Starting phenix.real_space_refine on Sun Jul 5 02:59:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq6_63294/07_2026/9lq6_63294.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.573 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 76 5.49 5 S 108 5.16 5 C 15488 2.51 5 N 4123 2.21 5 O 4873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24669 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3904 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain: "B" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4796 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 20, 'TRANS': 570} Chain breaks: 2 Chain: "C" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3043 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "F" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "G" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2534 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain: "K" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 676 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna2p': 5, 'rna3p': 26} Chain: "J" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 873 Classifications: {'RNA': 41} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 17, 'rna3p': 23} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 5.10, per 1000 atoms: 0.21 Number of scatterers: 24669 At special positions: 0 Unit cell: (105.316, 112.772, 200.38, 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) Mn 1 24.99 S 108 16.00 P 76 15.00 O 4873 8.00 N 4123 7.00 C 15488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5436 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 36 sheets defined 41.7% alpha, 16.3% beta 26 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 168 through 186 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.595A pdb=" N ASN A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.506A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.502A pdb=" N LYS A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.752A pdb=" N LYS A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.578A pdb=" N ILE A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.593A pdb=" N ARG A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.547A pdb=" N ALA B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 45 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 55 through 60 removed outlier: 4.197A pdb=" N GLN B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 60' Processing helix chain 'B' and resid 80 through 100 removed outlier: 3.719A pdb=" N ASP B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 135 through 151 Proline residue: B 141 - end of helix removed outlier: 3.571A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 227 through 238 removed outlier: 4.106A pdb=" N VAL B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 297 through 319 Processing helix chain 'B' and resid 343 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.617A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 409 through 419 removed outlier: 3.734A pdb=" N LYS B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.047A pdb=" N VAL B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.102A pdb=" N GLN B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.896A pdb=" N GLY B 528 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 560 removed outlier: 6.252A pdb=" N ASN B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 575 through 596 Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.670A pdb=" N LEU C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 410 removed outlier: 3.548A pdb=" N VAL C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 122 through 141 Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.516A pdb=" N GLN D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 240 through 252 Processing helix chain 'E' and resid 42 through 55 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 121 through 141 removed outlier: 3.774A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 189 through 197 Processing helix chain 'E' and resid 240 through 253 Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 121 through 141 removed outlier: 3.818A pdb=" N TYR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.578A pdb=" N GLN F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 240 through 253 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 81 removed outlier: 3.521A pdb=" N GLY G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.768A pdb=" N ARG G 131 " --> pdb=" O LYS G 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 45 removed outlier: 4.263A pdb=" N GLY H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.660A pdb=" N GLY H 70 " --> pdb=" O HIS H 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.540A pdb=" N THR H 89 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 112 through 132 removed outlier: 3.564A pdb=" N LEU H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 32 through 37 removed outlier: 3.720A pdb=" N GLU I 37 " --> pdb=" O THR I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 61 through 72 Processing helix chain 'I' and resid 116 through 127 removed outlier: 4.231A pdb=" N MET I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 removed outlier: 3.577A pdb=" N SER I 131 " --> pdb=" O PHE I 128 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU I 132 " --> pdb=" O PRO I 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 128 through 132' Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.540A pdb=" N LYS I 139 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG I 140 " --> pdb=" O SER I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 136 through 140' Processing helix chain 'I' and resid 141 through 161 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'I' and resid 192 through 196 removed outlier: 3.808A pdb=" N LYS I 196 " --> pdb=" O LEU I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 271 Processing helix chain 'I' and resid 283 through 299 Processing helix chain 'I' and resid 303 through 307 removed outlier: 3.562A pdb=" N GLY I 307 " --> pdb=" O THR I 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 6.656A pdb=" N THR A 5 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 204 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 7 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 8.511A pdb=" N PHE A 104 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU A 85 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE A 106 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 87 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.263A pdb=" N GLY A 119 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N LYS A 130 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 375 removed outlier: 4.710A pdb=" N ILE A 379 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL A 224 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 342 Processing sheet with id=AA8, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 326 removed outlier: 6.814A pdb=" N LEU B 331 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 325 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 378 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS B 434 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR B 387 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.695A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 151 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE C 163 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN C 229 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.695A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N PHE C 277 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 removed outlier: 4.193A pdb=" N PHE C 61 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AB8, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB9, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.899A pdb=" N PHE C 355 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 392 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 336 " --> pdb=" O ILE C 423 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 366 through 367 removed outlier: 4.092A pdb=" N ILE C 379 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.522A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 229 through 236 current: chain 'D' and resid 185 through 188 Processing sheet with id=AC3, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.522A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 92 current: chain 'D' and resid 268 through 275 removed outlier: 4.237A pdb=" N GLY D 269 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AC5, first strand: chain 'D' and resid 204 through 211 removed outlier: 6.266A pdb=" N LEU D 205 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR D 220 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG D 207 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 218 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN D 209 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.519A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 229 through 236 current: chain 'E' and resid 185 through 188 Processing sheet with id=AC7, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.519A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 92 current: chain 'E' and resid 270 through 275 Processing sheet with id=AC8, first strand: chain 'E' and resid 26 through 28 removed outlier: 5.103A pdb=" N ILE E 26 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN E 222 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN E 28 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU E 211 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.772A pdb=" N ILE E 163 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.526A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 229 through 235 current: chain 'F' and resid 185 through 188 Processing sheet with id=AD2, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.526A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 270 through 275 Processing sheet with id=AD3, first strand: chain 'F' and resid 204 through 211 removed outlier: 6.352A pdb=" N LEU F 205 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR F 220 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG F 207 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU F 218 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN F 209 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AD6, first strand: chain 'I' and resid 114 through 115 removed outlier: 6.470A pdb=" N THR I 242 " --> pdb=" O ALA I 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AD8, first strand: chain 'I' and resid 213 through 218 Processing sheet with id=AD9, first strand: chain 'I' and resid 258 through 260 removed outlier: 4.071A pdb=" N HIS I 253 " --> pdb=" O CYS I 260 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 2.67 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: 7558 1.34 - 1.46: 5499 1.46 - 1.58: 11944 1.58 - 1.70: 148 1.70 - 1.82: 183 Bond restraints: 25332 Sorted by residual: bond pdb=" CA ASP B 170 " pdb=" CB ASP B 170 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.21e-02 6.83e+03 1.86e+01 bond pdb=" C ASN D 37 " pdb=" N LEU D 38 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.20e+00 bond pdb=" C2 U J 21 " pdb=" N3 U J 21 " ideal model delta sigma weight residual 1.373 1.361 0.012 7.00e-03 2.04e+04 2.99e+00 bond pdb=" CB PHE A 263 " pdb=" CG PHE A 263 " ideal model delta sigma weight residual 1.502 1.463 0.039 2.30e-02 1.89e+03 2.88e+00 bond pdb=" N9 A J 9 " pdb=" C4 A J 9 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.74e+00 ... (remaining 25327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 34122 2.60 - 5.20: 396 5.20 - 7.80: 39 7.80 - 10.40: 6 10.40 - 13.00: 1 Bond angle restraints: 34564 Sorted by residual: angle pdb=" C LEU A 237 " pdb=" CA LEU A 237 " pdb=" CB LEU A 237 " ideal model delta sigma weight residual 116.54 108.29 8.25 1.15e+00 7.56e-01 5.15e+01 angle pdb=" CA LEU A 237 " pdb=" C LEU A 237 " pdb=" N ASP A 238 " ideal model delta sigma weight residual 119.52 115.36 4.16 7.90e-01 1.60e+00 2.77e+01 angle pdb=" CA ARG A 264 " pdb=" CB ARG A 264 " pdb=" CG ARG A 264 " ideal model delta sigma weight residual 114.10 124.05 -9.95 2.00e+00 2.50e-01 2.48e+01 angle pdb=" O2 U J 26 " pdb=" C2 U J 26 " pdb=" N3 U J 26 " ideal model delta sigma weight residual 122.20 119.28 2.92 7.00e-01 2.04e+00 1.75e+01 angle pdb=" CA ILE B 191 " pdb=" CB ILE B 191 " pdb=" CG1 ILE B 191 " ideal model delta sigma weight residual 110.40 117.23 -6.83 1.70e+00 3.46e-01 1.61e+01 ... (remaining 34559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 14628 35.67 - 71.34: 809 71.34 - 107.01: 45 107.01 - 142.68: 0 142.68 - 178.35: 3 Dihedral angle restraints: 15485 sinusoidal: 7059 harmonic: 8426 Sorted by residual: dihedral pdb=" O4' U J 14 " pdb=" C1' U J 14 " pdb=" N1 U J 14 " pdb=" C2 U J 14 " ideal model delta sinusoidal sigma weight residual -128.00 50.35 -178.35 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C K 18 " pdb=" C1' C K 18 " pdb=" N1 C K 18 " pdb=" C2 C K 18 " ideal model delta sinusoidal sigma weight residual -128.00 48.75 -176.75 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U J 26 " pdb=" C1' U J 26 " pdb=" N1 U J 26 " pdb=" C2 U J 26 " ideal model delta sinusoidal sigma weight residual -128.00 23.11 -151.11 1 1.70e+01 3.46e-03 6.23e+01 ... (remaining 15482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3404 0.065 - 0.130: 454 0.130 - 0.195: 24 0.195 - 0.260: 1 0.260 - 0.325: 1 Chirality restraints: 3884 Sorted by residual: chirality pdb=" CG LEU C 89 " pdb=" CB LEU C 89 " pdb=" CD1 LEU C 89 " pdb=" CD2 LEU C 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1' G J 15 " pdb=" O4' G J 15 " pdb=" C2' G J 15 " pdb=" N9 G J 15 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 237 " pdb=" CB LEU A 237 " pdb=" CD1 LEU A 237 " pdb=" CD2 LEU A 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 3881 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 320 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 321 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 191 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C ILE B 191 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE B 191 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO B 192 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 320 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" CD GLU C 320 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU C 320 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU C 320 " 0.015 2.00e-02 2.50e+03 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 591 2.66 - 3.22: 22733 3.22 - 3.78: 39631 3.78 - 4.34: 55171 4.34 - 4.90: 90383 Nonbonded interactions: 208509 Sorted by model distance: nonbonded pdb=" OD2 ASP B 329 " pdb=" O2' SAM B 702 " model vdw 2.105 3.040 nonbonded pdb=" OD1 ASN C 231 " pdb=" N ASN C 232 " model vdw 2.108 3.120 nonbonded pdb=" OG SER B 457 " pdb=" OE1 GLU B 546 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR H 84 " pdb=" OD2 ASP H 87 " model vdw 2.172 3.040 nonbonded pdb=" OE1 GLN C 126 " pdb=" NE ARG C 129 " model vdw 2.172 3.120 ... (remaining 208504 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 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 : 0.004 0.075 25332 Z= 0.193 Angle : 0.693 12.997 34564 Z= 0.403 Chirality : 0.044 0.325 3884 Planarity : 0.005 0.103 4149 Dihedral : 19.614 178.346 10049 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.51 % Favored : 93.96 % Rotamer: Outliers : 3.50 % Allowed : 34.89 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2829 helix: 1.02 (0.16), residues: 1076 sheet: 0.68 (0.23), residues: 456 loop : -1.28 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 432 TYR 0.022 0.001 TYR C 49 PHE 0.032 0.002 PHE C 106 TRP 0.010 0.001 TRP B 252 HIS 0.015 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (25332) covalent geometry : angle 0.69257 / 0.40 (34564) hydrogen bonds : bond 0.15527 / 10.64 ( 1046) hydrogen bonds : angle 6.09194 / 4.27 ( 2963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 342 time to evaluate : 1.023 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: A 237 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7473 (mm) REVERT: A 404 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7484 (tptt) REVERT: B 2 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8622 (tptt) REVERT: B 57 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8062 (tp30) REVERT: B 185 ARG cc_start: 0.8953 (mmm160) cc_final: 0.7568 (tpm-80) REVERT: B 314 GLU cc_start: 0.7926 (tp30) cc_final: 0.7556 (tp30) REVERT: B 394 GLU cc_start: 0.8188 (tt0) cc_final: 0.7893 (tt0) REVERT: B 466 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8704 (tp40) REVERT: C 150 MET cc_start: 0.9363 (ptm) cc_final: 0.8980 (ptm) REVERT: C 184 ASP cc_start: 0.6747 (m-30) cc_final: 0.6276 (m-30) REVERT: C 263 LYS cc_start: 0.6190 (pptt) cc_final: 0.5711 (pmtt) REVERT: C 334 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8112 (ppt90) REVERT: C 383 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 419 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: D 207 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8251 (mmm160) REVERT: G 3 ILE cc_start: 0.8929 (mt) cc_final: 0.8706 (mt) REVERT: G 85 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8228 (p) REVERT: G 94 SER cc_start: 0.8985 (t) cc_final: 0.8679 (p) REVERT: H 65 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8263 (ptt90) REVERT: H 104 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: H 108 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8276 (mt-10) REVERT: I 230 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8343 (ptpp) REVERT: I 280 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8735 (mttt) outliers start: 90 outliers final: 59 residues processed: 407 average time/residue: 0.7341 time to fit residues: 339.1668 Evaluate side-chains 405 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 335 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 280 LYS Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 340 GLN B 178 ASN B 239 ASN B 440 GLN C 297 GLN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.042235 restraints weight = 62588.589| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 1.96 r_work: 0.2292 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25332 Z= 0.172 Angle : 0.642 10.833 34564 Z= 0.349 Chirality : 0.044 0.273 3884 Planarity : 0.005 0.100 4149 Dihedral : 15.007 178.583 4397 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.27 % Favored : 94.17 % Rotamer: Outliers : 6.06 % Allowed : 30.73 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2829 helix: 1.21 (0.16), residues: 1088 sheet: 0.54 (0.23), residues: 477 loop : -1.23 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 432 TYR 0.031 0.001 TYR C 49 PHE 0.018 0.002 PHE B 461 TRP 0.008 0.001 TRP F 219 HIS 0.009 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (25332) covalent geometry : angle 0.64161 / 0.35 (34564) hydrogen bonds : bond 0.05216 / 3.50 ( 1046) hydrogen bonds : angle 5.00338 / 3.49 ( 2963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 349 time to evaluate : 0.916 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 133 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 139 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: A 315 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7823 (p0) REVERT: A 365 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8924 (ptp-170) REVERT: A 429 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 1 MET cc_start: 0.9124 (pmt) cc_final: 0.8890 (pmm) REVERT: B 57 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8210 (tp30) REVERT: B 75 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8827 (tmtm) REVERT: B 85 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: B 118 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8952 (tp) REVERT: B 185 ARG cc_start: 0.8925 (mmm160) cc_final: 0.7569 (tpm170) REVERT: B 253 ASP cc_start: 0.8429 (t0) cc_final: 0.8017 (t0) REVERT: B 314 GLU cc_start: 0.7882 (tp30) cc_final: 0.7532 (tp30) REVERT: B 394 GLU cc_start: 0.8240 (tt0) cc_final: 0.7899 (tt0) REVERT: C 47 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8590 (ptp-110) REVERT: C 184 ASP cc_start: 0.7094 (m-30) cc_final: 0.6770 (m-30) REVERT: C 334 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8641 (ppt90) REVERT: C 380 LYS cc_start: 0.9025 (tppp) cc_final: 0.8796 (mmtp) REVERT: D 80 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.9007 (tpt-90) REVERT: D 160 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8837 (mm-30) REVERT: D 164 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8791 (mtp85) REVERT: E 5 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8929 (ttt) REVERT: E 100 MET cc_start: 0.9397 (mmt) cc_final: 0.9044 (mmt) REVERT: F 245 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8348 (ttmm) REVERT: G 3 ILE cc_start: 0.8907 (mt) cc_final: 0.8673 (mt) REVERT: G 73 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8431 (tttt) REVERT: G 85 VAL cc_start: 0.8745 (t) cc_final: 0.8273 (p) REVERT: G 94 SER cc_start: 0.8987 (t) cc_final: 0.8696 (p) REVERT: H 65 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7869 (ptt90) REVERT: H 100 TYR cc_start: 0.8389 (t80) cc_final: 0.7890 (t80) REVERT: H 104 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: I 60 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8623 (mm-30) outliers start: 156 outliers final: 66 residues processed: 474 average time/residue: 0.7200 time to fit residues: 388.2759 Evaluate side-chains 413 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 329 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 80 ARG Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 3 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 157 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 178 ASN B 423 ASN E 13 ASN E 31 GLN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN I 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.053932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.043198 restraints weight = 62408.641| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 1.99 r_work: 0.2324 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2219 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25332 Z= 0.138 Angle : 0.605 10.344 34564 Z= 0.328 Chirality : 0.043 0.266 3884 Planarity : 0.005 0.098 4149 Dihedral : 14.671 178.974 4331 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.16 % Favored : 94.31 % Rotamer: Outliers : 5.79 % Allowed : 30.61 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2829 helix: 1.36 (0.16), residues: 1086 sheet: 0.63 (0.23), residues: 474 loop : -1.17 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 297 TYR 0.015 0.001 TYR C 49 PHE 0.021 0.001 PHE A 263 TRP 0.007 0.001 TRP A 147 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (25332) covalent geometry : angle 0.60542 / 0.33 (34564) hydrogen bonds : bond 0.04402 / 2.95 ( 1046) hydrogen bonds : angle 4.75507 / 3.33 ( 2963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 343 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8782 (p) REVERT: A 139 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: A 315 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7858 (p0) REVERT: A 332 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7537 (mmm-85) REVERT: A 365 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8912 (ptp-170) REVERT: A 429 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 57 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8233 (tp30) REVERT: B 75 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8854 (tmtm) REVERT: B 85 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8647 (tttp) REVERT: B 110 ASP cc_start: 0.8234 (t70) cc_final: 0.7814 (t70) REVERT: B 118 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 185 ARG cc_start: 0.8917 (mmm160) cc_final: 0.7882 (tpm170) REVERT: B 314 GLU cc_start: 0.7897 (tp30) cc_final: 0.7538 (tp30) REVERT: B 394 GLU cc_start: 0.8253 (tt0) cc_final: 0.7902 (tt0) REVERT: B 466 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: B 504 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8751 (mt0) REVERT: C 184 ASP cc_start: 0.7005 (m-30) cc_final: 0.6697 (m-30) REVERT: D 242 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: F 245 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8370 (ttmm) REVERT: G 1 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (pmm) REVERT: G 3 ILE cc_start: 0.8895 (mt) cc_final: 0.8674 (mt) REVERT: G 94 SER cc_start: 0.8992 (t) cc_final: 0.8698 (p) REVERT: H 65 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8331 (ptt90) REVERT: H 100 TYR cc_start: 0.8412 (t80) cc_final: 0.8012 (t80) REVERT: H 104 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: I 60 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8638 (mm-30) REVERT: I 230 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8229 (ptpp) REVERT: I 238 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8019 (ttp-110) outliers start: 149 outliers final: 62 residues processed: 456 average time/residue: 0.6859 time to fit residues: 356.6508 Evaluate side-chains 417 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 336 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 239 ASN B 553 ASN B 561 ASN D 238 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.052911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.042080 restraints weight = 62429.886| |-----------------------------------------------------------------------------| r_work (start): 0.2383 rms_B_bonded: 2.01 r_work: 0.2287 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2182 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25332 Z= 0.180 Angle : 0.630 10.431 34564 Z= 0.340 Chirality : 0.044 0.286 3884 Planarity : 0.005 0.097 4149 Dihedral : 14.527 178.693 4310 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.05 % Favored : 94.41 % Rotamer: Outliers : 5.75 % Allowed : 30.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2829 helix: 1.37 (0.16), residues: 1089 sheet: 0.65 (0.23), residues: 473 loop : -1.18 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 432 TYR 0.027 0.001 TYR C 49 PHE 0.018 0.002 PHE B 461 TRP 0.009 0.001 TRP F 219 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (25332) covalent geometry : angle 0.63037 / 0.34 (34564) hydrogen bonds : bond 0.04538 / 3.04 ( 1046) hydrogen bonds : angle 4.66211 / 3.26 ( 2963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 353 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 315 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 332 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7772 (mmm-85) REVERT: A 365 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (ptp-170) REVERT: A 429 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8110 (t80) REVERT: B 57 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8211 (tp30) REVERT: B 75 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8991 (tmtm) REVERT: B 85 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8728 (tttt) REVERT: B 161 GLU cc_start: 0.7885 (tp30) cc_final: 0.7426 (tp30) REVERT: B 219 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8137 (mp) REVERT: B 256 GLU cc_start: 0.8285 (pm20) cc_final: 0.8063 (pm20) REVERT: B 314 GLU cc_start: 0.7909 (tp30) cc_final: 0.7547 (tp30) REVERT: B 394 GLU cc_start: 0.8296 (tt0) cc_final: 0.7897 (tt0) REVERT: B 466 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: C 49 TYR cc_start: 0.8583 (m-80) cc_final: 0.8376 (m-80) REVERT: C 150 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9092 (ptm) REVERT: D 36 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9152 (p) REVERT: D 160 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8930 (mm-30) REVERT: D 242 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: F 18 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8838 (p) REVERT: F 20 GLU cc_start: 0.8515 (pm20) cc_final: 0.8038 (pm20) REVERT: G 1 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7591 (pmm) REVERT: G 3 ILE cc_start: 0.8914 (mt) cc_final: 0.8690 (mt) REVERT: G 94 SER cc_start: 0.8960 (t) cc_final: 0.8652 (p) REVERT: H 13 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: H 65 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8288 (ptt90) REVERT: H 100 TYR cc_start: 0.8462 (t80) cc_final: 0.8056 (t80) REVERT: H 104 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: H 108 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8269 (mt-10) REVERT: I 60 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: I 238 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8161 (ttp-110) outliers start: 148 outliers final: 77 residues processed: 461 average time/residue: 0.7143 time to fit residues: 375.6762 Evaluate side-chains 436 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 97 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 147 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 423 ASN B 495 HIS D 238 ASN E 238 ASN I 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.050886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.040208 restraints weight = 62976.254| |-----------------------------------------------------------------------------| r_work (start): 0.2330 rms_B_bonded: 1.94 r_work: 0.2232 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2125 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 25332 Z= 0.279 Angle : 0.712 11.499 34564 Z= 0.383 Chirality : 0.047 0.329 3884 Planarity : 0.006 0.096 4149 Dihedral : 14.525 178.269 4307 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.55 % Favored : 94.03 % Rotamer: Outliers : 6.25 % Allowed : 30.11 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2829 helix: 1.17 (0.16), residues: 1092 sheet: 0.54 (0.23), residues: 486 loop : -1.28 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 185 TYR 0.028 0.002 TYR C 49 PHE 0.021 0.002 PHE F 149 TRP 0.013 0.002 TRP F 219 HIS 0.016 0.002 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (25332) covalent geometry : angle 0.71153 / 0.38 (34564) hydrogen bonds : bond 0.05179 / 3.46 ( 1046) hydrogen bonds : angle 4.74829 / 3.32 ( 2963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 345 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 139 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: A 315 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (p0) REVERT: A 335 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 365 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8990 (ptp-170) REVERT: B 57 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8222 (tp30) REVERT: B 75 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8989 (tmtm) REVERT: B 85 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8757 (mtpt) REVERT: B 256 GLU cc_start: 0.8249 (pm20) cc_final: 0.8047 (pm20) REVERT: B 314 GLU cc_start: 0.7965 (tp30) cc_final: 0.7596 (tp30) REVERT: C 49 TYR cc_start: 0.8684 (m-80) cc_final: 0.8411 (m-80) REVERT: C 129 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7795 (mtt180) REVERT: C 150 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9079 (ptm) REVERT: C 334 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7886 (ppt90) REVERT: D 36 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9148 (p) REVERT: D 160 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8863 (mm-30) REVERT: E 100 MET cc_start: 0.9403 (mmt) cc_final: 0.9144 (mmt) REVERT: F 245 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8344 (ttmm) REVERT: G 94 SER cc_start: 0.8982 (t) cc_final: 0.8667 (p) REVERT: H 13 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: H 65 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8451 (ptt90) REVERT: H 100 TYR cc_start: 0.8520 (t80) cc_final: 0.8042 (t80) REVERT: H 104 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: I 60 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8548 (mm-30) outliers start: 161 outliers final: 89 residues processed: 467 average time/residue: 0.7039 time to fit residues: 375.0655 Evaluate side-chains 434 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 329 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 239 ASN B 423 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.040958 restraints weight = 62427.608| |-----------------------------------------------------------------------------| r_work (start): 0.2351 rms_B_bonded: 1.98 r_work: 0.2254 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2149 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25332 Z= 0.205 Angle : 0.665 12.046 34564 Z= 0.358 Chirality : 0.045 0.307 3884 Planarity : 0.005 0.093 4149 Dihedral : 14.504 178.127 4303 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.51 % Favored : 94.06 % Rotamer: Outliers : 6.06 % Allowed : 30.50 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2829 helix: 1.24 (0.16), residues: 1091 sheet: 0.56 (0.23), residues: 480 loop : -1.26 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 70 TYR 0.023 0.002 TYR C 49 PHE 0.019 0.002 PHE I 30 TRP 0.009 0.002 TRP E 219 HIS 0.013 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (25332) covalent geometry : angle 0.66455 / 0.36 (34564) hydrogen bonds : bond 0.04728 / 3.16 ( 1046) hydrogen bonds : angle 4.68839 / 3.27 ( 2963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 335 time to evaluate : 0.778 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 133 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 139 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 297 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8204 (tpp80) REVERT: A 315 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7863 (p0) REVERT: A 335 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8755 (mp) REVERT: A 365 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8947 (ptp-170) REVERT: A 429 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 57 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8272 (tp30) REVERT: B 75 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8957 (tmtm) REVERT: B 85 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8708 (tttt) REVERT: B 161 GLU cc_start: 0.7943 (tp30) cc_final: 0.7742 (tp30) REVERT: B 314 GLU cc_start: 0.7945 (tp30) cc_final: 0.7578 (tp30) REVERT: B 394 GLU cc_start: 0.8270 (tt0) cc_final: 0.7986 (tt0) REVERT: C 49 TYR cc_start: 0.8740 (m-80) cc_final: 0.8420 (m-80) REVERT: C 150 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8997 (ptm) REVERT: C 334 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8142 (ppt90) REVERT: D 36 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9149 (p) REVERT: D 160 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8825 (mm-30) REVERT: D 164 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: E 100 MET cc_start: 0.9408 (mmt) cc_final: 0.9146 (mmt) REVERT: G 94 SER cc_start: 0.8975 (t) cc_final: 0.8657 (p) REVERT: H 65 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8348 (ptt90) REVERT: H 100 TYR cc_start: 0.8524 (t80) cc_final: 0.8043 (t80) REVERT: H 104 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: H 117 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8660 (mttm) REVERT: I 60 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8553 (mm-30) REVERT: I 140 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8159 (ptm-80) outliers start: 156 outliers final: 92 residues processed: 448 average time/residue: 0.7204 time to fit residues: 368.2937 Evaluate side-chains 436 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 327 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 209 ASN A 360 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 423 ASN D 238 ASN G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.049394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.038823 restraints weight = 63399.033| |-----------------------------------------------------------------------------| r_work (start): 0.2287 rms_B_bonded: 1.94 r_work: 0.2187 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2081 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 25332 Z= 0.373 Angle : 0.800 11.646 34564 Z= 0.429 Chirality : 0.051 0.369 3884 Planarity : 0.006 0.094 4149 Dihedral : 14.531 178.603 4301 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.97 % Favored : 93.57 % Rotamer: Outliers : 6.57 % Allowed : 29.68 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2829 helix: 0.92 (0.16), residues: 1093 sheet: 0.51 (0.23), residues: 482 loop : -1.40 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 129 TYR 0.027 0.002 TYR C 49 PHE 0.026 0.003 PHE C 281 TRP 0.015 0.003 TRP F 219 HIS 0.018 0.002 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.37 (25332) covalent geometry : angle 0.80026 / 0.43 (34564) hydrogen bonds : bond 0.05731 / 3.82 ( 1046) hydrogen bonds : angle 4.87090 / 3.40 ( 2963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 332 time to evaluate : 1.003 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 133 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 139 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: A 315 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7971 (p0) REVERT: A 335 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 57 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8231 (tp30) REVERT: B 75 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8985 (tmtm) REVERT: B 85 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8711 (mtmm) REVERT: B 161 GLU cc_start: 0.8104 (tp30) cc_final: 0.7848 (tp30) REVERT: B 256 GLU cc_start: 0.8334 (pm20) cc_final: 0.8095 (pm20) REVERT: B 314 GLU cc_start: 0.8004 (tp30) cc_final: 0.7621 (tp30) REVERT: B 394 GLU cc_start: 0.8310 (tt0) cc_final: 0.7982 (tt0) REVERT: B 466 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: B 578 MET cc_start: 0.9243 (mmt) cc_final: 0.8941 (mmt) REVERT: C 76 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8234 (tp) REVERT: C 150 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9051 (ptm) REVERT: C 380 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8879 (mmtp) REVERT: D 36 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9145 (p) REVERT: D 160 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8755 (mm-30) REVERT: D 164 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8740 (mtp85) REVERT: D 207 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8319 (mmm160) REVERT: F 20 GLU cc_start: 0.8553 (pm20) cc_final: 0.8239 (pm20) REVERT: G 94 SER cc_start: 0.9009 (t) cc_final: 0.8698 (p) REVERT: H 13 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: H 65 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8505 (ptt90) REVERT: H 100 TYR cc_start: 0.8576 (t80) cc_final: 0.7970 (t80) REVERT: H 104 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: I 60 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8595 (mm-30) REVERT: I 140 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8226 (ptm-80) outliers start: 169 outliers final: 100 residues processed: 460 average time/residue: 0.7000 time to fit residues: 368.8068 Evaluate side-chains 446 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 327 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 54 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 chunk 271 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS B 423 ASN B 504 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN I 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.052431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.041717 restraints weight = 62334.294| |-----------------------------------------------------------------------------| r_work (start): 0.2375 rms_B_bonded: 1.96 r_work: 0.2277 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2171 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25332 Z= 0.152 Angle : 0.655 12.706 34564 Z= 0.353 Chirality : 0.044 0.290 3884 Planarity : 0.005 0.091 4149 Dihedral : 14.524 178.169 4298 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.23 % Favored : 94.34 % Rotamer: Outliers : 4.66 % Allowed : 31.86 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2829 helix: 1.22 (0.16), residues: 1087 sheet: 0.57 (0.23), residues: 479 loop : -1.28 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.018 0.001 TYR C 188 PHE 0.022 0.001 PHE A 263 TRP 0.011 0.001 TRP A 318 HIS 0.020 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (25332) covalent geometry : angle 0.65469 / 0.35 (34564) hydrogen bonds : bond 0.04384 / 2.94 ( 1046) hydrogen bonds : angle 4.67971 / 3.26 ( 2963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 350 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 139 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: A 315 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 335 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 429 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8118 (t80) REVERT: B 57 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8225 (tp30) REVERT: B 75 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8900 (tmtm) REVERT: B 85 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8707 (mtpt) REVERT: B 161 GLU cc_start: 0.7947 (tp30) cc_final: 0.7746 (tp30) REVERT: B 219 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 285 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8487 (mm-30) REVERT: B 314 GLU cc_start: 0.7946 (tp30) cc_final: 0.7567 (tp30) REVERT: B 394 GLU cc_start: 0.8280 (tt0) cc_final: 0.7967 (tt0) REVERT: B 466 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8531 (tm-30) REVERT: B 598 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8188 (mtpp) REVERT: C 47 ARG cc_start: 0.9041 (ptp-110) cc_final: 0.8811 (ptp-110) REVERT: C 49 TYR cc_start: 0.8813 (m-80) cc_final: 0.8468 (m-80) REVERT: C 150 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8995 (ptm) REVERT: D 2 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7257 (p) REVERT: D 36 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9137 (p) REVERT: D 124 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: D 160 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8818 (mm-30) REVERT: F 20 GLU cc_start: 0.8512 (pm20) cc_final: 0.8169 (pm20) REVERT: G 94 SER cc_start: 0.9005 (t) cc_final: 0.8689 (p) REVERT: H 65 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8310 (ptt90) REVERT: H 100 TYR cc_start: 0.8490 (t80) cc_final: 0.8000 (t80) REVERT: H 104 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: H 108 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 117 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8628 (mtpp) REVERT: I 60 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8619 (mm-30) REVERT: I 140 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8555 (ttp-110) outliers start: 120 outliers final: 64 residues processed: 443 average time/residue: 0.7138 time to fit residues: 361.5019 Evaluate side-chains 412 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 330 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 108 optimal weight: 0.6980 chunk 122 optimal weight: 0.3980 chunk 254 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 259 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN I 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.042216 restraints weight = 62298.796| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 1.98 r_work: 0.2292 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25332 Z= 0.152 Angle : 0.665 13.191 34564 Z= 0.356 Chirality : 0.043 0.281 3884 Planarity : 0.005 0.089 4149 Dihedral : 14.459 178.868 4297 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.37 % Favored : 94.24 % Rotamer: Outliers : 4.00 % Allowed : 32.94 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2829 helix: 1.30 (0.16), residues: 1093 sheet: 0.54 (0.23), residues: 485 loop : -1.17 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.017 0.001 TYR C 188 PHE 0.020 0.001 PHE B 126 TRP 0.010 0.001 TRP A 318 HIS 0.021 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (25332) covalent geometry : angle 0.66487 / 0.36 (34564) hydrogen bonds : bond 0.04255 / 2.85 ( 1046) hydrogen bonds : angle 4.61377 / 3.21 ( 2963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 339 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 139 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 263 PHE cc_start: 0.8133 (t80) cc_final: 0.7891 (t80) REVERT: A 297 ARG cc_start: 0.8443 (tpp80) cc_final: 0.8168 (tpp80) REVERT: A 315 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7958 (p0) REVERT: A 335 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 429 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 57 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8260 (tp30) REVERT: B 75 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8876 (tmtm) REVERT: B 85 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8714 (mtpt) REVERT: B 161 GLU cc_start: 0.7870 (tp30) cc_final: 0.7642 (tp30) REVERT: B 167 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7785 (tp-100) REVERT: B 314 GLU cc_start: 0.7943 (tp30) cc_final: 0.7564 (tp30) REVERT: B 394 GLU cc_start: 0.8305 (tt0) cc_final: 0.7978 (tt0) REVERT: B 466 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: B 598 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8175 (mtpp) REVERT: C 47 ARG cc_start: 0.9011 (ptp-110) cc_final: 0.8738 (ptp-110) REVERT: C 49 TYR cc_start: 0.8832 (m-80) cc_final: 0.8416 (m-80) REVERT: C 76 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8187 (tp) REVERT: C 150 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9032 (ptm) REVERT: D 2 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7182 (p) REVERT: D 36 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9142 (p) REVERT: F 20 GLU cc_start: 0.8547 (pm20) cc_final: 0.8218 (pm20) REVERT: G 94 SER cc_start: 0.8989 (t) cc_final: 0.8681 (p) REVERT: H 13 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: H 65 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7788 (ptt90) REVERT: H 100 TYR cc_start: 0.8483 (t80) cc_final: 0.8060 (t80) REVERT: H 104 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: H 108 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8262 (mt-10) REVERT: I 60 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8616 (mm-30) REVERT: I 140 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8476 (ttp-110) outliers start: 103 outliers final: 65 residues processed: 421 average time/residue: 0.7259 time to fit residues: 348.7036 Evaluate side-chains 416 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 333 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS B 423 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN I 50 GLN I 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.052423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.041698 restraints weight = 62720.193| |-----------------------------------------------------------------------------| r_work (start): 0.2374 rms_B_bonded: 1.97 r_work: 0.2277 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2172 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25332 Z= 0.183 Angle : 0.679 13.301 34564 Z= 0.363 Chirality : 0.044 0.293 3884 Planarity : 0.005 0.088 4149 Dihedral : 14.423 178.991 4297 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.87 % Favored : 93.74 % Rotamer: Outliers : 3.81 % Allowed : 33.26 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2829 helix: 1.29 (0.16), residues: 1092 sheet: 0.58 (0.23), residues: 479 loop : -1.19 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 70 TYR 0.016 0.001 TYR C 188 PHE 0.037 0.002 PHE B 393 TRP 0.010 0.001 TRP A 318 HIS 0.021 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (25332) covalent geometry : angle 0.67884 / 0.36 (34564) hydrogen bonds : bond 0.04414 / 2.95 ( 1046) hydrogen bonds : angle 4.64500 / 3.23 ( 2963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 335 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 139 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: A 263 PHE cc_start: 0.8155 (t80) cc_final: 0.7913 (t80) REVERT: A 335 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8719 (mp) REVERT: A 429 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 57 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8183 (tp30) REVERT: B 75 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8849 (tmtm) REVERT: B 85 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8811 (mtmt) REVERT: B 161 GLU cc_start: 0.7887 (tp30) cc_final: 0.7636 (tp30) REVERT: B 167 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7793 (tp-100) REVERT: B 285 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8498 (mm-30) REVERT: B 314 GLU cc_start: 0.7963 (tp30) cc_final: 0.7586 (tp30) REVERT: B 394 GLU cc_start: 0.8254 (tt0) cc_final: 0.7897 (tt0) REVERT: B 466 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: C 47 ARG cc_start: 0.9023 (ptp-110) cc_final: 0.8809 (ptp-110) REVERT: C 76 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8159 (tp) REVERT: C 150 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9009 (ptm) REVERT: D 36 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9143 (p) REVERT: D 124 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: F 20 GLU cc_start: 0.8551 (pm20) cc_final: 0.8236 (pm20) REVERT: G 94 SER cc_start: 0.8982 (t) cc_final: 0.8668 (p) REVERT: H 13 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: H 100 TYR cc_start: 0.8491 (t80) cc_final: 0.8072 (t80) REVERT: H 104 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: I 60 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: I 140 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8534 (ttp-110) outliers start: 98 outliers final: 71 residues processed: 415 average time/residue: 0.7222 time to fit residues: 341.9192 Evaluate side-chains 421 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 334 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 13 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 137 optimal weight: 0.0770 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.053901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.043165 restraints weight = 62255.792| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 1.97 r_work: 0.2321 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2216 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25332 Z= 0.142 Angle : 0.657 14.053 34564 Z= 0.350 Chirality : 0.043 0.273 3884 Planarity : 0.005 0.086 4149 Dihedral : 14.397 179.594 4292 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.44 % Favored : 94.20 % Rotamer: Outliers : 3.42 % Allowed : 33.49 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2829 helix: 1.37 (0.16), residues: 1094 sheet: 0.55 (0.24), residues: 467 loop : -1.09 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.017 0.001 TYR C 188 PHE 0.020 0.001 PHE B 126 TRP 0.012 0.001 TRP A 318 HIS 0.019 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (25332) covalent geometry : angle 0.65743 / 0.35 (34564) hydrogen bonds : bond 0.04008 / 2.69 ( 1046) hydrogen bonds : angle 4.58324 / 3.18 ( 2963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8650.57 seconds wall clock time: 148 minutes 38.36 seconds (8918.36 seconds total)