A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.689A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 106 through 107 removed outlier: 4.048A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE3, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE4, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE6, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.591A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE8, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 332 through 333 Processing sheet with id=AF1, first strand: chain 'P' and resid 7 through 8 removed outlier: 3.544A pdb=" N TRP P 8 " --> pdb=" O THR Q 27 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR Q 27 " --> pdb=" O TRP P 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 166 through 167 removed outlier: 3.612A pdb=" N GLN P 172 " --> pdb=" O CYS P 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 55 through 57 Processing sheet with id=AF4, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.646A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE Q 168 " --> pdb=" O CYS Q 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 1321 hydrogen bonds defined for protein. 3669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 13.19 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9809 1.34 - 1.46: 9111 1.46 - 1.59: 14378 1.59 - 1.71: 309 1.71 - 1.84: 187 Bond restraints: 33794 Sorted by residual: bond pdb=" C SER A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.329 1.355 -0.026 1.18e-02 7.18e+03 4.91e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.44e+00 bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.68e+00 bond pdb=" O5' U M 20 " pdb=" C5' U M 20 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.74e+00 bond pdb=" C LEU I 379 " pdb=" O LEU I 379 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.15e-02 7.56e+03 2.58e+00 ... (remaining 33789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 45394 2.01 - 4.02: 834 4.02 - 6.03: 99 6.03 - 8.05: 22 8.05 - 10.06: 2 Bond angle restraints: 46351 Sorted by residual: angle pdb=" C4' G M 3 " pdb=" C3' G M 3 " pdb=" O3' G M 3 " ideal model delta sigma weight residual 109.40 117.22 -7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" O3' DA N 23 " pdb=" C3' DA N 23 " pdb=" C2' DA N 23 " ideal model delta sigma weight residual 111.50 104.03 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" N LEU J 103 " pdb=" CA LEU J 103 " pdb=" C LEU J 103 " ideal model delta sigma weight residual 110.97 105.85 5.12 1.09e+00 8.42e-01 2.20e+01 angle pdb=" N TYR K 108 " pdb=" CA TYR K 108 " pdb=" C TYR K 108 " ideal model delta sigma weight residual 112.90 107.11 5.79 1.31e+00 5.83e-01 1.96e+01 angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta sigma weight residual 119.76 115.32 4.44 1.03e+00 9.43e-01 1.86e+01 ... (remaining 46346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 18971 35.81 - 71.62: 1017 71.62 - 107.43: 61 107.43 - 143.24: 4 143.24 - 179.05: 5 Dihedral angle restraints: 20058 sinusoidal: 9538 harmonic: 10520 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 58.37 141.63 1 1.50e+01 4.44e-03 7.61e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 20055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4011 0.045 - 0.091: 765 0.091 - 0.136: 209 0.136 - 0.182: 20 0.182 - 0.227: 6 Chirality restraints: 5011 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5008 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE J 61 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 61 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C PHE K 61 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE K 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 62 " -0.018 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 407 2.58 - 3.16: 27945 3.16 - 3.74: 55156 3.74 - 4.32: 76341 4.32 - 4.90: 121425 Nonbonded interactions: 281274 Sorted by model distance: nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR Q 64 " pdb="MG MG Q 601 " model vdw 2.052 2.170 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 3.120 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.165 3.120 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 3.040 ... (remaining 281269 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 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 77.730 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.150 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.003 0.059 33794 Z= 0.157 Angle : 0.647 10.058 46351 Z= 0.369 Chirality : 0.040 0.227 5011 Planarity : 0.004 0.088 5356 Dihedral : 19.406 179.052 13308 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 0.72 % Allowed : 20.38 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3552 helix: 1.26 (0.14), residues: 1332 sheet: -0.91 (0.20), residues: 640 loop : -0.72 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 PHE 0.019 0.001 PHE G 234 TYR 0.038 0.001 TYR C 244 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.17445 ( 1407) hydrogen bonds : angle 6.70653 ( 3939) covalent geometry : bond 0.00309 (33794) covalent geometry : angle 0.64728 (46351) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 414 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6431 (tpt) cc_final: 0.6144 (tpt) REVERT: A 116 LEU cc_start: 0.9273 (tp) cc_final: 0.9016 (tp) REVERT: A 166 ASP cc_start: 0.7416 (t0) cc_final: 0.7192 (t0) REVERT: A 202 ASP cc_start: 0.8014 (p0) cc_final: 0.7730 (p0) REVERT: A 209 GLN cc_start: 0.8822 (tt0) cc_final: 0.8542 (mt0) REVERT: B 43 HIS cc_start: 0.8980 (t70) cc_final: 0.8729 (t70) REVERT: B 118 ARG cc_start: 0.5291 (tmt170) cc_final: 0.4265 (ttt-90) REVERT: B 213 ARG cc_start: 0.4448 (tpp80) cc_final: 0.3957 (tpp80) REVERT: C 227 VAL cc_start: 0.9296 (t) cc_final: 0.9057 (p) REVERT: E 256 GLN cc_start: 0.8592 (tp40) cc_final: 0.8300 (tp-100) REVERT: I 358 TRP cc_start: 0.5735 (OUTLIER) cc_final: 0.5470 (p90) REVERT: J 37 LYS cc_start: 0.7961 (pttt) cc_final: 0.7733 (pttp) REVERT: J 87 LEU cc_start: 0.9233 (tp) cc_final: 0.8988 (tp) REVERT: K 5 SER cc_start: 0.8481 (t) cc_final: 0.8213 (p) REVERT: K 20 GLN cc_start: 0.8797 (tp40) cc_final: 0.8421 (tp40) REVERT: P 132 PHE cc_start: 0.7367 (m-80) cc_final: 0.7035 (m-10) REVERT: Q 79 LEU cc_start: 0.7910 (tp) cc_final: 0.7547 (mt) REVERT: Q 95 GLU cc_start: 0.4823 (tt0) cc_final: 0.4519 (pp20) REVERT: Q 124 HIS cc_start: 0.7081 (m-70) cc_final: 0.6790 (m-70) REVERT: Q 164 HIS cc_start: 0.8634 (t-90) cc_final: 0.8340 (t70) REVERT: Q 176 PHE cc_start: 0.6010 (m-80) cc_final: 0.5673 (m-80) REVERT: Q 321 GLU cc_start: 0.4913 (tt0) cc_final: 0.4625 (mm-30) outliers start: 23 outliers final: 6 residues processed: 428 average time/residue: 0.5031 time to fit residues: 345.5230 Evaluate side-chains 292 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 285 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain P residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 333 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.107039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071480 restraints weight = 93075.975| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.80 r_work: 0.3013 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33794 Z= 0.195 Angle : 0.629 8.567 46351 Z= 0.337 Chirality : 0.041 0.188 5011 Planarity : 0.005 0.092 5356 Dihedral : 19.093 175.747 6017 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.48 % Favored : 93.10 % Rotamer: Outliers : 2.83 % Allowed : 18.74 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3552 helix: 1.50 (0.14), residues: 1338 sheet: -0.98 (0.21), residues: 604 loop : -0.63 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 PHE 0.019 0.001 PHE I 362 TYR 0.018 0.002 TYR G 182 ARG 0.008 0.001 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1407) hydrogen bonds : angle 4.93192 ( 3939) covalent geometry : bond 0.00434 (33794) covalent geometry : angle 0.62919 (46351) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8236 (p0) cc_final: 0.7750 (p0) REVERT: B 43 HIS cc_start: 0.9079 (t70) cc_final: 0.8825 (t70) REVERT: B 118 ARG cc_start: 0.5011 (tmt170) cc_final: 0.3872 (ttt-90) REVERT: B 213 ARG cc_start: 0.4265 (tpp80) cc_final: 0.3751 (tpp80) REVERT: D 136 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7104 (ttt90) REVERT: E 247 PRO cc_start: 0.7260 (Cg_exo) cc_final: 0.6971 (Cg_endo) REVERT: E 256 GLN cc_start: 0.8450 (tp40) cc_final: 0.8080 (tp-100) REVERT: F 28 SER cc_start: 0.8759 (m) cc_final: 0.8473 (m) REVERT: F 30 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7787 (m110) REVERT: F 137 MET cc_start: 0.8366 (tpp) cc_final: 0.8150 (tpp) REVERT: G 77 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7639 (mtm-85) REVERT: G 160 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8716 (mttp) REVERT: I 62 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: I 152 PHE cc_start: 0.8108 (t80) cc_final: 0.7756 (t80) REVERT: I 303 MET cc_start: 0.8747 (mmp) cc_final: 0.8092 (mmm) REVERT: I 358 TRP cc_start: 0.5611 (OUTLIER) cc_final: 0.5317 (p90) REVERT: I 451 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8733 (tp30) REVERT: J 63 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8133 (mp0) REVERT: K 20 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8723 (tp40) REVERT: L 99 ILE cc_start: 0.9475 (mp) cc_final: 0.9268 (mp) REVERT: L 103 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9118 (mm) REVERT: P 40 TYR cc_start: 0.8828 (t80) cc_final: 0.8543 (t80) REVERT: P 132 PHE cc_start: 0.7316 (m-80) cc_final: 0.6884 (m-80) REVERT: P 154 TYR cc_start: 0.8286 (p90) cc_final: 0.7807 (p90) REVERT: Q 14 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6903 (mmm160) REVERT: Q 95 GLU cc_start: 0.5576 (tt0) cc_final: 0.5185 (pp20) outliers start: 90 outliers final: 26 residues processed: 379 average time/residue: 0.4952 time to fit residues: 307.5511 Evaluate side-chains 307 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 238 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.108051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072534 restraints weight = 93539.828| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.77 r_work: 0.3016 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33794 Z= 0.146 Angle : 0.585 11.344 46351 Z= 0.312 Chirality : 0.040 0.191 5011 Planarity : 0.005 0.094 5356 Dihedral : 18.952 174.516 6009 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.36 % Favored : 93.24 % Rotamer: Outliers : 2.51 % Allowed : 18.30 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3552 helix: 1.61 (0.14), residues: 1335 sheet: -0.88 (0.21), residues: 594 loop : -0.60 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 63 HIS 0.007 0.001 HIS Q 30 PHE 0.025 0.001 PHE Q 270 TYR 0.020 0.001 TYR G 182 ARG 0.007 0.000 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1407) hydrogen bonds : angle 4.61784 ( 3939) covalent geometry : bond 0.00324 (33794) covalent geometry : angle 0.58489 (46351) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6545 (tpt) cc_final: 0.6036 (tpt) REVERT: A 92 TYR cc_start: 0.8924 (m-80) cc_final: 0.8720 (m-80) REVERT: A 146 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7617 (tttp) REVERT: A 202 ASP cc_start: 0.8201 (p0) cc_final: 0.7715 (p0) REVERT: A 209 GLN cc_start: 0.8954 (tt0) cc_final: 0.8569 (mt0) REVERT: B 43 HIS cc_start: 0.9033 (t70) cc_final: 0.8794 (t70) REVERT: B 118 ARG cc_start: 0.4547 (tmt170) cc_final: 0.3465 (mtp180) REVERT: B 166 ASN cc_start: 0.8904 (m-40) cc_final: 0.8668 (p0) REVERT: B 204 MET cc_start: 0.8194 (tpp) cc_final: 0.7876 (tpt) REVERT: B 213 ARG cc_start: 0.4253 (tpp80) cc_final: 0.3298 (mmm-85) REVERT: C 244 TYR cc_start: 0.6976 (t80) cc_final: 0.6562 (t80) REVERT: E 152 ASP cc_start: 0.9135 (p0) cc_final: 0.8666 (p0) REVERT: E 256 GLN cc_start: 0.8403 (tp40) cc_final: 0.8000 (tp-100) REVERT: F 30 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7888 (m-40) REVERT: F 137 MET cc_start: 0.8336 (tpp) cc_final: 0.8047 (tpp) REVERT: G 77 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7659 (mtm-85) REVERT: G 160 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8695 (mtmm) REVERT: H 251 GLU cc_start: 0.8524 (mp0) cc_final: 0.8033 (tm-30) REVERT: I 62 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: I 152 PHE cc_start: 0.8057 (t80) cc_final: 0.7752 (t80) REVERT: I 303 MET cc_start: 0.8658 (mmp) cc_final: 0.7825 (mmm) REVERT: I 358 TRP cc_start: 0.5588 (OUTLIER) cc_final: 0.5270 (p90) REVERT: J 107 SER cc_start: 0.8883 (m) cc_final: 0.8553 (p) REVERT: K 20 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8582 (tp40) REVERT: K 107 SER cc_start: 0.8291 (p) cc_final: 0.7618 (t) REVERT: L 82 GLN cc_start: 0.8080 (mt0) cc_final: 0.7726 (mt0) REVERT: L 103 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9069 (mm) REVERT: P 132 PHE cc_start: 0.7210 (m-80) cc_final: 0.6803 (m-10) REVERT: Q 95 GLU cc_start: 0.5317 (tt0) cc_final: 0.5018 (pp20) REVERT: Q 123 ASP cc_start: 0.9018 (p0) cc_final: 0.8717 (t0) outliers start: 80 outliers final: 38 residues processed: 373 average time/residue: 0.5185 time to fit residues: 317.0711 Evaluate side-chains 318 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 64 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 361 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067588 restraints weight = 93908.738| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.79 r_work: 0.2894 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 33794 Z= 0.315 Angle : 0.699 12.024 46351 Z= 0.368 Chirality : 0.043 0.221 5011 Planarity : 0.005 0.097 5356 Dihedral : 18.938 173.597 6009 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.07 % Favored : 92.48 % Rotamer: Outliers : 3.96 % Allowed : 18.27 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3552 helix: 1.43 (0.14), residues: 1331 sheet: -0.96 (0.21), residues: 595 loop : -0.65 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 63 HIS 0.007 0.001 HIS B 51 PHE 0.022 0.002 PHE C 221 TYR 0.024 0.002 TYR D 183 ARG 0.007 0.001 ARG H 302 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1407) hydrogen bonds : angle 4.76889 ( 3939) covalent geometry : bond 0.00704 (33794) covalent geometry : angle 0.69940 (46351) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 264 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8383 (p0) cc_final: 0.8024 (p0) REVERT: A 209 GLN cc_start: 0.8869 (tt0) cc_final: 0.8611 (mt0) REVERT: B 118 ARG cc_start: 0.4744 (tmt170) cc_final: 0.3384 (mtp180) REVERT: C 179 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8153 (ptp90) REVERT: C 244 TYR cc_start: 0.7180 (t80) cc_final: 0.6784 (t80) REVERT: E 152 ASP cc_start: 0.9155 (p0) cc_final: 0.8762 (p0) REVERT: E 181 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.9045 (pt0) REVERT: E 256 GLN cc_start: 0.8433 (tp40) cc_final: 0.8054 (tp-100) REVERT: F 137 MET cc_start: 0.8467 (tpp) cc_final: 0.8007 (tpt) REVERT: G 77 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7716 (mtm-85) REVERT: G 160 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8809 (mtmm) REVERT: G 164 GLU cc_start: 0.9210 (tp30) cc_final: 0.8998 (pm20) REVERT: H 181 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: I 62 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7315 (m-10) REVERT: I 152 PHE cc_start: 0.8102 (t80) cc_final: 0.7817 (t80) REVERT: I 358 TRP cc_start: 0.5691 (OUTLIER) cc_final: 0.5375 (p90) REVERT: I 451 GLU cc_start: 0.9194 (tp30) cc_final: 0.8922 (tp30) REVERT: K 82 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: L 103 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9172 (mm) outliers start: 126 outliers final: 60 residues processed: 371 average time/residue: 0.4539 time to fit residues: 279.6404 Evaluate side-chains 308 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 239 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 15 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071018 restraints weight = 92955.224| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.79 r_work: 0.2975 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33794 Z= 0.143 Angle : 0.590 12.155 46351 Z= 0.314 Chirality : 0.040 0.199 5011 Planarity : 0.005 0.098 5356 Dihedral : 18.834 173.614 6007 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.53 % Favored : 93.05 % Rotamer: Outliers : 3.01 % Allowed : 19.50 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3552 helix: 1.61 (0.14), residues: 1336 sheet: -0.88 (0.22), residues: 583 loop : -0.57 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.019 0.001 PHE Q 176 TYR 0.020 0.001 TYR G 182 ARG 0.007 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1407) hydrogen bonds : angle 4.43722 ( 3939) covalent geometry : bond 0.00321 (33794) covalent geometry : angle 0.58985 (46351) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6313 (tpt) cc_final: 0.5585 (tpt) REVERT: A 202 ASP cc_start: 0.8275 (p0) cc_final: 0.7806 (p0) REVERT: A 209 GLN cc_start: 0.8817 (tt0) cc_final: 0.8568 (mt0) REVERT: B 43 HIS cc_start: 0.9076 (t70) cc_final: 0.8830 (t70) REVERT: B 99 TYR cc_start: 0.8174 (m-80) cc_final: 0.7617 (m-80) REVERT: B 118 ARG cc_start: 0.4569 (tmt170) cc_final: 0.3516 (mmm-85) REVERT: B 213 ARG cc_start: 0.4685 (tpp80) cc_final: 0.3987 (tpp80) REVERT: C 244 TYR cc_start: 0.7078 (t80) cc_final: 0.6627 (t80) REVERT: C 294 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7903 (t0) REVERT: E 137 MET cc_start: 0.8931 (tpp) cc_final: 0.8716 (tpp) REVERT: E 152 ASP cc_start: 0.9116 (p0) cc_final: 0.8674 (p0) REVERT: E 181 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8994 (pt0) REVERT: E 247 PRO cc_start: 0.7690 (Cg_exo) cc_final: 0.7463 (Cg_endo) REVERT: E 256 GLN cc_start: 0.8455 (tp40) cc_final: 0.8046 (tp-100) REVERT: F 28 SER cc_start: 0.8813 (m) cc_final: 0.8529 (m) REVERT: F 137 MET cc_start: 0.8310 (tpp) cc_final: 0.7816 (tpt) REVERT: G 77 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: G 160 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8793 (mtmm) REVERT: I 62 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: I 152 PHE cc_start: 0.8003 (t80) cc_final: 0.7703 (t80) REVERT: I 222 LYS cc_start: 0.8051 (tptp) cc_final: 0.7817 (mmmt) REVERT: I 358 TRP cc_start: 0.5558 (OUTLIER) cc_final: 0.5323 (p90) REVERT: I 451 GLU cc_start: 0.9147 (tp30) cc_final: 0.8855 (tp30) REVERT: J 112 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.4725 (p0) REVERT: K 20 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8704 (tp40) REVERT: K 49 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8832 (tmm-80) REVERT: K 82 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8280 (mm110) REVERT: L 95 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8842 (mp10) REVERT: L 103 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9067 (mm) REVERT: P 154 TYR cc_start: 0.8380 (p90) cc_final: 0.8057 (p90) outliers start: 96 outliers final: 54 residues processed: 365 average time/residue: 0.4438 time to fit residues: 270.4171 Evaluate side-chains 323 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 306 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068419 restraints weight = 93849.273| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.81 r_work: 0.2907 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33794 Z= 0.245 Angle : 0.636 11.152 46351 Z= 0.336 Chirality : 0.041 0.206 5011 Planarity : 0.005 0.100 5356 Dihedral : 18.817 173.962 6004 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.87 % Favored : 92.71 % Rotamer: Outliers : 3.42 % Allowed : 19.43 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3552 helix: 1.56 (0.14), residues: 1333 sheet: -0.89 (0.22), residues: 583 loop : -0.58 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 63 HIS 0.009 0.001 HIS K 81 PHE 0.019 0.001 PHE C 221 TYR 0.022 0.002 TYR G 182 ARG 0.008 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 1407) hydrogen bonds : angle 4.53715 ( 3939) covalent geometry : bond 0.00549 (33794) covalent geometry : angle 0.63642 (46351) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 267 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6456 (tpt) cc_final: 0.5786 (tpt) REVERT: A 24 MET cc_start: 0.8297 (tpp) cc_final: 0.8068 (tpp) REVERT: A 202 ASP cc_start: 0.8361 (p0) cc_final: 0.7916 (p0) REVERT: B 99 TYR cc_start: 0.8273 (m-80) cc_final: 0.7612 (m-80) REVERT: B 118 ARG cc_start: 0.4532 (tmt170) cc_final: 0.3465 (mtp180) REVERT: B 187 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 213 ARG cc_start: 0.4501 (tpp80) cc_final: 0.3818 (tpp80) REVERT: C 244 TYR cc_start: 0.7240 (t80) cc_final: 0.6797 (t80) REVERT: D 77 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8495 (mtm-85) REVERT: E 137 MET cc_start: 0.9001 (tpp) cc_final: 0.8746 (tpp) REVERT: E 152 ASP cc_start: 0.9196 (p0) cc_final: 0.8815 (p0) REVERT: E 181 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9016 (pt0) REVERT: E 256 GLN cc_start: 0.8473 (tp40) cc_final: 0.8063 (tp-100) REVERT: F 77 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9038 (mtm110) REVERT: F 137 MET cc_start: 0.8417 (tpp) cc_final: 0.8029 (tpt) REVERT: G 77 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7694 (mtm-85) REVERT: G 152 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8697 (p0) REVERT: G 160 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8805 (mtmm) REVERT: G 181 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: G 229 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: I 26 MET cc_start: 0.8839 (mmm) cc_final: 0.8287 (mmt) REVERT: I 52 TRP cc_start: 0.7421 (p90) cc_final: 0.6955 (p90) REVERT: I 62 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: I 152 PHE cc_start: 0.8136 (t80) cc_final: 0.7870 (t80) REVERT: J 112 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.4791 (p0) REVERT: L 95 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8956 (mp10) REVERT: L 103 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9076 (mm) REVERT: P 54 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7586 (ttmm) REVERT: P 154 TYR cc_start: 0.8583 (p90) cc_final: 0.8213 (p90) REVERT: Q 271 TYR cc_start: 0.0861 (OUTLIER) cc_final: 0.0364 (m-10) outliers start: 109 outliers final: 68 residues processed: 355 average time/residue: 0.4529 time to fit residues: 260.3371 Evaluate side-chains 329 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 248 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 124 HIS Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 108 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 336 optimal weight: 30.0000 chunk 234 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 362 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN K 82 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.105722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070235 restraints weight = 93690.056| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.84 r_work: 0.2988 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33794 Z= 0.157 Angle : 0.598 11.067 46351 Z= 0.317 Chirality : 0.040 0.194 5011 Planarity : 0.005 0.100 5356 Dihedral : 18.757 173.758 6002 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.53 % Favored : 93.05 % Rotamer: Outliers : 3.11 % Allowed : 19.84 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3552 helix: 1.64 (0.14), residues: 1334 sheet: -0.78 (0.22), residues: 577 loop : -0.50 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 63 HIS 0.020 0.001 HIS Q 124 PHE 0.015 0.001 PHE G 234 TYR 0.035 0.001 TYR A 37 ARG 0.009 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 1407) hydrogen bonds : angle 4.38695 ( 3939) covalent geometry : bond 0.00355 (33794) covalent geometry : angle 0.59763 (46351) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 276 time to evaluate : 3.807 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: A 1 MET cc_start: 0.6485 (tpt) cc_final: 0.5838 (tpt) REVERT: A 202 ASP cc_start: 0.8358 (p0) cc_final: 0.7894 (p0) REVERT: A 209 GLN cc_start: 0.8873 (mt0) cc_final: 0.8596 (mt0) REVERT: B 99 TYR cc_start: 0.8250 (m-80) cc_final: 0.7719 (m-80) REVERT: B 118 ARG cc_start: 0.4407 (tmt170) cc_final: 0.3470 (mtp180) REVERT: B 187 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 204 MET cc_start: 0.8219 (tpp) cc_final: 0.7807 (tpt) REVERT: C 244 TYR cc_start: 0.7188 (t80) cc_final: 0.6796 (t80) REVERT: D 77 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8161 (ttp-170) REVERT: D 156 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8971 (tptt) REVERT: D 226 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9074 (mt) REVERT: E 137 MET cc_start: 0.8951 (tpp) cc_final: 0.8712 (tpp) REVERT: E 152 ASP cc_start: 0.9080 (p0) cc_final: 0.8630 (p0) REVERT: E 181 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8935 (pt0) REVERT: E 256 GLN cc_start: 0.8528 (tp40) cc_final: 0.8093 (tp-100) REVERT: F 137 MET cc_start: 0.8283 (tpp) cc_final: 0.7948 (tpt) REVERT: G 77 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7738 (mtm-85) REVERT: G 152 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8692 (p0) REVERT: G 160 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8823 (mtmm) REVERT: G 181 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: I 26 MET cc_start: 0.8805 (mmm) cc_final: 0.8236 (mmt) REVERT: I 52 TRP cc_start: 0.7338 (p90) cc_final: 0.6963 (p90) REVERT: I 62 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: I 222 LYS cc_start: 0.8151 (tptp) cc_final: 0.7898 (mmmt) REVERT: J 112 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.4603 (p0) REVERT: K 20 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8716 (tp40) REVERT: K 82 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: L 95 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8820 (mp10) REVERT: L 103 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9083 (mm) REVERT: P 154 TYR cc_start: 0.8540 (p90) cc_final: 0.8203 (p90) REVERT: Q 271 TYR cc_start: 0.0778 (OUTLIER) cc_final: 0.0246 (m-10) outliers start: 99 outliers final: 65 residues processed: 351 average time/residue: 0.4381 time to fit residues: 252.0161 Evaluate side-chains 341 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 317 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 337 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069525 restraints weight = 93574.278| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.77 r_work: 0.2976 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33794 Z= 0.188 Angle : 0.610 10.723 46351 Z= 0.322 Chirality : 0.040 0.198 5011 Planarity : 0.005 0.101 5356 Dihedral : 18.748 173.559 6002 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.64 % Favored : 92.96 % Rotamer: Outliers : 3.08 % Allowed : 20.22 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3552 helix: 1.65 (0.14), residues: 1334 sheet: -0.81 (0.22), residues: 577 loop : -0.51 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 63 HIS 0.008 0.001 HIS K 81 PHE 0.021 0.001 PHE F 234 TYR 0.023 0.001 TYR G 182 ARG 0.007 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1407) hydrogen bonds : angle 4.40004 ( 3939) covalent geometry : bond 0.00426 (33794) covalent geometry : angle 0.60978 (46351) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 271 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8360 (p0) cc_final: 0.7904 (p0) REVERT: A 209 GLN cc_start: 0.8862 (mt0) cc_final: 0.8558 (mt0) REVERT: B 99 TYR cc_start: 0.8301 (m-80) cc_final: 0.7714 (m-80) REVERT: B 118 ARG cc_start: 0.4469 (tmt170) cc_final: 0.3454 (mtp180) REVERT: B 187 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 204 MET cc_start: 0.8205 (tpp) cc_final: 0.7817 (tpt) REVERT: C 244 TYR cc_start: 0.7251 (t80) cc_final: 0.6839 (t80) REVERT: D 77 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8190 (ttp-170) REVERT: D 156 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8944 (tptt) REVERT: E 137 MET cc_start: 0.8933 (tpp) cc_final: 0.8677 (tpp) REVERT: E 152 ASP cc_start: 0.9092 (p0) cc_final: 0.8655 (p0) REVERT: E 181 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8937 (pt0) REVERT: E 256 GLN cc_start: 0.8527 (tp40) cc_final: 0.8103 (tp-100) REVERT: F 32 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8372 (t70) REVERT: F 137 MET cc_start: 0.8185 (tpp) cc_final: 0.7841 (tpp) REVERT: F 234 PHE cc_start: 0.7938 (t80) cc_final: 0.7730 (t80) REVERT: F 247 PRO cc_start: 0.9040 (Cg_exo) cc_final: 0.8816 (Cg_endo) REVERT: G 77 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: G 160 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8726 (mtmm) REVERT: G 181 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: I 26 MET cc_start: 0.8829 (mmm) cc_final: 0.8266 (mmt) REVERT: I 52 TRP cc_start: 0.7236 (p90) cc_final: 0.6991 (p90) REVERT: I 62 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7160 (m-10) REVERT: I 396 ASP cc_start: 0.7103 (t0) cc_final: 0.6509 (t70) REVERT: I 451 GLU cc_start: 0.9209 (tp30) cc_final: 0.8981 (tp30) REVERT: J 20 GLN cc_start: 0.9422 (tp40) cc_final: 0.8840 (tm-30) REVERT: J 112 ASP cc_start: 0.5960 (OUTLIER) cc_final: 0.4623 (p0) REVERT: K 20 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8745 (tp40) REVERT: L 95 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8954 (mp10) REVERT: L 103 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9107 (mm) REVERT: P 54 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7600 (tptt) REVERT: P 154 TYR cc_start: 0.8599 (p90) cc_final: 0.8158 (p90) REVERT: Q 42 ARG cc_start: 0.7781 (tpt90) cc_final: 0.7211 (ptp-110) REVERT: Q 271 TYR cc_start: 0.0807 (OUTLIER) cc_final: 0.0208 (m-80) outliers start: 98 outliers final: 73 residues processed: 345 average time/residue: 0.4656 time to fit residues: 263.9478 Evaluate side-chains 348 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 263 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 124 HIS Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 65 optimal weight: 0.0370 chunk 175 optimal weight: 0.0050 chunk 53 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 366 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.106288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071049 restraints weight = 93210.925| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.76 r_work: 0.3009 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33794 Z= 0.144 Angle : 0.591 12.071 46351 Z= 0.311 Chirality : 0.040 0.195 5011 Planarity : 0.005 0.101 5356 Dihedral : 18.697 172.845 6002 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.25 % Favored : 93.38 % Rotamer: Outliers : 2.51 % Allowed : 20.75 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3552 helix: 1.67 (0.14), residues: 1342 sheet: -0.78 (0.22), residues: 586 loop : -0.52 (0.17), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.022 0.001 PHE I 338 TYR 0.028 0.001 TYR A 37 ARG 0.007 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 1407) hydrogen bonds : angle 4.33420 ( 3939) covalent geometry : bond 0.00324 (33794) covalent geometry : angle 0.59144 (46351) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 281 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6150 (tpt) cc_final: 0.5208 (tpt) REVERT: A 202 ASP cc_start: 0.8337 (p0) cc_final: 0.7864 (p0) REVERT: B 99 TYR cc_start: 0.8250 (m-80) cc_final: 0.7668 (m-80) REVERT: B 118 ARG cc_start: 0.4286 (tmt170) cc_final: 0.3441 (mtp180) REVERT: B 204 MET cc_start: 0.8156 (tpp) cc_final: 0.7819 (tpt) REVERT: C 244 TYR cc_start: 0.7247 (t80) cc_final: 0.6791 (t80) REVERT: D 77 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: D 156 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8964 (tptt) REVERT: E 137 MET cc_start: 0.8885 (tpp) cc_final: 0.8656 (tpp) REVERT: E 152 ASP cc_start: 0.9012 (p0) cc_final: 0.8577 (p0) REVERT: E 181 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8903 (pt0) REVERT: E 256 GLN cc_start: 0.8522 (tp40) cc_final: 0.8093 (tp-100) REVERT: F 32 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8214 (t70) REVERT: F 137 MET cc_start: 0.8162 (tpp) cc_final: 0.7833 (tpp) REVERT: F 247 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8807 (Cg_endo) REVERT: G 77 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: G 152 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8690 (p0) REVERT: G 160 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8813 (mtmm) REVERT: G 181 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: H 251 GLU cc_start: 0.8664 (mp0) cc_final: 0.8153 (tt0) REVERT: I 26 MET cc_start: 0.8779 (mmm) cc_final: 0.8205 (mmt) REVERT: I 60 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8271 (mm-30) REVERT: I 62 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7220 (m-10) REVERT: I 396 ASP cc_start: 0.7149 (t0) cc_final: 0.6525 (t70) REVERT: J 112 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.4625 (p0) REVERT: K 20 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8582 (tp40) REVERT: L 95 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8804 (mp10) REVERT: L 103 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9059 (mm) REVERT: P 40 TYR cc_start: 0.8680 (t80) cc_final: 0.8389 (t80) REVERT: Q 42 ARG cc_start: 0.7815 (tpt90) cc_final: 0.7269 (ptp-110) REVERT: Q 271 TYR cc_start: 0.0863 (OUTLIER) cc_final: 0.0289 (m-80) REVERT: Q 318 MET cc_start: 0.4578 (ptt) cc_final: 0.4294 (tmm) outliers start: 80 outliers final: 57 residues processed: 340 average time/residue: 0.4373 time to fit residues: 246.7505 Evaluate side-chains 329 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 259 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 55 CYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 10 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 128 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 288 optimal weight: 0.5980 chunk 213 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.105954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070697 restraints weight = 92809.055| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.74 r_work: 0.3003 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33794 Z= 0.155 Angle : 0.597 11.930 46351 Z= 0.316 Chirality : 0.040 0.193 5011 Planarity : 0.004 0.102 5356 Dihedral : 18.682 171.785 6002 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.56 % Favored : 93.07 % Rotamer: Outliers : 2.35 % Allowed : 21.13 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3552 helix: 1.70 (0.14), residues: 1337 sheet: -0.74 (0.22), residues: 585 loop : -0.51 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.013 0.001 PHE G 234 TYR 0.025 0.001 TYR I 324 ARG 0.006 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1407) hydrogen bonds : angle 4.31837 ( 3939) covalent geometry : bond 0.00350 (33794) covalent geometry : angle 0.59744 (46351) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 276 time to evaluate : 4.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6128 (tpt) cc_final: 0.5230 (tpt) REVERT: A 202 ASP cc_start: 0.8336 (p0) cc_final: 0.7854 (p0) REVERT: B 99 TYR cc_start: 0.8248 (m-80) cc_final: 0.7689 (m-80) REVERT: B 118 ARG cc_start: 0.4347 (tmt170) cc_final: 0.3506 (mtp180) REVERT: B 187 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 204 MET cc_start: 0.8236 (tpp) cc_final: 0.7902 (tpt) REVERT: C 244 TYR cc_start: 0.7276 (t80) cc_final: 0.6805 (t80) REVERT: D 77 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8196 (ttp-170) REVERT: D 156 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8965 (tptt) REVERT: E 137 MET cc_start: 0.8890 (tpp) cc_final: 0.8659 (tpp) REVERT: E 152 ASP cc_start: 0.8990 (p0) cc_final: 0.8560 (p0) REVERT: E 181 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8919 (pt0) REVERT: E 256 GLN cc_start: 0.8524 (tp40) cc_final: 0.8100 (tp-100) REVERT: F 32 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8309 (t70) REVERT: F 137 MET cc_start: 0.8096 (tpp) cc_final: 0.7779 (tpp) REVERT: F 247 PRO cc_start: 0.9051 (Cg_exo) cc_final: 0.8825 (Cg_endo) REVERT: G 77 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7783 (mtm-85) REVERT: G 152 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8692 (p0) REVERT: G 160 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8734 (mtmm) REVERT: G 181 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: H 251 GLU cc_start: 0.8617 (mp0) cc_final: 0.8117 (tt0) REVERT: H 302 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (mtt90) REVERT: I 26 MET cc_start: 0.8818 (mmm) cc_final: 0.8244 (mmt) REVERT: I 62 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7327 (m-10) REVERT: I 396 ASP cc_start: 0.7074 (t0) cc_final: 0.6419 (t70) REVERT: J 112 ASP cc_start: 0.5910 (OUTLIER) cc_final: 0.4672 (p0) REVERT: K 20 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8718 (tp40) REVERT: L 95 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8907 (mp10) REVERT: L 103 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9073 (mm) REVERT: P 40 TYR cc_start: 0.8699 (t80) cc_final: 0.8428 (t80) REVERT: Q 42 ARG cc_start: 0.7869 (tpt90) cc_final: 0.7353 (ptp-110) REVERT: Q 271 TYR cc_start: 0.0947 (OUTLIER) cc_final: 0.0338 (m-80) REVERT: Q 318 MET cc_start: 0.4823 (ptt) cc_final: 0.4572 (tmm) outliers start: 75 outliers final: 56 residues processed: 333 average time/residue: 0.4692 time to fit residues: 259.3914 Evaluate side-chains 336 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 266 time to evaluate : 5.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 284 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 3 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.107127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072133 restraints weight = 92690.383| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.72 r_work: 0.3033 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33794 Z= 0.128 Angle : 0.593 23.644 46351 Z= 0.309 Chirality : 0.039 0.272 5011 Planarity : 0.005 0.180 5356 Dihedral : 18.637 172.848 6002 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.91 % Favored : 93.75 % Rotamer: Outliers : 2.23 % Allowed : 21.19 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3552 helix: 1.70 (0.14), residues: 1346 sheet: -0.69 (0.22), residues: 585 loop : -0.48 (0.17), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.012 0.001 PHE G 234 TYR 0.029 0.001 TYR A 37 ARG 0.006 0.000 ARG Q 42 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1407) hydrogen bonds : angle 4.24463 ( 3939) covalent geometry : bond 0.00285 (33794) covalent geometry : angle 0.59265 (46351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21188.77 seconds wall clock time: 375 minutes 25.66 seconds (22525.66 seconds total)