Starting phenix.real_space_refine on Fri Feb 6 09:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.map" model { file = "/net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq5_63293/02_2026/9lq5_63293.cif" } resolution = 2.97 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= -0.017 sd= 0.470 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 41 5.49 5 S 107 5.16 5 C 15175 2.51 5 N 3994 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 23974 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3895 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4828 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 574} Chain breaks: 1 Chain: "C" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3044 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2218 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "E" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2218 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "F" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2218 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "G" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1072 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1072 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2535 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 297} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.23 Number of scatterers: 23974 At special positions: 0 Unit cell: (105.316, 110.908, 205.972, 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 107 16.00 P 41 15.00 O 4656 8.00 N 3994 7.00 C 15175 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 33 sheets defined 42.3% alpha, 16.0% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.642A pdb=" N VAL A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' 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 removed outlier: 3.703A pdb=" N GLY A 195 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.796A pdb=" N LEU A 237 " --> pdb=" O GLN A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.802A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 285 through 298 removed outlier: 3.659A pdb=" N LYS A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.592A pdb=" N ALA A 333 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.576A pdb=" N THR B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 45 removed outlier: 3.764A pdb=" N PHE B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.681A pdb=" N GLN B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 3.579A 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 79 through 100 removed outlier: 3.620A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 removed outlier: 3.519A pdb=" N ILE B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 Proline residue: B 141 - end of helix removed outlier: 3.767A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.504A 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 205 Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.236A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 removed outlier: 4.138A pdb=" N GLU B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.698A pdb=" N ASN B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) 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 318 Processing helix chain 'B' and resid 343 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 409 through 419 removed outlier: 3.586A pdb=" N LYS B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.600A 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: 4.104A pdb=" N VAL B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 495 through 505 removed outlier: 3.530A pdb=" N ASN B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 531 through 560 removed outlier: 3.764A pdb=" N GLN B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG B 554 " --> pdb=" O ASP B 550 " (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 115 through 124 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.701A pdb=" N TYR C 220 " --> pdb=" O HIS C 217 " (cutoff:3.500A) 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 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' 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: 3.734A pdb=" N LEU C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 410 Processing helix chain 'C' and resid 411 through 418 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 121 through 141 removed outlier: 3.818A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (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 253 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: 3.885A 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 252 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'F' and resid 18 through 22 removed outlier: 4.098A pdb=" N VAL F 21 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN F 22 " --> pdb=" O GLY F 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 42 through 55 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: 3.930A pdb=" N TYR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.593A 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 'F' and resid 263 through 267 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.338A pdb=" N GLY G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 65 through 82 removed outlier: 3.891A pdb=" N ILE G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 Processing helix chain 'G' and resid 113 through 131 Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 46 removed outlier: 4.328A pdb=" N GLY H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.510A pdb=" N GLY H 70 " --> pdb=" O HIS H 66 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 111 through 133 removed outlier: 3.600A pdb=" N TYR H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 20 through 23 removed outlier: 3.544A pdb=" N ARG I 23 " --> pdb=" O ASP I 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 20 through 23' Processing helix chain 'I' and resid 32 through 37 removed outlier: 4.252A pdb=" N GLU I 37 " --> pdb=" O THR I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 53 Processing helix chain 'I' and resid 61 through 72 Processing helix chain 'I' and resid 116 through 127 removed outlier: 4.081A pdb=" N MET I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 removed outlier: 3.637A pdb=" N SER I 131 " --> pdb=" O PHE I 128 " (cutoff:3.500A) removed outlier: 4.454A 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 141 through 161 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 261 through 271 removed outlier: 3.745A pdb=" N LYS I 270 " --> pdb=" O GLU I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 299 Processing helix chain 'I' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.571A pdb=" N PHE A 160 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A 5 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 204 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.473A 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: 6.628A pdb=" N GLU A 85 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 106 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.129A 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: 6.361A pdb=" N GLY A 119 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 129 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 139 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 375 removed outlier: 4.730A pdb=" N ILE A 379 " --> pdb=" O LYS A 227 " (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 344 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.619A pdb=" N LYS C 185 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 326 removed outlier: 6.685A pdb=" N LEU B 331 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 325 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS B 434 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 387 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.480A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.011A 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: 4.948A pdb=" N GLN C 229 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.480A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N PHE C 277 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 176 Processing sheet with id=AB7, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.969A pdb=" N SER C 392 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 393 " --> pdb=" O MET C 356 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N MET C 356 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR C 395 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.706A 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=AB9, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.706A 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 274 through 275 Processing sheet with id=AC1, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.770A pdb=" N ILE D 163 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 204 through 211 removed outlier: 6.097A pdb=" N LEU D 205 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR D 220 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG D 207 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 218 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN D 209 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AC4, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.583A 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 235 current: chain 'E' and resid 185 through 188 Processing sheet with id=AC5, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.583A 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=AC6, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.781A pdb=" N ILE E 163 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 204 through 211 removed outlier: 6.382A pdb=" N LEU E 205 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 220 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG E 207 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU E 218 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN E 209 " --> pdb=" O ALA E 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.549A 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=AC9, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.549A 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=AD1, first strand: chain 'F' and resid 204 through 211 removed outlier: 5.898A pdb=" N GLU F 211 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AD3, first strand: chain 'I' and resid 114 through 115 removed outlier: 5.717A pdb=" N VAL I 204 " --> pdb=" O ASN I 244 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN I 244 " --> pdb=" O VAL I 204 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL I 241 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AD5, first strand: chain 'I' and resid 213 through 218 Processing sheet with id=AD6, first strand: chain 'I' and resid 258 through 260 removed outlier: 4.218A pdb=" N HIS I 253 " --> pdb=" O CYS I 260 " (cutoff:3.500A) 997 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7482 1.34 - 1.46: 4642 1.46 - 1.58: 12170 1.58 - 1.70: 81 1.70 - 1.82: 180 Bond restraints: 24555 Sorted by residual: bond pdb=" C TYR A 280 " pdb=" N PRO A 281 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.81e+00 bond pdb=" CB LYS B 188 " pdb=" CG LYS B 188 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLN C 233 " pdb=" CG GLN C 233 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" CB GLU I 223 " pdb=" CG GLU I 223 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CG LYS A 116 " pdb=" CD LYS A 116 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 ... (remaining 24550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 32921 2.29 - 4.57: 360 4.57 - 6.86: 54 6.86 - 9.14: 17 9.14 - 11.43: 6 Bond angle restraints: 33358 Sorted by residual: angle pdb=" CA ILE A 311 " pdb=" CB ILE A 311 " pdb=" CG1 ILE A 311 " ideal model delta sigma weight residual 110.40 117.68 -7.28 1.70e+00 3.46e-01 1.83e+01 angle pdb=" CB LYS A 404 " pdb=" CG LYS A 404 " pdb=" CD LYS A 404 " ideal model delta sigma weight residual 111.30 120.77 -9.47 2.30e+00 1.89e-01 1.70e+01 angle pdb=" CB LYS A 116 " pdb=" CG LYS A 116 " pdb=" CD LYS A 116 " ideal model delta sigma weight residual 111.30 120.29 -8.99 2.30e+00 1.89e-01 1.53e+01 angle pdb=" CA LYS B 477 " pdb=" CB LYS B 477 " pdb=" CG LYS B 477 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CB MET C 45 " pdb=" CG MET C 45 " pdb=" SD MET C 45 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 ... (remaining 33353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14514 35.94 - 71.87: 442 71.87 - 107.81: 17 107.81 - 143.74: 0 143.74 - 179.68: 4 Dihedral angle restraints: 14977 sinusoidal: 6543 harmonic: 8434 Sorted by residual: dihedral pdb=" O4' C J 28 " pdb=" C1' C J 28 " pdb=" N1 C J 28 " pdb=" C2 C J 28 " ideal model delta sinusoidal sigma weight residual 200.00 36.14 163.86 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' C J 39 " pdb=" C1' C J 39 " pdb=" N1 C J 39 " pdb=" C2 C J 39 " ideal model delta sinusoidal sigma weight residual 200.00 49.43 150.57 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' C J 29 " pdb=" C1' C J 29 " pdb=" N1 C J 29 " pdb=" C2 C J 29 " ideal model delta sinusoidal sigma weight residual 200.00 55.13 144.87 1 1.50e+01 4.44e-03 7.76e+01 ... (remaining 14974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3064 0.053 - 0.106: 547 0.106 - 0.159: 102 0.159 - 0.212: 4 0.212 - 0.265: 1 Chirality restraints: 3718 Sorted by residual: chirality pdb=" C1' U J 18 " pdb=" O4' U J 18 " pdb=" C2' U J 18 " pdb=" N1 U J 18 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1' A J 24 " pdb=" O4' A J 24 " pdb=" C2' A J 24 " pdb=" N9 A J 24 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 295 " pdb=" N ILE B 295 " pdb=" C ILE B 295 " pdb=" CB ILE B 295 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3715 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G J 37 " -0.034 2.00e-02 2.50e+03 1.56e-02 7.33e+00 pdb=" N9 G J 37 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G J 37 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G J 37 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G J 37 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G J 37 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G J 37 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G J 37 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G J 37 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G J 37 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G J 37 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G J 37 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A J 24 " -0.036 2.00e-02 2.50e+03 1.62e-02 7.19e+00 pdb=" N9 A J 24 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A J 24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A J 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A J 24 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A J 24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A J 24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A J 24 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A J 24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A J 24 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A J 24 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U J 18 " -0.036 2.00e-02 2.50e+03 1.77e-02 7.04e+00 pdb=" N1 U J 18 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U J 18 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U J 18 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U J 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U J 18 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U J 18 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U J 18 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U J 18 " 0.007 2.00e-02 2.50e+03 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 511 2.67 - 3.23: 22702 3.23 - 3.79: 37562 3.79 - 4.34: 52475 4.34 - 4.90: 86381 Nonbonded interactions: 199631 Sorted by model distance: nonbonded pdb=" OH TYR H 10 " pdb=" OE1 GLN H 82 " model vdw 2.118 3.040 nonbonded pdb=" OD2 ASP B 328 " pdb="MN MN B 701 " model vdw 2.127 2.320 nonbonded pdb=" OH TYR F 220 " pdb=" O4 U J 27 " model vdw 2.154 3.040 nonbonded pdb=" O ASN B 260 " pdb=" NZ LYS B 263 " model vdw 2.161 3.120 nonbonded pdb=" O SER D 67 " pdb=" O2' G J 6 " model vdw 2.190 3.040 ... (remaining 199626 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: 4.090 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.580 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 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 0.046 24555 Z= 0.162 Angle : 0.637 11.429 33358 Z= 0.332 Chirality : 0.042 0.265 3718 Planarity : 0.004 0.082 4129 Dihedral : 16.234 179.675 9537 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.29 % Allowed : 20.93 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.16), residues: 2834 helix: 1.51 (0.16), residues: 1075 sheet: 0.61 (0.24), residues: 481 loop : -0.90 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 70 TYR 0.017 0.001 TYR C 75 PHE 0.017 0.002 PHE I 44 TRP 0.012 0.001 TRP B 25 HIS 0.004 0.001 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00383 (24555) covalent geometry : angle 0.63678 (33358) hydrogen bonds : bond 0.14775 ( 987) hydrogen bonds : angle 6.18228 ( 2847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8787 (mm) REVERT: A 139 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8467 (mm-30) REVERT: A 263 PHE cc_start: 0.8590 (t80) cc_final: 0.7950 (t80) REVERT: A 264 ARG cc_start: 0.8634 (mpp80) cc_final: 0.8242 (mpp80) REVERT: A 299 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.5737 (p90) REVERT: A 342 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: A 350 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: A 360 ASN cc_start: 0.8815 (p0) cc_final: 0.8358 (p0) REVERT: A 421 HIS cc_start: 0.8498 (p-80) cc_final: 0.7881 (p90) REVERT: A 422 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8136 (mp) REVERT: B 59 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: B 207 MET cc_start: 0.6799 (tpp) cc_final: 0.6353 (tpp) REVERT: B 227 ASN cc_start: 0.8639 (m-40) cc_final: 0.8419 (m110) REVERT: B 329 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: B 475 MET cc_start: 0.8375 (mmt) cc_final: 0.8027 (mmt) REVERT: B 491 MET cc_start: 0.8579 (mtp) cc_final: 0.7114 (tmt) REVERT: C 108 TYR cc_start: 0.7762 (p90) cc_final: 0.7557 (p90) REVERT: C 320 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 134 ASP cc_start: 0.8692 (m-30) cc_final: 0.8408 (m-30) REVERT: D 233 MET cc_start: 0.9435 (mmt) cc_final: 0.8812 (mmt) REVERT: E 33 ASP cc_start: 0.8707 (t0) cc_final: 0.8478 (t70) REVERT: G 60 ASP cc_start: 0.7886 (t0) cc_final: 0.7632 (t0) REVERT: I 238 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7264 (ttp80) outliers start: 59 outliers final: 33 residues processed: 388 average time/residue: 0.8180 time to fit residues: 357.1431 Evaluate side-chains 382 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 238 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 59 GLN B 342 ASN B 561 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN G 19 ASN G 56 ASN H 77 ASN H 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.051611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.041640 restraints weight = 63598.596| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 2.24 r_work: 0.2298 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2181 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24555 Z= 0.258 Angle : 0.657 12.620 33358 Z= 0.352 Chirality : 0.045 0.252 3718 Planarity : 0.005 0.051 4129 Dihedral : 12.654 179.599 3819 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 5.31 % Allowed : 17.29 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.16), residues: 2834 helix: 1.41 (0.16), residues: 1088 sheet: 0.62 (0.23), residues: 484 loop : -0.94 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 16 TYR 0.018 0.002 TYR E 270 PHE 0.026 0.002 PHE I 44 TRP 0.011 0.001 TRP B 25 HIS 0.005 0.001 HIS C 386 Details of bonding type rmsd covalent geometry : bond 0.00612 (24555) covalent geometry : angle 0.65687 (33358) hydrogen bonds : bond 0.05347 ( 987) hydrogen bonds : angle 5.03539 ( 2847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 352 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8475 (mm-30) REVERT: A 231 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6327 (tm) REVERT: A 263 PHE cc_start: 0.8724 (t80) cc_final: 0.7992 (t80) REVERT: A 264 ARG cc_start: 0.8626 (mpp80) cc_final: 0.8131 (mpp80) REVERT: A 299 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6123 (p90) REVERT: A 350 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: A 360 ASN cc_start: 0.8917 (p0) cc_final: 0.8480 (p0) REVERT: A 401 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8323 (tp30) REVERT: A 408 MET cc_start: 0.8539 (pmm) cc_final: 0.8270 (pmm) REVERT: A 422 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 207 MET cc_start: 0.6869 (tpp) cc_final: 0.6498 (tpp) REVERT: B 475 MET cc_start: 0.8437 (mmt) cc_final: 0.8094 (mmt) REVERT: B 491 MET cc_start: 0.8667 (mtp) cc_final: 0.7170 (tmt) REVERT: C 184 ASP cc_start: 0.8152 (m-30) cc_final: 0.7734 (m-30) REVERT: C 320 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 21 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (p) REVERT: D 134 ASP cc_start: 0.8708 (m-30) cc_final: 0.8435 (m-30) REVERT: F 52 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: F 124 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: F 204 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9113 (p) REVERT: G 60 ASP cc_start: 0.7959 (t0) cc_final: 0.7665 (t0) REVERT: I 238 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7318 (ttp80) outliers start: 137 outliers final: 60 residues processed: 448 average time/residue: 0.7526 time to fit residues: 382.5060 Evaluate side-chains 404 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 238 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 110 optimal weight: 0.2980 chunk 235 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.0040 chunk 195 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN C 248 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN H 77 ASN H 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.044352 restraints weight = 62596.470| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 2.24 r_work: 0.2380 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2266 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24555 Z= 0.129 Angle : 0.561 10.649 33358 Z= 0.299 Chirality : 0.042 0.267 3718 Planarity : 0.004 0.051 4129 Dihedral : 12.311 178.565 3791 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 4.22 % Allowed : 18.49 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.16), residues: 2834 helix: 1.69 (0.16), residues: 1089 sheet: 0.91 (0.23), residues: 445 loop : -0.87 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 16 TYR 0.023 0.001 TYR A 326 PHE 0.014 0.001 PHE B 126 TRP 0.010 0.001 TRP B 25 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00289 (24555) covalent geometry : angle 0.56100 (33358) hydrogen bonds : bond 0.04091 ( 987) hydrogen bonds : angle 4.72138 ( 2847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 351 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 139 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 231 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6322 (tm) REVERT: A 263 PHE cc_start: 0.8649 (t80) cc_final: 0.7961 (t80) REVERT: A 264 ARG cc_start: 0.8532 (mpp80) cc_final: 0.8171 (mpp80) REVERT: A 299 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.6083 (p90) REVERT: A 360 ASN cc_start: 0.8876 (p0) cc_final: 0.8437 (p0) REVERT: A 401 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8200 (tp30) REVERT: A 408 MET cc_start: 0.8444 (pmm) cc_final: 0.8177 (pmm) REVERT: A 421 HIS cc_start: 0.8512 (p-80) cc_final: 0.7757 (p-80) REVERT: A 422 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 207 MET cc_start: 0.6820 (tpp) cc_final: 0.6428 (tpp) REVERT: B 250 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: B 329 ASP cc_start: 0.8496 (m-30) cc_final: 0.8257 (m-30) REVERT: B 475 MET cc_start: 0.8342 (mmt) cc_final: 0.8050 (mmt) REVERT: C 184 ASP cc_start: 0.8003 (m-30) cc_final: 0.7621 (m-30) REVERT: C 320 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 356 MET cc_start: 0.8843 (mtt) cc_final: 0.8619 (mtt) REVERT: C 422 TYR cc_start: 0.8363 (p90) cc_final: 0.8109 (p90) REVERT: D 134 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: E 58 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: E 188 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9131 (mt) REVERT: F 52 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: G 60 ASP cc_start: 0.7807 (t0) cc_final: 0.7528 (t0) outliers start: 109 outliers final: 44 residues processed: 427 average time/residue: 0.7585 time to fit residues: 366.9327 Evaluate side-chains 390 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 337 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN B 342 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN G 18 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN H 77 ASN H 111 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.053414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.043407 restraints weight = 62946.406| |-----------------------------------------------------------------------------| r_work (start): 0.2456 rms_B_bonded: 2.24 r_work: 0.2351 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2235 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24555 Z= 0.166 Angle : 0.587 10.536 33358 Z= 0.311 Chirality : 0.043 0.247 3718 Planarity : 0.004 0.047 4129 Dihedral : 12.215 179.016 3778 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 4.19 % Allowed : 18.88 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.16), residues: 2834 helix: 1.73 (0.16), residues: 1090 sheet: 0.73 (0.23), residues: 472 loop : -0.85 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 16 TYR 0.020 0.001 TYR A 326 PHE 0.017 0.002 PHE I 44 TRP 0.008 0.001 TRP B 25 HIS 0.003 0.001 HIS C 386 Details of bonding type rmsd covalent geometry : bond 0.00389 (24555) covalent geometry : angle 0.58699 (33358) hydrogen bonds : bond 0.04299 ( 987) hydrogen bonds : angle 4.69789 ( 2847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 353 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 139 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8541 (mm-30) REVERT: A 231 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6263 (tm) REVERT: A 263 PHE cc_start: 0.8628 (t80) cc_final: 0.8022 (t80) REVERT: A 264 ARG cc_start: 0.8551 (mpp80) cc_final: 0.8241 (mpp80) REVERT: A 299 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.6118 (p90) REVERT: A 360 ASN cc_start: 0.8877 (p0) cc_final: 0.8446 (p0) REVERT: A 401 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8143 (tp30) REVERT: A 408 MET cc_start: 0.8369 (pmm) cc_final: 0.8166 (pmm) REVERT: A 421 HIS cc_start: 0.8569 (p-80) cc_final: 0.7803 (p-80) REVERT: A 422 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 59 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 191 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8990 (pp) REVERT: B 207 MET cc_start: 0.6761 (tpp) cc_final: 0.6387 (tpp) REVERT: B 250 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: B 475 MET cc_start: 0.8492 (mmt) cc_final: 0.8180 (mmt) REVERT: C 184 ASP cc_start: 0.8109 (m-30) cc_final: 0.7741 (m-30) REVERT: C 320 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 134 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: D 233 MET cc_start: 0.9358 (mmt) cc_final: 0.8846 (mmt) REVERT: E 58 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: E 188 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9156 (mt) REVERT: F 52 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: F 204 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9149 (p) REVERT: G 60 ASP cc_start: 0.7808 (t0) cc_final: 0.7548 (t0) REVERT: I 240 ASP cc_start: 0.8996 (t0) cc_final: 0.8756 (t0) outliers start: 108 outliers final: 57 residues processed: 428 average time/residue: 0.7669 time to fit residues: 371.7249 Evaluate side-chains 407 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 338 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 190 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN G 56 ASN G 95 GLN H 77 ASN H 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.052738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.042785 restraints weight = 62813.791| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 2.22 r_work: 0.2333 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2216 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24555 Z= 0.191 Angle : 0.611 10.613 33358 Z= 0.323 Chirality : 0.044 0.239 3718 Planarity : 0.004 0.048 4129 Dihedral : 12.222 179.400 3774 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 4.73 % Allowed : 19.50 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.16), residues: 2834 helix: 1.69 (0.16), residues: 1089 sheet: 0.62 (0.23), residues: 478 loop : -0.86 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 193 TYR 0.018 0.001 TYR A 326 PHE 0.020 0.002 PHE I 44 TRP 0.009 0.001 TRP B 25 HIS 0.004 0.001 HIS B 592 Details of bonding type rmsd covalent geometry : bond 0.00452 (24555) covalent geometry : angle 0.61113 (33358) hydrogen bonds : bond 0.04479 ( 987) hydrogen bonds : angle 4.72721 ( 2847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 347 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 139 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8500 (mm-30) REVERT: A 231 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6280 (tm) REVERT: A 263 PHE cc_start: 0.8641 (t80) cc_final: 0.8028 (t80) REVERT: A 264 ARG cc_start: 0.8540 (mpp80) cc_final: 0.8215 (mpp80) REVERT: A 299 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6319 (p90) REVERT: A 346 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: A 360 ASN cc_start: 0.8893 (p0) cc_final: 0.8467 (p0) REVERT: A 401 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8138 (tp30) REVERT: A 408 MET cc_start: 0.8432 (pmm) cc_final: 0.8207 (pmm) REVERT: A 421 HIS cc_start: 0.8606 (p-80) cc_final: 0.7823 (p-80) REVERT: A 422 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 59 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: B 191 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 207 MET cc_start: 0.6777 (tpp) cc_final: 0.6408 (tpp) REVERT: B 263 LYS cc_start: 0.9176 (ptpp) cc_final: 0.8815 (mtpp) REVERT: B 329 ASP cc_start: 0.8628 (m-30) cc_final: 0.8387 (m-30) REVERT: B 475 MET cc_start: 0.8547 (mmt) cc_final: 0.8201 (mmt) REVERT: B 491 MET cc_start: 0.8574 (mtp) cc_final: 0.7205 (tmt) REVERT: C 184 ASP cc_start: 0.8114 (m-30) cc_final: 0.7723 (m-30) REVERT: C 320 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 134 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: D 233 MET cc_start: 0.9368 (mmt) cc_final: 0.8845 (mmt) REVERT: E 58 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: E 188 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9193 (mt) REVERT: F 52 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: F 204 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9150 (p) REVERT: G 60 ASP cc_start: 0.7876 (t0) cc_final: 0.7621 (t0) REVERT: I 238 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7299 (ttp80) REVERT: I 240 ASP cc_start: 0.9019 (t0) cc_final: 0.8769 (t0) outliers start: 122 outliers final: 78 residues processed: 436 average time/residue: 0.7359 time to fit residues: 364.6092 Evaluate side-chains 424 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 333 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 238 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 231 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN C 268 GLN E 42 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN H 77 ASN H 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.052757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.042729 restraints weight = 62971.937| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 2.23 r_work: 0.2333 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24555 Z= 0.199 Angle : 0.623 10.474 33358 Z= 0.330 Chirality : 0.044 0.239 3718 Planarity : 0.004 0.051 4129 Dihedral : 12.254 179.567 3774 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 5.00 % Allowed : 19.96 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.16), residues: 2834 helix: 1.66 (0.16), residues: 1089 sheet: 0.62 (0.22), residues: 488 loop : -0.88 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 193 TYR 0.019 0.002 TYR A 267 PHE 0.021 0.002 PHE I 44 TRP 0.009 0.001 TRP B 25 HIS 0.004 0.001 HIS B 592 Details of bonding type rmsd covalent geometry : bond 0.00473 (24555) covalent geometry : angle 0.62334 (33358) hydrogen bonds : bond 0.04537 ( 987) hydrogen bonds : angle 4.73583 ( 2847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 338 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 139 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8498 (mm-30) REVERT: A 170 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8619 (p0) REVERT: A 231 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6339 (tm) REVERT: A 263 PHE cc_start: 0.8675 (t80) cc_final: 0.7916 (t80) REVERT: A 264 ARG cc_start: 0.8497 (mpp80) cc_final: 0.8092 (mpp80) REVERT: A 299 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6392 (p90) REVERT: A 346 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 360 ASN cc_start: 0.8868 (p0) cc_final: 0.8452 (p0) REVERT: A 401 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8201 (tp30) REVERT: A 422 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 59 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: B 160 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: B 191 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9029 (pp) REVERT: B 207 MET cc_start: 0.6894 (tpp) cc_final: 0.6516 (tpp) REVERT: B 250 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: B 329 ASP cc_start: 0.8615 (m-30) cc_final: 0.8395 (m-30) REVERT: B 475 MET cc_start: 0.8426 (mmt) cc_final: 0.8075 (mmt) REVERT: B 491 MET cc_start: 0.8569 (mtp) cc_final: 0.7217 (tmt) REVERT: C 184 ASP cc_start: 0.8063 (m-30) cc_final: 0.7744 (m-30) REVERT: C 320 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 422 TYR cc_start: 0.8407 (p90) cc_final: 0.8207 (p90) REVERT: D 134 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: D 233 MET cc_start: 0.9366 (mmt) cc_final: 0.8891 (mmt) REVERT: E 58 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: E 188 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9212 (mt) REVERT: F 52 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: F 204 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9127 (p) REVERT: G 60 ASP cc_start: 0.7880 (t0) cc_final: 0.7601 (t0) REVERT: I 238 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7386 (ttp80) REVERT: I 240 ASP cc_start: 0.8978 (t0) cc_final: 0.8713 (t0) outliers start: 129 outliers final: 81 residues processed: 436 average time/residue: 0.7377 time to fit residues: 366.3008 Evaluate side-chains 427 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 330 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU 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 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 238 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 254 optimal weight: 0.9990 chunk 203 optimal weight: 0.0870 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 263 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN G 56 ASN G 95 GLN H 77 ASN H 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.044367 restraints weight = 62474.563| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 2.23 r_work: 0.2382 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24555 Z= 0.140 Angle : 0.601 9.557 33358 Z= 0.315 Chirality : 0.042 0.308 3718 Planarity : 0.004 0.051 4129 Dihedral : 12.234 178.924 3774 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 4.26 % Allowed : 21.12 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.16), residues: 2834 helix: 1.84 (0.16), residues: 1084 sheet: 0.85 (0.23), residues: 458 loop : -0.84 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 432 TYR 0.017 0.001 TYR A 464 PHE 0.017 0.001 PHE B 126 TRP 0.010 0.001 TRP B 25 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00325 (24555) covalent geometry : angle 0.60067 (33358) hydrogen bonds : bond 0.03941 ( 987) hydrogen bonds : angle 4.59970 ( 2847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 350 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 139 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8493 (mm-30) REVERT: A 231 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6288 (tm) REVERT: A 263 PHE cc_start: 0.8641 (t80) cc_final: 0.7757 (t80) REVERT: A 264 ARG cc_start: 0.8437 (mpp80) cc_final: 0.7954 (mpp80) REVERT: A 299 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6145 (p90) REVERT: A 360 ASN cc_start: 0.8843 (p0) cc_final: 0.8415 (p0) REVERT: A 401 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8089 (tp30) REVERT: A 408 MET cc_start: 0.8238 (pmm) cc_final: 0.7847 (pmm) REVERT: A 422 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7875 (mp) REVERT: B 207 MET cc_start: 0.6846 (tpp) cc_final: 0.6526 (tpp) REVERT: B 250 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: B 256 GLU cc_start: 0.8127 (tp30) cc_final: 0.7819 (mm-30) REVERT: B 263 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8581 (mttm) REVERT: B 475 MET cc_start: 0.8407 (mmt) cc_final: 0.8059 (mmt) REVERT: C 110 GLU cc_start: 0.8081 (pm20) cc_final: 0.7856 (mp0) REVERT: C 184 ASP cc_start: 0.7965 (m-30) cc_final: 0.7646 (m-30) REVERT: C 320 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7980 (tm-30) REVERT: D 134 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: D 233 MET cc_start: 0.9330 (mmt) cc_final: 0.8819 (mmt) REVERT: E 58 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: E 188 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9198 (mt) REVERT: F 52 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: F 204 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9146 (p) REVERT: G 60 ASP cc_start: 0.7761 (t0) cc_final: 0.7448 (t0) REVERT: I 240 ASP cc_start: 0.8958 (t0) cc_final: 0.8708 (t0) outliers start: 110 outliers final: 62 residues processed: 424 average time/residue: 0.7689 time to fit residues: 369.5731 Evaluate side-chains 409 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 336 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 LEU 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 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 150 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 152 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 212 optimal weight: 0.2980 chunk 140 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 316 ASN B 227 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 81 GLN G 95 GLN H 77 ASN H 111 ASN I 272 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.054718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.044660 restraints weight = 62466.561| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.24 r_work: 0.2389 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2273 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24555 Z= 0.142 Angle : 0.613 10.002 33358 Z= 0.320 Chirality : 0.043 0.290 3718 Planarity : 0.004 0.056 4129 Dihedral : 12.175 178.913 3770 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 3.99 % Allowed : 21.82 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.16), residues: 2834 helix: 1.89 (0.16), residues: 1077 sheet: 0.79 (0.23), residues: 464 loop : -0.81 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 312 TYR 0.014 0.001 TYR I 145 PHE 0.016 0.001 PHE B 126 TRP 0.009 0.001 TRP B 25 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00332 (24555) covalent geometry : angle 0.61341 (33358) hydrogen bonds : bond 0.03918 ( 987) hydrogen bonds : angle 4.55917 ( 2847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 344 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 139 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8499 (mm-30) REVERT: A 231 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6252 (tm) REVERT: A 263 PHE cc_start: 0.8655 (t80) cc_final: 0.7757 (t80) REVERT: A 264 ARG cc_start: 0.8407 (mpp80) cc_final: 0.7894 (mpp80) REVERT: A 299 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6499 (p90) REVERT: A 346 GLU cc_start: 0.8356 (pm20) cc_final: 0.8026 (pm20) REVERT: A 360 ASN cc_start: 0.8851 (p0) cc_final: 0.8426 (p0) REVERT: A 401 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8132 (tp30) REVERT: A 408 MET cc_start: 0.8265 (pmm) cc_final: 0.7912 (pmm) REVERT: A 422 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 59 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: B 207 MET cc_start: 0.6813 (tpp) cc_final: 0.6496 (tpp) REVERT: B 250 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: B 263 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8654 (mttm) REVERT: B 329 ASP cc_start: 0.8574 (m-30) cc_final: 0.8321 (m-30) REVERT: B 475 MET cc_start: 0.8409 (mmt) cc_final: 0.8072 (mmt) REVERT: C 184 ASP cc_start: 0.8006 (m-30) cc_final: 0.7694 (m-30) REVERT: C 320 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 134 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: D 233 MET cc_start: 0.9333 (mmt) cc_final: 0.8842 (mmt) REVERT: E 58 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: E 188 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9200 (mt) REVERT: F 52 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: F 204 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9151 (p) REVERT: G 60 ASP cc_start: 0.7784 (t0) cc_final: 0.7463 (t0) REVERT: I 240 ASP cc_start: 0.8968 (t0) cc_final: 0.8724 (t0) outliers start: 103 outliers final: 68 residues processed: 415 average time/residue: 0.7672 time to fit residues: 361.2643 Evaluate side-chains 415 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 336 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 LEU 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 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 212 MET Chi-restraints excluded: chain I residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 15 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 271 optimal weight: 0.0270 chunk 60 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN H 77 ASN H 111 ASN I 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.052787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.042778 restraints weight = 63272.276| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 2.24 r_work: 0.2335 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2219 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24555 Z= 0.210 Angle : 0.679 10.996 33358 Z= 0.355 Chirality : 0.045 0.285 3718 Planarity : 0.005 0.062 4129 Dihedral : 12.232 179.638 3770 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.95 % Allowed : 22.09 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.16), residues: 2834 helix: 1.70 (0.16), residues: 1085 sheet: 0.59 (0.23), residues: 482 loop : -0.85 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 432 TYR 0.016 0.002 TYR H 100 PHE 0.024 0.002 PHE I 44 TRP 0.008 0.001 TRP D 219 HIS 0.005 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00504 (24555) covalent geometry : angle 0.67897 (33358) hydrogen bonds : bond 0.04556 ( 987) hydrogen bonds : angle 4.71321 ( 2847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 335 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8804 (mm) REVERT: A 139 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8530 (mm-30) REVERT: A 231 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6302 (tm) REVERT: A 263 PHE cc_start: 0.8696 (t80) cc_final: 0.7969 (t80) REVERT: A 264 ARG cc_start: 0.8390 (mpp80) cc_final: 0.7990 (mpp80) REVERT: A 299 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6410 (p90) REVERT: A 360 ASN cc_start: 0.8846 (p0) cc_final: 0.8426 (p0) REVERT: A 401 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8164 (tp30) REVERT: A 408 MET cc_start: 0.8401 (pmm) cc_final: 0.7910 (pmm) REVERT: A 422 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 59 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: B 207 MET cc_start: 0.6940 (tpp) cc_final: 0.6596 (tpp) REVERT: B 250 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: B 263 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8651 (mttm) REVERT: B 329 ASP cc_start: 0.8654 (m-30) cc_final: 0.8415 (m-30) REVERT: B 475 MET cc_start: 0.8454 (mmt) cc_final: 0.8112 (mmt) REVERT: B 491 MET cc_start: 0.8550 (mtp) cc_final: 0.7190 (tmt) REVERT: C 184 ASP cc_start: 0.8042 (m-30) cc_final: 0.7716 (m-30) REVERT: C 320 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 134 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: D 233 MET cc_start: 0.9372 (mmt) cc_final: 0.8893 (mmt) REVERT: E 58 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: E 188 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9210 (mt) REVERT: F 52 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: F 204 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9142 (p) REVERT: G 60 ASP cc_start: 0.7814 (t0) cc_final: 0.7518 (t0) REVERT: I 240 ASP cc_start: 0.8990 (t0) cc_final: 0.8738 (t0) outliers start: 102 outliers final: 73 residues processed: 411 average time/residue: 0.7633 time to fit residues: 355.8618 Evaluate side-chains 412 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU 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 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 212 MET Chi-restraints excluded: chain I residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 0 optimal weight: 3.9990 chunk 267 optimal weight: 0.0570 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 224 optimal weight: 0.2980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 82 GLN H 77 ASN H 111 ASN I 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.055187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.045196 restraints weight = 62911.309| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 2.25 r_work: 0.2406 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2291 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24555 Z= 0.136 Angle : 0.644 11.675 33358 Z= 0.335 Chirality : 0.043 0.271 3718 Planarity : 0.004 0.062 4129 Dihedral : 12.195 178.338 3770 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 3.18 % Allowed : 22.98 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.16), residues: 2834 helix: 1.89 (0.16), residues: 1082 sheet: 0.94 (0.23), residues: 437 loop : -0.81 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 193 TYR 0.015 0.001 TYR I 145 PHE 0.034 0.001 PHE A 112 TRP 0.011 0.001 TRP B 25 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00320 (24555) covalent geometry : angle 0.64400 (33358) hydrogen bonds : bond 0.03762 ( 987) hydrogen bonds : angle 4.53634 ( 2847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 344 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 139 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8495 (mm-30) REVERT: A 231 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6238 (tm) REVERT: A 263 PHE cc_start: 0.8624 (t80) cc_final: 0.7854 (t80) REVERT: A 264 ARG cc_start: 0.8338 (mpp80) cc_final: 0.7916 (mpp80) REVERT: A 299 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6676 (p90) REVERT: A 360 ASN cc_start: 0.8817 (p0) cc_final: 0.8392 (p0) REVERT: A 408 MET cc_start: 0.8321 (pmm) cc_final: 0.7869 (pmm) REVERT: A 422 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 207 MET cc_start: 0.6751 (tpp) cc_final: 0.6432 (tpp) REVERT: B 250 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: B 256 GLU cc_start: 0.8121 (tp30) cc_final: 0.7847 (mm-30) REVERT: B 263 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8652 (mttm) REVERT: B 329 ASP cc_start: 0.8530 (m-30) cc_final: 0.8275 (m-30) REVERT: B 475 MET cc_start: 0.8445 (mmt) cc_final: 0.8111 (mmt) REVERT: C 184 ASP cc_start: 0.7948 (m-30) cc_final: 0.7641 (m-30) REVERT: C 254 HIS cc_start: 0.8870 (t-90) cc_final: 0.8582 (t-90) REVERT: C 320 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7947 (tm-30) REVERT: E 58 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: E 188 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9188 (mt) REVERT: F 52 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: F 204 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9142 (p) REVERT: G 60 ASP cc_start: 0.7768 (t0) cc_final: 0.7466 (t0) REVERT: I 240 ASP cc_start: 0.8960 (t0) cc_final: 0.8709 (t0) outliers start: 82 outliers final: 61 residues processed: 408 average time/residue: 0.7695 time to fit residues: 355.6332 Evaluate side-chains 407 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 336 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 LEU 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 259 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 203 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 240 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN H 77 ASN H 111 ASN I 272 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.052893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.042938 restraints weight = 63187.429| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 2.22 r_work: 0.2338 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2222 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24555 Z= 0.208 Angle : 0.698 11.620 33358 Z= 0.364 Chirality : 0.045 0.273 3718 Planarity : 0.005 0.061 4129 Dihedral : 12.231 179.578 3770 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 3.41 % Allowed : 23.06 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.16), residues: 2834 helix: 1.73 (0.16), residues: 1086 sheet: 0.62 (0.22), residues: 493 loop : -0.84 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 70 TYR 0.029 0.002 TYR B 414 PHE 0.039 0.002 PHE A 112 TRP 0.008 0.001 TRP D 219 HIS 0.005 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00500 (24555) covalent geometry : angle 0.69822 (33358) hydrogen bonds : bond 0.04537 ( 987) hydrogen bonds : angle 4.69029 ( 2847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8910.27 seconds wall clock time: 153 minutes 5.38 seconds (9185.38 seconds total)