Starting phenix.real_space_refine on Fri Feb 6 11:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq6_63294/02_2026/9lq6_63294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq6_63294/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lq6_63294/02_2026/9lq6_63294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq6_63294/02_2026/9lq6_63294.map" model { file = "/net/cci-nas-00/data/ceres_data/9lq6_63294/02_2026/9lq6_63294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq6_63294/02_2026/9lq6_63294.cif" } 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-2.0-5952/lib/python3.9/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, 59 Unusual residues: {' MN': 1, 'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.92, per 1000 atoms: 0.24 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 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: 3.08 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: 5.26 Time building geometry restraints manager: 2.83 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=" 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=" CB GLU B 19 " pdb=" CG GLU B 19 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" CD1 PHE A 263 " pdb=" CE1 PHE A 263 " ideal model delta sigma weight residual 1.382 1.335 0.047 3.00e-02 1.11e+03 2.46e+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=" 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 angle pdb=" N MET B 290 " pdb=" CA MET B 290 " pdb=" C MET B 290 " ideal model delta sigma weight residual 113.19 108.48 4.71 1.19e+00 7.06e-01 1.57e+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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.580 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 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= 0.181 Angle : 0.693 12.997 34564 Z= 0.378 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 covalent geometry : bond 0.00410 (25332) covalent geometry : angle 0.69255 (34564) hydrogen bonds : bond 0.15527 ( 1046) hydrogen bonds : angle 6.09194 ( 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 : 1.096 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: 0.8078 time to fit residues: 372.2540 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 : 1.082 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 314 ASN A 340 GLN B 178 ASN B 239 ASN B 440 GLN C 297 GLN E 13 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.053109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.042382 restraints weight = 62621.919| |-----------------------------------------------------------------------------| r_work (start): 0.2393 rms_B_bonded: 1.98 r_work: 0.2297 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2192 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25332 Z= 0.166 Angle : 0.628 10.254 34564 Z= 0.338 Chirality : 0.043 0.245 3884 Planarity : 0.005 0.103 4149 Dihedral : 14.866 178.203 4397 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.23 % Favored : 94.24 % Rotamer: Outliers : 6.06 % Allowed : 30.19 % 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: 0.11 (0.16), residues: 2829 helix: 1.27 (0.16), residues: 1085 sheet: 0.56 (0.23), residues: 477 loop : -1.19 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 432 TYR 0.028 0.001 TYR C 49 PHE 0.018 0.002 PHE B 461 TRP 0.008 0.001 TRP A 147 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00380 (25332) covalent geometry : angle 0.62849 (34564) hydrogen bonds : bond 0.04523 ( 1046) hydrogen bonds : angle 4.83220 ( 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 510 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 354 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 139 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 263 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 365 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (ptp-170) REVERT: A 429 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 57 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8255 (tp30) REVERT: B 85 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8651 (tttp) REVERT: B 118 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 185 ARG cc_start: 0.8929 (mmm160) cc_final: 0.7598 (tpm170) REVERT: B 314 GLU cc_start: 0.7893 (tp30) cc_final: 0.7529 (tp30) REVERT: B 394 GLU cc_start: 0.8243 (tt0) cc_final: 0.7892 (tt0) REVERT: C 47 ARG cc_start: 0.8949 (ttm110) cc_final: 0.8574 (ptp-110) REVERT: C 49 TYR cc_start: 0.8520 (m-80) cc_final: 0.8260 (m-80) REVERT: C 184 ASP cc_start: 0.7062 (m-30) cc_final: 0.6788 (m-30) REVERT: C 380 LYS cc_start: 0.9010 (tppp) cc_final: 0.8789 (mmtp) REVERT: D 80 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.9000 (tpt-90) REVERT: D 164 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8788 (mtp85) REVERT: F 242 GLU cc_start: 0.8514 (pm20) cc_final: 0.8288 (pm20) REVERT: F 245 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8322 (ttmm) REVERT: G 3 ILE cc_start: 0.8898 (mt) cc_final: 0.8666 (mt) REVERT: G 94 SER cc_start: 0.8983 (t) cc_final: 0.8702 (p) REVERT: G 108 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7900 (mt-10) REVERT: H 65 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7895 (ptt90) REVERT: H 100 TYR cc_start: 0.8372 (t80) cc_final: 0.7793 (t80) REVERT: H 104 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: H 108 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8353 (mt-10) REVERT: I 60 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (mm-30) outliers start: 156 outliers final: 58 residues processed: 478 average time/residue: 0.7862 time to fit residues: 425.8800 Evaluate side-chains 405 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 263 PHE 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 364 SER Chi-restraints excluded: chain A residue 365 ARG 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 85 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 257 ILE 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 131 THR 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 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 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 86 THR Chi-restraints excluded: chain G residue 87 ASP 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 209 ASP Chi-restraints excluded: chain I residue 223 GLU 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: 3.9990 chunk 234 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 360 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 423 ASN B 553 ASN B 561 ASN E 31 GLN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.054051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.043243 restraints weight = 62517.365| |-----------------------------------------------------------------------------| r_work (start): 0.2415 rms_B_bonded: 1.99 r_work: 0.2321 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25332 Z= 0.140 Angle : 0.598 11.999 34564 Z= 0.320 Chirality : 0.042 0.235 3884 Planarity : 0.005 0.100 4149 Dihedral : 14.468 178.841 4318 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.30 % Favored : 94.20 % Rotamer: Outliers : 5.75 % Allowed : 30.54 % Favored : 63.71 % 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: 0.26 (0.16), residues: 2829 helix: 1.42 (0.16), residues: 1092 sheet: 0.65 (0.23), residues: 472 loop : -1.16 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 418 TYR 0.023 0.001 TYR C 49 PHE 0.017 0.001 PHE B 461 TRP 0.008 0.001 TRP A 147 HIS 0.009 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00317 (25332) covalent geometry : angle 0.59830 (34564) hydrogen bonds : bond 0.04112 ( 1046) hydrogen bonds : angle 4.60270 ( 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 501 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 353 time to evaluate : 0.994 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 133 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 332 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7656 (mmm-85) REVERT: A 365 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8935 (ptp-170) REVERT: A 429 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8086 (t80) REVERT: B 57 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8248 (tp30) REVERT: B 85 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8651 (tttt) REVERT: B 161 GLU cc_start: 0.7841 (tp30) cc_final: 0.7371 (tp30) REVERT: B 167 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7538 (tp-100) REVERT: B 314 GLU cc_start: 0.7885 (tp30) cc_final: 0.7536 (tp30) REVERT: B 394 GLU cc_start: 0.8274 (tt0) cc_final: 0.7893 (tt0) REVERT: B 466 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: B 598 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8221 (mtpp) REVERT: C 47 ARG cc_start: 0.8945 (ttm110) cc_final: 0.8635 (ptp-110) REVERT: C 49 TYR cc_start: 0.8605 (m-80) cc_final: 0.8306 (m-80) REVERT: C 150 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9079 (ptm) REVERT: C 184 ASP cc_start: 0.7045 (m-30) cc_final: 0.6842 (m-30) REVERT: C 189 ASN cc_start: 0.8456 (t0) cc_final: 0.8201 (t0) REVERT: D 80 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8922 (tpt-90) REVERT: D 242 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7898 (pp20) REVERT: G 3 ILE cc_start: 0.8897 (mt) cc_final: 0.8673 (mt) REVERT: G 94 SER cc_start: 0.8951 (t) cc_final: 0.8651 (p) REVERT: H 13 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: H 65 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8226 (ptt90) REVERT: H 100 TYR cc_start: 0.8350 (t80) cc_final: 0.7870 (t80) REVERT: H 104 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: I 60 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: I 238 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8188 (ttp-110) outliers start: 148 outliers final: 61 residues processed: 466 average time/residue: 0.7715 time to fit residues: 407.9355 Evaluate side-chains 412 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 237 LEU 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 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 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 200 THR 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 466 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 352 LEU 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 114 MET Chi-restraints excluded: chain D residue 166 THR 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 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 244 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 96 VAL 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 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 189 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 252 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 239 ASN B 423 ASN D 238 ASN ** 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 = 0.2667 r_free = 0.2667 target = 0.052213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.041406 restraints weight = 62651.968| |-----------------------------------------------------------------------------| r_work (start): 0.2362 rms_B_bonded: 1.99 r_work: 0.2266 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2161 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25332 Z= 0.206 Angle : 0.646 12.537 34564 Z= 0.345 Chirality : 0.044 0.267 3884 Planarity : 0.005 0.098 4149 Dihedral : 14.423 178.001 4310 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.37 % Favored : 94.17 % Rotamer: Outliers : 5.67 % Allowed : 30.38 % Favored : 63.95 % 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: 1.36 (0.16), residues: 1087 sheet: 0.64 (0.23), residues: 476 loop : -1.17 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 185 TYR 0.024 0.002 TYR C 49 PHE 0.018 0.002 PHE I 30 TRP 0.011 0.002 TRP F 219 HIS 0.018 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00479 (25332) covalent geometry : angle 0.64554 (34564) hydrogen bonds : bond 0.04570 ( 1046) hydrogen bonds : angle 4.63917 ( 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 500 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 354 time to evaluate : 1.088 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 133 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 315 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 365 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8946 (ptp-170) REVERT: B 57 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8244 (tp30) REVERT: B 85 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8676 (mtpt) REVERT: B 161 GLU cc_start: 0.7904 (tp30) cc_final: 0.7654 (tp30) REVERT: B 167 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7655 (tp-100) REVERT: B 256 GLU cc_start: 0.8326 (pm20) cc_final: 0.8083 (pm20) REVERT: B 314 GLU cc_start: 0.7934 (tp30) cc_final: 0.7566 (tp30) REVERT: C 47 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8584 (ptp-110) REVERT: C 49 TYR cc_start: 0.8732 (m-80) cc_final: 0.8375 (m-80) REVERT: C 150 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9084 (ptm) REVERT: C 184 ASP cc_start: 0.7181 (m-30) cc_final: 0.6966 (m-30) REVERT: D 36 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9152 (p) REVERT: E 100 MET cc_start: 0.9395 (mmt) cc_final: 0.9060 (mmt) REVERT: E 242 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: F 245 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8291 (ttmm) REVERT: G 94 SER cc_start: 0.8969 (t) cc_final: 0.8672 (p) REVERT: H 13 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: H 65 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8299 (ptt90) REVERT: H 100 TYR cc_start: 0.8439 (t80) cc_final: 0.8099 (t80) REVERT: H 104 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: H 108 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8385 (mt-10) REVERT: I 60 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: I 238 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8129 (ttp-110) outliers start: 146 outliers final: 77 residues processed: 464 average time/residue: 0.7692 time to fit residues: 405.8395 Evaluate side-chains 425 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 334 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG 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 B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE 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 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 159 SER Chi-restraints excluded: chain C residue 295 ILE 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 118 ASN 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 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 E residue 242 GLU Chi-restraints excluded: chain F residue 3 THR 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 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 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 189 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 97 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 314 ASN A 360 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 423 ASN D 238 ASN E 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.040704 restraints weight = 62739.302| |-----------------------------------------------------------------------------| r_work (start): 0.2342 rms_B_bonded: 1.97 r_work: 0.2245 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2138 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25332 Z= 0.227 Angle : 0.673 14.621 34564 Z= 0.357 Chirality : 0.045 0.276 3884 Planarity : 0.005 0.097 4149 Dihedral : 14.374 177.644 4302 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.51 % Favored : 93.99 % Rotamer: Outliers : 6.22 % Allowed : 29.84 % Favored : 63.95 % 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: 0.12 (0.16), residues: 2829 helix: 1.25 (0.16), residues: 1090 sheet: 0.59 (0.23), residues: 479 loop : -1.20 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 70 TYR 0.021 0.002 TYR C 49 PHE 0.019 0.002 PHE I 30 TRP 0.010 0.002 TRP D 219 HIS 0.021 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00530 (25332) covalent geometry : angle 0.67264 (34564) hydrogen bonds : bond 0.04697 ( 1046) hydrogen bonds : angle 4.65187 ( 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: 160 poor density : 346 time to evaluate : 1.000 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 133 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 315 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7983 (p0) REVERT: A 335 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 429 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8185 (t80) REVERT: B 57 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8231 (tp30) REVERT: B 85 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8726 (mtpt) REVERT: B 161 GLU cc_start: 0.7920 (tp30) cc_final: 0.7462 (tp30) REVERT: B 167 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7523 (tp-100) REVERT: B 256 GLU cc_start: 0.8277 (pm20) cc_final: 0.8000 (pm20) REVERT: B 314 GLU cc_start: 0.7935 (tp30) cc_final: 0.7565 (tp30) REVERT: B 394 GLU cc_start: 0.8280 (tt0) cc_final: 0.7974 (tt0) REVERT: B 466 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: C 47 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8569 (ptp-110) REVERT: C 49 TYR cc_start: 0.8828 (m-80) cc_final: 0.8470 (m-80) REVERT: C 150 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.9084 (ptm) REVERT: D 36 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9152 (p) REVERT: D 160 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: E 100 MET cc_start: 0.9408 (mmt) cc_final: 0.9141 (mmt) REVERT: E 242 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: G 94 SER cc_start: 0.8987 (t) cc_final: 0.8682 (p) REVERT: H 65 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8318 (ptt90) REVERT: H 100 TYR cc_start: 0.8525 (t80) cc_final: 0.8037 (t80) REVERT: H 104 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: I 60 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8557 (mm-30) REVERT: I 140 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8151 (ptm-80) outliers start: 160 outliers final: 88 residues processed: 468 average time/residue: 0.7296 time to fit residues: 389.9998 Evaluate side-chains 437 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 334 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain A residue 133 SER 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 398 SER 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 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE 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 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 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 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 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 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 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 242 GLU Chi-restraints excluded: chain F residue 3 THR 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 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 116 LEU 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 85 VAL 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 140 ARG Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 209 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 237 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN D 238 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.053653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.042892 restraints weight = 62320.676| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 1.98 r_work: 0.2311 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2208 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25332 Z= 0.136 Angle : 0.612 14.542 34564 Z= 0.324 Chirality : 0.042 0.232 3884 Planarity : 0.005 0.094 4149 Dihedral : 14.316 178.943 4299 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.44 % Favored : 94.10 % Rotamer: Outliers : 5.32 % Allowed : 31.04 % 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: 0.32 (0.16), residues: 2829 helix: 1.46 (0.16), residues: 1094 sheet: 0.68 (0.23), residues: 472 loop : -1.11 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 185 TYR 0.017 0.001 TYR C 188 PHE 0.017 0.001 PHE B 461 TRP 0.009 0.001 TRP A 318 HIS 0.019 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00308 (25332) covalent geometry : angle 0.61245 (34564) hydrogen bonds : bond 0.03897 ( 1046) hydrogen bonds : angle 4.48437 ( 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 493 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 356 time to evaluate : 0.933 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: 0.8982 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 139 GLU cc_start: 0.8675 (tp30) cc_final: 0.8354 (mp0) REVERT: A 263 PHE cc_start: 0.8025 (t80) cc_final: 0.7637 (t80) REVERT: A 315 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7954 (p0) REVERT: A 335 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 362 CYS cc_start: 0.9004 (p) cc_final: 0.8629 (p) REVERT: A 429 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 57 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8276 (tp30) REVERT: B 75 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8986 (tmtm) REVERT: B 85 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8643 (mtpt) REVERT: B 161 GLU cc_start: 0.7774 (tp30) cc_final: 0.7332 (tp30) REVERT: B 167 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7417 (tp-100) REVERT: B 256 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: B 285 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 314 GLU cc_start: 0.7901 (tp30) cc_final: 0.7542 (tp30) REVERT: B 393 PHE cc_start: 0.8374 (t80) cc_final: 0.8173 (t80) REVERT: B 394 GLU cc_start: 0.8274 (tt0) cc_final: 0.7987 (tt0) REVERT: B 466 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: C 47 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8629 (ptp-110) REVERT: C 49 TYR cc_start: 0.8813 (m-80) cc_final: 0.8444 (m-80) REVERT: C 76 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8168 (tp) REVERT: C 150 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9034 (ptm) REVERT: D 36 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9142 (p) REVERT: D 70 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7883 (mtp180) REVERT: D 124 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: D 242 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7915 (pp20) REVERT: E 5 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8649 (ttt) REVERT: E 74 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8848 (t) REVERT: G 94 SER cc_start: 0.8964 (t) cc_final: 0.8660 (p) REVERT: H 13 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: H 100 TYR cc_start: 0.8468 (t80) cc_final: 0.8118 (t80) REVERT: H 104 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: I 60 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: I 140 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8438 (ttp-110) REVERT: I 238 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8128 (ttp-110) outliers start: 137 outliers final: 62 residues processed: 456 average time/residue: 0.7444 time to fit residues: 387.5457 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 : 1.022 ------------------------------------------------------------------------------- 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 133 SER 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 409 ARG Chi-restraints excluded: chain A residue 415 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 167 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 256 GLU 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 364 GLN 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 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 293 SER Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 LEU 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 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 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 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 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 34 SER Chi-restraints excluded: chain F residue 96 VAL 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 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 162 ASN 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 238 ARG Chi-restraints excluded: chain I residue 304 THR 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 261 optimal weight: 0.0270 chunk 213 optimal weight: 2.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 397 HIS B 423 ASN ** 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 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 = 0.2665 r_free = 0.2665 target = 0.052143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.041397 restraints weight = 62703.026| |-----------------------------------------------------------------------------| r_work (start): 0.2367 rms_B_bonded: 1.96 r_work: 0.2268 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2162 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25332 Z= 0.197 Angle : 0.667 15.009 34564 Z= 0.352 Chirality : 0.044 0.264 3884 Planarity : 0.005 0.093 4149 Dihedral : 14.277 178.476 4291 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.51 % Favored : 94.03 % Rotamer: Outliers : 5.24 % Allowed : 31.12 % 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: 0.22 (0.16), residues: 2829 helix: 1.35 (0.16), residues: 1094 sheet: 0.62 (0.23), residues: 479 loop : -1.14 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 185 TYR 0.017 0.002 TYR F 270 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.001 TRP F 219 HIS 0.013 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00461 (25332) covalent geometry : angle 0.66668 (34564) hydrogen bonds : bond 0.04420 ( 1046) hydrogen bonds : angle 4.56152 ( 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 476 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 341 time to evaluate : 0.975 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: 0.8982 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 139 GLU cc_start: 0.8723 (tp30) cc_final: 0.8380 (mp0) REVERT: A 335 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 429 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8210 (t80) REVERT: B 57 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8244 (tp30) REVERT: B 75 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9065 (tmtt) REVERT: B 85 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8723 (mtpt) REVERT: B 161 GLU cc_start: 0.7806 (tp30) cc_final: 0.7363 (tm-30) REVERT: B 167 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7244 (tp-100) REVERT: B 256 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: B 267 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8781 (mmt-90) REVERT: B 285 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 314 GLU cc_start: 0.7932 (tp30) cc_final: 0.7571 (tp30) REVERT: B 393 PHE cc_start: 0.8305 (t80) cc_final: 0.7884 (t80) REVERT: B 394 GLU cc_start: 0.8317 (tt0) cc_final: 0.7965 (tt0) REVERT: B 466 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: C 47 ARG cc_start: 0.8916 (ttm110) cc_final: 0.8695 (ptp-110) REVERT: C 49 TYR cc_start: 0.8901 (m-80) cc_final: 0.8657 (m-80) REVERT: C 76 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8151 (tp) REVERT: C 116 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8305 (mtpt) REVERT: C 150 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.9006 (ptm) REVERT: D 36 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9149 (p) REVERT: D 160 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8636 (mm-30) REVERT: D 164 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8783 (mtp85) REVERT: D 242 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7936 (pp20) REVERT: E 5 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8890 (ttt) REVERT: G 94 SER cc_start: 0.8990 (t) cc_final: 0.8691 (p) REVERT: H 13 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: H 100 TYR cc_start: 0.8502 (t80) cc_final: 0.7939 (t80) REVERT: H 104 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: I 60 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8619 (mm-30) REVERT: I 140 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8550 (ttp-110) outliers start: 135 outliers final: 78 residues processed: 437 average time/residue: 0.7197 time to fit residues: 358.7886 Evaluate side-chains 424 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 326 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 133 SER 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 398 SER 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 167 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 267 ARG 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 397 HIS 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 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 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 75 LEU Chi-restraints excluded: chain D residue 79 VAL 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 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 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 211 GLU Chi-restraints excluded: chain E residue 234 LEU 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 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 89 THR Chi-restraints excluded: chain G residue 95 GLN 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 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 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 119 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 54 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 242 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 271 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS B 423 ASN D 238 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.052941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.042162 restraints weight = 62303.398| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 1.97 r_work: 0.2289 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2185 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25332 Z= 0.163 Angle : 0.646 13.797 34564 Z= 0.341 Chirality : 0.043 0.246 3884 Planarity : 0.005 0.091 4149 Dihedral : 14.226 179.085 4288 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.59 % Favored : 94.06 % Rotamer: Outliers : 4.78 % Allowed : 31.93 % Favored : 63.29 % 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: 0.28 (0.16), residues: 2829 helix: 1.41 (0.16), residues: 1093 sheet: 0.68 (0.23), residues: 472 loop : -1.12 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 418 TYR 0.015 0.001 TYR C 49 PHE 0.017 0.002 PHE I 30 TRP 0.009 0.001 TRP A 318 HIS 0.010 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00379 (25332) covalent geometry : angle 0.64625 (34564) hydrogen bonds : bond 0.04127 ( 1046) hydrogen bonds : angle 4.52127 ( 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 458 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 335 time to evaluate : 1.094 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: 0.8932 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 139 GLU cc_start: 0.8688 (tp30) cc_final: 0.8344 (mp0) REVERT: A 315 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7884 (p0) REVERT: A 335 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 429 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 57 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8220 (tp30) REVERT: B 75 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9066 (tmtt) REVERT: B 77 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 85 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8670 (mtpt) REVERT: B 126 PHE cc_start: 0.9103 (p90) cc_final: 0.8712 (p90) REVERT: B 161 GLU cc_start: 0.7756 (tp30) cc_final: 0.7346 (tm-30) REVERT: B 167 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7250 (tp-100) REVERT: B 256 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: B 267 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8787 (mmt-90) REVERT: B 285 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 314 GLU cc_start: 0.7920 (tp30) cc_final: 0.7545 (tp30) REVERT: B 394 GLU cc_start: 0.8334 (tt0) cc_final: 0.7975 (tt0) REVERT: B 466 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: C 49 TYR cc_start: 0.8921 (m-80) cc_final: 0.8666 (m-80) REVERT: C 76 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 116 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8296 (mtpt) REVERT: C 150 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9002 (ptm) REVERT: C 334 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7933 (ppt90) REVERT: D 36 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9142 (p) REVERT: D 242 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: E 5 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8689 (ttt) REVERT: F 20 GLU cc_start: 0.8636 (pm20) cc_final: 0.8431 (pm20) REVERT: G 94 SER cc_start: 0.8979 (t) cc_final: 0.8668 (p) REVERT: H 13 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: H 104 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: I 60 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: I 140 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8462 (ttp-110) outliers start: 123 outliers final: 75 residues processed: 429 average time/residue: 0.7583 time to fit residues: 370.7598 Evaluate side-chains 424 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 133 SER 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 398 SER 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 167 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 VAL 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 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 343 VAL 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 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 123 THR 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 4 ARG Chi-restraints excluded: chain E residue 5 MET 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 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 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 95 GLN 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 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 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 119 SER Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 108 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 254 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 259 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 252 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN G 104 GLN I 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.044167 restraints weight = 62042.871| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 1.98 r_work: 0.2350 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2247 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1733 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= 0.129 Angle : 0.628 14.877 34564 Z= 0.329 Chirality : 0.042 0.221 3884 Planarity : 0.005 0.089 4149 Dihedral : 14.159 179.849 4286 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.44 % Favored : 94.20 % Rotamer: Outliers : 4.23 % Allowed : 32.48 % Favored : 63.29 % 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: 0.40 (0.16), residues: 2829 helix: 1.50 (0.16), residues: 1097 sheet: 0.73 (0.24), residues: 471 loop : -1.05 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 70 TYR 0.018 0.001 TYR C 375 PHE 0.016 0.001 PHE B 461 TRP 0.009 0.001 TRP A 318 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00297 (25332) covalent geometry : angle 0.62841 (34564) hydrogen bonds : bond 0.03641 ( 1046) hydrogen bonds : angle 4.41017 ( 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 448 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 339 time to evaluate : 0.966 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 133 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 139 GLU cc_start: 0.8682 (tp30) cc_final: 0.8363 (mp0) REVERT: A 312 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7797 (mtm-85) REVERT: A 315 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7955 (p0) REVERT: A 429 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 16 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8215 (tp30) REVERT: B 57 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8258 (tp30) REVERT: B 77 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 85 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8745 (mtmt) REVERT: B 126 PHE cc_start: 0.9091 (p90) cc_final: 0.8677 (p90) REVERT: B 161 GLU cc_start: 0.7652 (tp30) cc_final: 0.7269 (tm-30) REVERT: B 167 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7296 (tp-100) REVERT: B 256 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: B 267 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8766 (mmt-90) REVERT: B 285 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8476 (mm-30) REVERT: B 389 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8818 (tmtt) REVERT: B 393 PHE cc_start: 0.7705 (t80) cc_final: 0.7478 (t80) REVERT: B 394 GLU cc_start: 0.8313 (tt0) cc_final: 0.7979 (tt0) REVERT: C 47 ARG cc_start: 0.8913 (ptp-110) cc_final: 0.8598 (ptp-110) REVERT: C 49 TYR cc_start: 0.8844 (m-80) cc_final: 0.8563 (m-80) REVERT: C 76 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8141 (tp) REVERT: C 150 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9023 (ptm) REVERT: C 334 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7898 (ppt90) REVERT: D 36 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9147 (p) REVERT: D 194 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8132 (m) REVERT: E 74 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8858 (t) REVERT: E 242 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: H 13 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: H 57 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8856 (mt-10) REVERT: H 104 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: I 60 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: I 140 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8507 (ttp-110) outliers start: 109 outliers final: 65 residues processed: 424 average time/residue: 0.7838 time to fit residues: 380.2037 Evaluate side-chains 410 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 328 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 210 ILE 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 354 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 316 VAL 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 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 293 SER Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 343 VAL 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 75 LEU Chi-restraints excluded: chain D residue 79 VAL 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 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 242 GLU Chi-restraints excluded: chain E residue 244 LEU 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 G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR 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 89 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 209 ASP 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: 3.9990 chunk 204 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS B 423 ASN D 238 ASN I 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.040717 restraints weight = 62476.896| |-----------------------------------------------------------------------------| r_work (start): 0.2343 rms_B_bonded: 1.95 r_work: 0.2246 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2141 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25332 Z= 0.240 Angle : 0.719 13.962 34564 Z= 0.378 Chirality : 0.046 0.284 3884 Planarity : 0.005 0.089 4149 Dihedral : 14.163 178.070 4283 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.76 % Favored : 93.85 % Rotamer: Outliers : 3.81 % Allowed : 32.87 % Favored : 63.33 % 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: 1.28 (0.16), residues: 1095 sheet: 0.58 (0.23), residues: 483 loop : -1.15 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.021 0.002 TYR C 49 PHE 0.018 0.002 PHE B 461 TRP 0.017 0.002 TRP F 219 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00567 (25332) covalent geometry : angle 0.71908 (34564) hydrogen bonds : bond 0.04663 ( 1046) hydrogen bonds : angle 4.65023 ( 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 424 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 326 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 139 GLU cc_start: 0.8679 (tp30) cc_final: 0.8321 (mp0) REVERT: A 263 PHE cc_start: 0.7699 (t80) cc_final: 0.7380 (t80) REVERT: A 297 ARG cc_start: 0.8242 (tpp-160) cc_final: 0.7974 (tpp80) REVERT: A 312 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: A 315 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7966 (p0) REVERT: A 335 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 429 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8320 (t80) REVERT: B 57 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8220 (tp30) REVERT: B 75 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8922 (tmtt) REVERT: B 77 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 85 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8817 (mtmt) REVERT: B 161 GLU cc_start: 0.7832 (tp30) cc_final: 0.7445 (tm-30) REVERT: B 167 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7345 (tp-100) REVERT: B 256 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: B 267 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8778 (mmt-90) REVERT: B 285 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8565 (mm-30) REVERT: B 389 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8721 (tmtt) REVERT: B 394 GLU cc_start: 0.8272 (tt0) cc_final: 0.7892 (tt0) REVERT: C 47 ARG cc_start: 0.9014 (ptp-110) cc_final: 0.8768 (ptp-110) REVERT: C 116 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8328 (mtpt) REVERT: C 150 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9004 (ptm) REVERT: C 320 GLU cc_start: 0.8646 (tt0) cc_final: 0.8105 (pt0) REVERT: D 36 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9149 (p) REVERT: E 100 MET cc_start: 0.9387 (mmt) cc_final: 0.9067 (mmt) REVERT: E 242 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: H 13 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: H 104 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: I 60 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8566 (mm-30) REVERT: I 140 ARG cc_start: 0.9071 (ptm-80) cc_final: 0.8538 (ttp-110) outliers start: 98 outliers final: 67 residues processed: 402 average time/residue: 0.7473 time to fit residues: 341.2839 Evaluate side-chains 402 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 320 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 211 CYS 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 398 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 74 PHE 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 98 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 316 VAL 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 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 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 75 LEU 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 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 211 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 242 GLU 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 G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR 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 89 THR Chi-restraints excluded: chain H residue 104 GLN 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 119 SER Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 189 ILE 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: 0.0970 chunk 153 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 504 GLN D 238 ASN F 240 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 = 0.2685 r_free = 0.2685 target = 0.052889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.042065 restraints weight = 62437.419| |-----------------------------------------------------------------------------| r_work (start): 0.2384 rms_B_bonded: 1.99 r_work: 0.2287 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2182 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1638 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= 0.169 Angle : 0.679 14.262 34564 Z= 0.355 Chirality : 0.044 0.246 3884 Planarity : 0.005 0.088 4149 Dihedral : 14.153 179.016 4283 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.76 % Favored : 93.88 % Rotamer: Outliers : 3.89 % Allowed : 32.87 % Favored : 63.25 % 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: 0.22 (0.16), residues: 2829 helix: 1.36 (0.16), residues: 1093 sheet: 0.60 (0.24), residues: 476 loop : -1.14 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 185 TYR 0.019 0.001 TYR C 375 PHE 0.018 0.001 PHE I 30 TRP 0.008 0.001 TRP A 147 HIS 0.009 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00395 (25332) covalent geometry : angle 0.67854 (34564) hydrogen bonds : bond 0.04121 ( 1046) hydrogen bonds : angle 4.57747 ( 2963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9157.13 seconds wall clock time: 157 minutes 17.98 seconds (9437.98 seconds total)