Starting phenix.real_space_refine on Tue May 5 16:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333.map" model { file = "/net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib6_35333/05_2026/8ib6_35333_neut.cif" } resolution = 3.3 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= 0.001 sd= 0.089 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 242 5.16 5 C 20842 2.51 5 N 5100 2.21 5 O 5615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31822 Number of models: 1 Model: "" Number of chains: 33 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "J" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1205 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain breaks: 2 Chain: "K" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 4798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4798 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Chain: "M" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3622 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain: "N" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2694 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain: "O" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2599 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "U" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "X" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 4, 'TRANS': 22} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1030 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "c" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 988 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "e" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 475 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 858 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "h" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1146 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 11, 'TRANS': 124} Chain: "i" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 796 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 569 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "l" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1328 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 18, 'TRANS': 139} Chain: "m" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1054 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 11, 'TRANS': 115} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1027 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "p" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1438 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 388 Unusual residues: {'3PE': 5, 'CDL': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 67 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'3PE': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 6.88, per 1000 atoms: 0.22 Number of scatterers: 31822 At special positions: 0 Unit cell: (184.8, 138.6, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 242 16.00 P 23 15.00 O 5615 8.00 N 5100 7.00 C 20842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS Y 20 " - pdb=" SG CYS Y 77 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 97 " - pdb=" SG CYS Y 117 " distance=2.36 Simple disulfide: pdb=" SG CYS e 33 " - pdb=" SG CYS e 66 " distance=2.02 Simple disulfide: pdb=" SG CYS e 43 " - pdb=" SG CYS e 56 " distance=2.05 Simple disulfide: pdb=" SG CYS o 59 " - pdb=" SG CYS o 90 " distance=2.02 Simple disulfide: pdb=" SG CYS o 69 " - pdb=" SG CYS o 80 " distance=2.36 Simple disulfide: pdb=" SG CYS p 77 " - pdb=" SG CYS p 84 " distance=2.04 Simple disulfide: pdb=" SG CYS p 113 " - pdb=" SG CYS p 125 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7240 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 4 sheets defined 67.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.746A pdb=" N GLN D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 21 Processing helix chain 'J' and resid 26 through 44 removed outlier: 3.578A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 59 removed outlier: 3.709A pdb=" N PHE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 removed outlier: 3.525A pdb=" N MET J 73 " --> pdb=" O TYR J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 109 Processing helix chain 'J' and resid 140 through 146 removed outlier: 3.506A pdb=" N TYR J 145 " --> pdb=" O ALA J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 171 removed outlier: 4.067A pdb=" N MET J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 153 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 168 " --> pdb=" O PHE J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'K' and resid 25 through 51 removed outlier: 4.169A pdb=" N THR K 29 " --> pdb=" O HIS K 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 85 removed outlier: 3.811A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU K 64 " --> pdb=" O PRO K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'L' and resid 2 through 24 removed outlier: 4.113A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 25 through 30 removed outlier: 4.419A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 83 through 108 removed outlier: 3.560A pdb=" N GLN L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 133 Processing helix chain 'L' and resid 136 through 156 removed outlier: 3.548A pdb=" N LEU L 140 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 191 removed outlier: 3.607A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 202 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 237 removed outlier: 3.676A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 247 Processing helix chain 'L' and resid 250 through 263 removed outlier: 3.536A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 270 removed outlier: 4.061A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 295 removed outlier: 3.836A pdb=" N LEU L 274 " --> pdb=" O ASN L 270 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN L 295 " --> pdb=" O CYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 319 Processing helix chain 'L' and resid 321 through 350 removed outlier: 3.504A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 Processing helix chain 'L' and resid 361 through 366 Processing helix chain 'L' and resid 366 through 381 Processing helix chain 'L' and resid 386 through 402 removed outlier: 3.530A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 431 Processing helix chain 'L' and resid 447 through 472 Proline residue: L 453 - end of helix removed outlier: 5.302A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 488 Processing helix chain 'L' and resid 488 through 510 removed outlier: 3.694A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS L 510 " --> pdb=" O ASN L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 525 Processing helix chain 'L' and resid 528 through 534 removed outlier: 3.564A pdb=" N HIS L 534 " --> pdb=" O PRO L 530 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 548 removed outlier: 3.628A pdb=" N LEU L 542 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU L 544 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER L 545 " --> pdb=" O SER L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 561 Processing helix chain 'L' and resid 562 through 579 removed outlier: 3.683A pdb=" N THR L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER L 567 " --> pdb=" O PRO L 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 605 removed outlier: 3.501A pdb=" N TYR L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 Processing helix chain 'M' and resid 10 through 18 Processing helix chain 'M' and resid 22 through 39 Processing helix chain 'M' and resid 40 through 43 Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.508A pdb=" N ILE M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU M 68 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 91 through 111 removed outlier: 3.577A pdb=" N GLN M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 125 Processing helix chain 'M' and resid 125 through 137 removed outlier: 3.542A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 171 removed outlier: 3.851A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 191 through 207 removed outlier: 3.936A pdb=" N LEU M 197 " --> pdb=" O ASN M 193 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.743A pdb=" N GLU M 222 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 234 Processing helix chain 'M' and resid 234 through 247 removed outlier: 4.145A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 258 removed outlier: 3.510A pdb=" N ALA M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.504A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 Processing helix chain 'M' and resid 305 through 338 Processing helix chain 'M' and resid 347 through 351 Processing helix chain 'M' and resid 352 through 367 removed outlier: 3.519A pdb=" N ALA M 356 " --> pdb=" O PHE M 352 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 389 Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.144A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE M 400 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE M 401 " --> pdb=" O GLY M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 450 Proline residue: M 443 - end of helix removed outlier: 3.762A pdb=" N SER M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 455 Processing helix chain 'N' and resid 2 through 23 Proline residue: N 17 - end of helix removed outlier: 3.553A pdb=" N THR N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 removed outlier: 3.530A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.579A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS N 79 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 107 Processing helix chain 'N' and resid 109 through 112 Processing helix chain 'N' and resid 113 through 120 removed outlier: 3.854A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 132 Processing helix chain 'N' and resid 132 through 145 removed outlier: 4.240A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.505A pdb=" N ILE N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 172 removed outlier: 3.755A pdb=" N ILE N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 193 Processing helix chain 'N' and resid 197 through 222 removed outlier: 3.835A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.750A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 232 Processing helix chain 'N' and resid 232 through 237 Processing helix chain 'N' and resid 239 through 252 removed outlier: 4.194A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 273 removed outlier: 4.129A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 301 removed outlier: 3.834A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 317 Processing helix chain 'N' and resid 323 through 333 removed outlier: 3.704A pdb=" N SER N 327 " --> pdb=" O ASN N 323 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR N 328 " --> pdb=" O LEU N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 338 No H-bonds generated for 'chain 'N' and resid 336 through 338' Processing helix chain 'N' and resid 339 through 344 Processing helix chain 'O' and resid 39 through 45 Processing helix chain 'O' and resid 48 through 53 removed outlier: 4.060A pdb=" N LEU O 53 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 82 removed outlier: 3.547A pdb=" N LEU O 73 " --> pdb=" O GLY O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 98 Processing helix chain 'O' and resid 113 through 120 Processing helix chain 'O' and resid 126 through 153 Processing helix chain 'O' and resid 162 through 176 removed outlier: 4.103A pdb=" N PHE O 167 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL O 168 " --> pdb=" O TYR O 164 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE O 169 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU O 170 " --> pdb=" O ASP O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 195 Processing helix chain 'O' and resid 196 through 198 No H-bonds generated for 'chain 'O' and resid 196 through 198' Processing helix chain 'O' and resid 210 through 221 Processing helix chain 'O' and resid 230 through 244 Processing helix chain 'O' and resid 244 through 253 removed outlier: 3.735A pdb=" N MET O 252 " --> pdb=" O LYS O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 276 Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 287 through 299 removed outlier: 4.567A pdb=" N TYR O 293 " --> pdb=" O TRP O 289 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 294 " --> pdb=" O THR O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 300 through 305 Processing helix chain 'O' and resid 306 through 310 removed outlier: 3.651A pdb=" N ILE O 310 " --> pdb=" O TYR O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 332 Processing helix chain 'U' and resid 75 through 88 removed outlier: 3.551A pdb=" N ASP U 81 " --> pdb=" O ASP U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 126 removed outlier: 3.714A pdb=" N GLU U 117 " --> pdb=" O LEU U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 136 Processing helix chain 'U' and resid 142 through 152 removed outlier: 3.519A pdb=" N ALA U 149 " --> pdb=" O VAL U 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.901A pdb=" N TYR Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS Y 12 " --> pdb=" O PHE Y 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 45 Processing helix chain 'Y' and resid 50 through 84 removed outlier: 3.534A pdb=" N PHE Y 72 " --> pdb=" O ILE Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 107 removed outlier: 3.765A pdb=" N TYR Y 92 " --> pdb=" O ASP Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 134 Processing helix chain 'c' and resid 40 through 73 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 28 through 49 Processing helix chain 'd' and resid 57 through 97 removed outlier: 3.609A pdb=" N LEU d 62 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG d 78 " --> pdb=" O PHE d 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 11 Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 33 through 42 removed outlier: 3.600A pdb=" N LYS e 38 " --> pdb=" O HIS e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 52 Processing helix chain 'e' and resid 57 through 67 removed outlier: 3.636A pdb=" N GLU e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU e 67 " --> pdb=" O PHE e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 89 removed outlier: 3.784A pdb=" N MET e 73 " --> pdb=" O ARG e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 100 removed outlier: 3.578A pdb=" N GLY e 100 " --> pdb=" O HIS e 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 34 removed outlier: 3.637A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 86 Processing helix chain 'g' and resid 87 through 93 Processing helix chain 'g' and resid 98 through 106 Processing helix chain 'g' and resid 109 through 111 No H-bonds generated for 'chain 'g' and resid 109 through 111' Processing helix chain 'g' and resid 112 through 131 removed outlier: 3.825A pdb=" N ARG g 117 " --> pdb=" O GLN g 113 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG g 118 " --> pdb=" O GLU g 114 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 93 removed outlier: 3.726A pdb=" N PHE h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU h 68 " --> pdb=" O ASP h 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE h 73 " --> pdb=" O ARG h 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET h 76 " --> pdb=" O LYS h 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR h 78 " --> pdb=" O TYR h 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE h 80 " --> pdb=" O MET h 76 " (cutoff:3.500A) Proline residue: h 81 - end of helix Processing helix chain 'h' and resid 108 through 113 Processing helix chain 'h' and resid 115 through 126 removed outlier: 4.012A pdb=" N ALA h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 164 removed outlier: 4.071A pdb=" N ASN h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG h 161 " --> pdb=" O ARG h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 175 through 179 removed outlier: 3.725A pdb=" N PHE h 178 " --> pdb=" O GLU h 175 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 27 removed outlier: 3.574A pdb=" N GLN i 13 " --> pdb=" O LYS i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 89 removed outlier: 3.562A pdb=" N HIS i 74 " --> pdb=" O PHE i 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Proline residue: i 78 - end of helix removed outlier: 3.584A pdb=" N PHE i 81 " --> pdb=" O ILE i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 76 removed outlier: 3.601A pdb=" N VAL j 55 " --> pdb=" O THR j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 92 removed outlier: 4.189A pdb=" N TRP j 92 " --> pdb=" O PRO j 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 98 removed outlier: 3.520A pdb=" N LEU j 97 " --> pdb=" O THR j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 33 through 46 removed outlier: 4.163A pdb=" N THR k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 54 removed outlier: 4.268A pdb=" N ARG k 53 " --> pdb=" O PRO k 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 61 removed outlier: 4.335A pdb=" N TYR k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY k 61 " --> pdb=" O TRP k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 3.514A pdb=" N VAL k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 90 Processing helix chain 'l' and resid 33 through 37 Processing helix chain 'l' and resid 44 through 55 removed outlier: 3.545A pdb=" N ALA l 52 " --> pdb=" O ARG l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 86 Processing helix chain 'l' and resid 125 through 150 Processing helix chain 'l' and resid 161 through 166 removed outlier: 4.183A pdb=" N ASN l 165 " --> pdb=" O TYR l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 24 removed outlier: 3.568A pdb=" N TYR m 23 " --> pdb=" O ASP m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 48 removed outlier: 3.986A pdb=" N SER m 38 " --> pdb=" O VAL m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 74 removed outlier: 3.596A pdb=" N ILE m 66 " --> pdb=" O ASP m 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP m 68 " --> pdb=" O ALA m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 Processing helix chain 'm' and resid 95 through 101 Processing helix chain 'm' and resid 101 through 119 removed outlier: 3.811A pdb=" N THR m 107 " --> pdb=" O TYR m 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 18 removed outlier: 3.733A pdb=" N LYS n 15 " --> pdb=" O THR n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 18 through 26 removed outlier: 3.630A pdb=" N ARG n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 50 removed outlier: 3.525A pdb=" N MET n 44 " --> pdb=" O PHE n 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA n 46 " --> pdb=" O CYS n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 74 removed outlier: 3.635A pdb=" N GLU n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 96 removed outlier: 3.970A pdb=" N CYS n 96 " --> pdb=" O ARG n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 110 through 114 Processing helix chain 'n' and resid 115 through 143 removed outlier: 3.710A pdb=" N PHE n 119 " --> pdb=" O TYR n 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN n 124 " --> pdb=" O SER n 120 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP n 134 " --> pdb=" O MET n 130 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG n 135 " --> pdb=" O GLU n 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 9 removed outlier: 4.435A pdb=" N THR o 6 " --> pdb=" O GLY o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 49 Processing helix chain 'o' and resid 52 through 56 Processing helix chain 'o' and resid 59 through 72 removed outlier: 3.624A pdb=" N ARG o 65 " --> pdb=" O HIS o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 119 removed outlier: 3.551A pdb=" N LYS o 118 " --> pdb=" O ARG o 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 41 removed outlier: 3.740A pdb=" N TYR p 32 " --> pdb=" O ASN p 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU p 33 " --> pdb=" O PRO p 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU p 39 " --> pdb=" O LYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 59 removed outlier: 4.254A pdb=" N ASN p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 113 removed outlier: 3.523A pdb=" N TRP p 92 " --> pdb=" O ALA p 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE p 102 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET p 103 " --> pdb=" O ASP p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 140 removed outlier: 3.733A pdb=" N GLU p 130 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN p 131 " --> pdb=" O LYS p 127 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA p 138 " --> pdb=" O LYS p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 174 removed outlier: 3.758A pdb=" N ARG p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA p 170 " --> pdb=" O GLU p 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 81 removed outlier: 6.889A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP L 66 " --> pdb=" O MET L 78 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE L 80 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR L 64 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 440 through 441 Processing sheet with id=AA3, first strand: chain 'O' and resid 84 through 85 removed outlier: 6.329A pdb=" N LYS O 84 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL O 59 " --> pdb=" O ALA O 203 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE O 205 " --> pdb=" O VAL O 59 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR O 61 " --> pdb=" O ILE O 205 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE O 207 " --> pdb=" O THR O 61 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL O 204 " --> pdb=" O LEU O 256 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR O 258 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR O 206 " --> pdb=" O TYR O 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 97 through 98 removed outlier: 5.941A pdb=" N GLU h 97 " --> pdb=" O TYR p 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 1697 hydrogen bonds defined for protein. 4935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4840 1.29 - 1.42: 8516 1.42 - 1.55: 18744 1.55 - 1.69: 116 1.69 - 1.82: 438 Bond restraints: 32654 Sorted by residual: bond pdb=" O6 EHZ n 201 " pdb=" P1 EHZ n 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" N PRO O 247 " pdb=" CD PRO O 247 " ideal model delta sigma weight residual 1.473 1.706 -0.233 1.40e-02 5.10e+03 2.77e+02 bond pdb=" N PRO d 115 " pdb=" CD PRO d 115 " ideal model delta sigma weight residual 1.473 1.277 0.196 1.40e-02 5.10e+03 1.95e+02 bond pdb=" N PRO L 265 " pdb=" CD PRO L 265 " ideal model delta sigma weight residual 1.473 1.667 -0.194 1.40e-02 5.10e+03 1.92e+02 bond pdb=" N PRO N 255 " pdb=" CD PRO N 255 " ideal model delta sigma weight residual 1.473 1.283 0.190 1.40e-02 5.10e+03 1.83e+02 ... (remaining 32649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 43510 6.66 - 13.33: 592 13.33 - 19.99: 28 19.99 - 26.66: 1 26.66 - 33.32: 2 Bond angle restraints: 44133 Sorted by residual: angle pdb=" N PRO N 255 " pdb=" CA PRO N 255 " pdb=" C PRO N 255 " ideal model delta sigma weight residual 110.70 128.50 -17.80 1.22e+00 6.72e-01 2.13e+02 angle pdb=" N PRO M 370 " pdb=" CA PRO M 370 " pdb=" C PRO M 370 " ideal model delta sigma weight residual 110.70 128.50 -17.80 1.22e+00 6.72e-01 2.13e+02 angle pdb=" O MET O 83 " pdb=" C MET O 83 " pdb=" N LYS O 84 " ideal model delta sigma weight residual 122.89 140.50 -17.61 1.22e+00 6.72e-01 2.08e+02 angle pdb=" N TYR O 118 " pdb=" CA TYR O 118 " pdb=" C TYR O 118 " ideal model delta sigma weight residual 111.07 125.92 -14.85 1.07e+00 8.73e-01 1.93e+02 angle pdb=" C MET O 83 " pdb=" N LYS O 84 " pdb=" CA LYS O 84 " ideal model delta sigma weight residual 120.75 100.06 20.69 1.51e+00 4.39e-01 1.88e+02 ... (remaining 44128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.47: 18996 28.47 - 56.94: 739 56.94 - 85.41: 83 85.41 - 113.88: 5 113.88 - 142.35: 2 Dihedral angle restraints: 19825 sinusoidal: 8622 harmonic: 11203 Sorted by residual: dihedral pdb=" CB CYS p 77 " pdb=" SG CYS p 77 " pdb=" SG CYS p 84 " pdb=" CB CYS p 84 " ideal model delta sinusoidal sigma weight residual -86.00 -167.16 81.16 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS e 43 " pdb=" SG CYS e 43 " pdb=" SG CYS e 56 " pdb=" CB CYS e 56 " ideal model delta sinusoidal sigma weight residual 93.00 160.90 -67.90 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" O2A ADP O 402 " pdb=" O3A ADP O 402 " pdb=" PA ADP O 402 " pdb=" PB ADP O 402 " ideal model delta sinusoidal sigma weight residual 300.00 157.66 142.35 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 19822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3546 0.104 - 0.209: 961 0.209 - 0.313: 228 0.313 - 0.418: 47 0.418 - 0.522: 15 Chirality restraints: 4797 Sorted by residual: chirality pdb=" CA ASP L 554 " pdb=" N ASP L 554 " pdb=" C ASP L 554 " pdb=" CB ASP L 554 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA LEU d 113 " pdb=" N LEU d 113 " pdb=" C LEU d 113 " pdb=" CB LEU d 113 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CA LEU L 525 " pdb=" N LEU L 525 " pdb=" C LEU L 525 " pdb=" CB LEU L 525 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 4794 not shown) Planarity restraints: 5412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET O 83 " -0.022 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C MET O 83 " 0.098 2.00e-02 2.50e+03 pdb=" O MET O 83 " -0.043 2.00e-02 2.50e+03 pdb=" N LYS O 84 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER l 125 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER l 125 " -0.071 2.00e-02 2.50e+03 pdb=" O SER l 125 " 0.027 2.00e-02 2.50e+03 pdb=" N TRP l 126 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 546 " -0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU L 546 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU L 546 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS L 547 " -0.022 2.00e-02 2.50e+03 ... (remaining 5409 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 770 2.61 - 3.18: 32385 3.18 - 3.75: 51492 3.75 - 4.33: 74541 4.33 - 4.90: 116092 Nonbonded interactions: 275280 Sorted by model distance: nonbonded pdb=" O ASN L 605 " pdb=" OD1 ASN L 605 " model vdw 2.034 3.040 nonbonded pdb=" O ASN L 579 " pdb=" OD1 ASN L 579 " model vdw 2.062 3.040 nonbonded pdb=" OD1 ASN N 323 " pdb=" N LEU N 324 " model vdw 2.083 3.120 nonbonded pdb=" O ARG m 123 " pdb=" NE2 GLN p 140 " model vdw 2.127 3.120 nonbonded pdb=" O PRO g 108 " pdb=" OD1 ASP g 109 " model vdw 2.132 3.040 ... (remaining 275275 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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 : 0.014 0.731 32662 Z= 0.987 Angle : 1.964 42.461 44149 Z= 1.401 Chirality : 0.106 0.522 4797 Planarity : 0.007 0.069 5412 Dihedral : 14.269 142.346 12561 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 44.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 0.24 % Allowed : 5.75 % Favored : 94.02 % Cbeta Deviations : 1.33 % 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: -2.28 (0.13), residues: 3763 helix: -0.95 (0.10), residues: 2374 sheet: -2.81 (1.05), residues: 22 loop : -2.38 (0.15), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG p 162 TYR 0.035 0.002 TYR l 153 PHE 0.038 0.002 PHE X 168 TRP 0.029 0.002 TRP L 407 HIS 0.008 0.002 HIS l 106 Details of bonding type rmsd covalent geometry : bond 0.01390 (32654) covalent geometry : angle 1.95292 (44133) SS BOND : bond 0.16471 ( 8) SS BOND : angle 11.06676 ( 16) hydrogen bonds : bond 0.22802 ( 1697) hydrogen bonds : angle 8.63223 ( 4935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1426 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 TYR cc_start: 0.5662 (m-80) cc_final: 0.5370 (m-80) REVERT: J 149 THR cc_start: 0.8177 (t) cc_final: 0.7957 (p) REVERT: K 1 MET cc_start: 0.5489 (tmm) cc_final: 0.4911 (tmm) REVERT: K 24 SER cc_start: 0.9033 (m) cc_final: 0.8828 (m) REVERT: K 78 LEU cc_start: 0.8600 (tt) cc_final: 0.8233 (tt) REVERT: K 96 LEU cc_start: 0.8320 (mt) cc_final: 0.8103 (mp) REVERT: L 132 THR cc_start: 0.8903 (m) cc_final: 0.8692 (p) REVERT: L 208 ASP cc_start: 0.7668 (t0) cc_final: 0.7270 (t0) REVERT: L 493 ILE cc_start: 0.8249 (tp) cc_final: 0.7943 (tp) REVERT: M 173 THR cc_start: 0.8083 (p) cc_final: 0.7563 (t) REVERT: M 294 MET cc_start: 0.8740 (mmp) cc_final: 0.8490 (mmm) REVERT: M 366 ASN cc_start: 0.8759 (t0) cc_final: 0.8476 (t0) REVERT: N 243 MET cc_start: 0.7013 (mmm) cc_final: 0.6763 (mmm) REVERT: N 278 MET cc_start: 0.6903 (mmm) cc_final: 0.6447 (mmm) REVERT: U 122 MET cc_start: 0.8807 (mmp) cc_final: 0.8412 (mmt) REVERT: U 130 ILE cc_start: 0.9326 (mm) cc_final: 0.9047 (mm) REVERT: U 151 LYS cc_start: 0.8656 (tptm) cc_final: 0.8251 (tptt) REVERT: Y 60 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7669 (ttp-110) REVERT: d 33 TYR cc_start: 0.9033 (t80) cc_final: 0.8738 (t80) REVERT: d 44 MET cc_start: 0.8266 (tpt) cc_final: 0.7947 (tpt) REVERT: e 82 GLN cc_start: 0.8504 (tp40) cc_final: 0.7852 (tt0) REVERT: g 135 MET cc_start: 0.8785 (ttm) cc_final: 0.8585 (ttp) REVERT: i 120 MET cc_start: 0.8493 (mtp) cc_final: 0.8141 (mtm) REVERT: k 77 PHE cc_start: 0.8971 (t80) cc_final: 0.8729 (t80) REVERT: k 81 PHE cc_start: 0.8589 (t80) cc_final: 0.8224 (t80) REVERT: k 88 LEU cc_start: 0.8737 (tp) cc_final: 0.8530 (tt) REVERT: m 62 ASP cc_start: 0.7979 (t0) cc_final: 0.7694 (t0) REVERT: n 33 HIS cc_start: 0.7138 (m-70) cc_final: 0.6687 (m-70) REVERT: n 85 SER cc_start: 0.9055 (m) cc_final: 0.8836 (t) REVERT: o 72 ASP cc_start: 0.7997 (m-30) cc_final: 0.7778 (m-30) REVERT: p 137 LYS cc_start: 0.7656 (tptp) cc_final: 0.7429 (tppt) REVERT: p 146 LEU cc_start: 0.8389 (mt) cc_final: 0.8053 (mp) outliers start: 8 outliers final: 2 residues processed: 1428 average time/residue: 0.1985 time to fit residues: 449.3574 Evaluate side-chains 978 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 976 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain i residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 60 HIS K 7 ASN L 56 HIS L 113 ASN L 135 ASN L 139 GLN L 199 GLN L 321 GLN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 517 ASN L 572 ASN M 48 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 139 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS M 331 ASN M 374 ASN M 390 ASN M 422 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN N 204 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 ASN O 71 ASN O 79 GLN O 132 GLN O 175 ASN O 299 GLN O 323 GLN O 329 ASN U 101 ASN Y 19 GLN Y 91 ASN Y 108 HIS d 97 HIS ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 HIS f 13 HIS f 45 GLN g 68 ASN h 109 HIS h 170 GLN i 83 HIS ** j 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 39 GLN l 31 HIS l 80 ASN l 106 HIS ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 GLN n 33 HIS n 53 ASN o 54 GLN p 100 GLN p 140 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110369 restraints weight = 49105.261| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.19 r_work: 0.3238 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32662 Z= 0.197 Angle : 0.792 14.396 44149 Z= 0.407 Chirality : 0.047 0.355 4797 Planarity : 0.006 0.086 5412 Dihedral : 13.015 138.118 4970 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 2.80 % Allowed : 13.65 % Favored : 83.55 % 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: -0.51 (0.13), residues: 3763 helix: 0.24 (0.10), residues: 2439 sheet: -2.25 (1.18), residues: 22 loop : -1.28 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 26 TYR 0.039 0.002 TYR L 422 PHE 0.053 0.002 PHE X 169 TRP 0.019 0.002 TRP L 557 HIS 0.010 0.002 HIS L 332 Details of bonding type rmsd covalent geometry : bond 0.00439 (32654) covalent geometry : angle 0.78828 (44133) SS BOND : bond 0.00681 ( 8) SS BOND : angle 4.26359 ( 16) hydrogen bonds : bond 0.06084 ( 1697) hydrogen bonds : angle 5.15817 ( 4935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1014 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 TYR cc_start: 0.4622 (m-80) cc_final: 0.4416 (m-80) REVERT: J 44 LEU cc_start: 0.8565 (mt) cc_final: 0.8337 (mm) REVERT: J 64 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8413 (mp) REVERT: J 144 MET cc_start: 0.9070 (mtt) cc_final: 0.8732 (mtt) REVERT: J 149 THR cc_start: 0.9026 (t) cc_final: 0.8820 (p) REVERT: K 24 SER cc_start: 0.9317 (m) cc_final: 0.9110 (p) REVERT: K 27 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: K 96 LEU cc_start: 0.8354 (mt) cc_final: 0.8145 (mp) REVERT: L 24 SER cc_start: 0.8073 (t) cc_final: 0.7643 (p) REVERT: L 170 GLN cc_start: 0.8816 (tt0) cc_final: 0.8524 (tt0) REVERT: L 198 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8322 (mt) REVERT: L 366 MET cc_start: 0.8677 (mtp) cc_final: 0.8233 (mtm) REVERT: L 493 ILE cc_start: 0.8716 (tp) cc_final: 0.8459 (tp) REVERT: L 510 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7522 (mmtt) REVERT: L 598 ILE cc_start: 0.8639 (mt) cc_final: 0.8432 (mm) REVERT: M 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8786 (m110) REVERT: M 246 ILE cc_start: 0.9278 (tt) cc_final: 0.9073 (tt) REVERT: M 271 MET cc_start: 0.8589 (mmm) cc_final: 0.8188 (mtp) REVERT: M 278 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (mtm110) REVERT: M 308 SER cc_start: 0.9037 (m) cc_final: 0.8697 (p) REVERT: M 366 ASN cc_start: 0.9160 (t0) cc_final: 0.8685 (t0) REVERT: M 421 ASN cc_start: 0.7729 (p0) cc_final: 0.6955 (m-40) REVERT: N 149 LEU cc_start: 0.8774 (pp) cc_final: 0.8311 (mp) REVERT: N 175 MET cc_start: 0.8345 (tpp) cc_final: 0.7980 (tpp) REVERT: N 187 MET cc_start: 0.8660 (tpp) cc_final: 0.8327 (mmm) REVERT: N 190 MET cc_start: 0.8312 (mtm) cc_final: 0.7847 (mtm) REVERT: N 243 MET cc_start: 0.8109 (mmm) cc_final: 0.7577 (mmm) REVERT: N 271 MET cc_start: 0.9310 (mmm) cc_final: 0.9031 (mmm) REVERT: N 314 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: O 195 LEU cc_start: 0.8062 (tt) cc_final: 0.7854 (tp) REVERT: O 208 ASP cc_start: 0.7325 (t70) cc_final: 0.6738 (p0) REVERT: O 231 SER cc_start: 0.8922 (p) cc_final: 0.8629 (t) REVERT: O 332 ARG cc_start: 0.6675 (tpp-160) cc_final: 0.6405 (tpm170) REVERT: U 101 ASN cc_start: 0.8643 (m-40) cc_final: 0.8185 (m-40) REVERT: U 125 GLU cc_start: 0.8277 (tp30) cc_final: 0.7770 (tp30) REVERT: U 130 ILE cc_start: 0.9294 (mm) cc_final: 0.8920 (mm) REVERT: U 143 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7970 (mt-10) REVERT: U 151 LYS cc_start: 0.8761 (tptm) cc_final: 0.8489 (tttp) REVERT: X 155 GLU cc_start: 0.8212 (tp30) cc_final: 0.7777 (mt-10) REVERT: Y 18 THR cc_start: 0.7771 (m) cc_final: 0.7400 (p) REVERT: Y 60 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7008 (ttp80) REVERT: Y 81 GLN cc_start: 0.8601 (tp40) cc_final: 0.8399 (tp40) REVERT: Y 88 ASP cc_start: 0.8516 (t0) cc_final: 0.8248 (t0) REVERT: Y 133 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8256 (mt-10) REVERT: c 31 VAL cc_start: 0.8380 (t) cc_final: 0.8045 (m) REVERT: c 65 ASP cc_start: 0.8944 (m-30) cc_final: 0.8736 (m-30) REVERT: c 69 TYR cc_start: 0.8001 (t80) cc_final: 0.7178 (t80) REVERT: c 71 ARG cc_start: 0.8317 (ptp90) cc_final: 0.8068 (ptp90) REVERT: d 2 MET cc_start: 0.6081 (tpp) cc_final: 0.5780 (mmm) REVERT: d 27 ASN cc_start: 0.7690 (p0) cc_final: 0.7319 (p0) REVERT: d 34 MET cc_start: 0.8833 (mmm) cc_final: 0.8442 (mmm) REVERT: d 107 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8478 (mtmt) REVERT: e 15 ASP cc_start: 0.7329 (t0) cc_final: 0.7102 (t0) REVERT: e 28 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mmmt) REVERT: e 37 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6996 (tm-30) REVERT: e 39 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7068 (mt-10) REVERT: e 59 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7509 (mt-10) REVERT: e 82 GLN cc_start: 0.8090 (tp40) cc_final: 0.7486 (tt0) REVERT: f 5 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7333 (mp10) REVERT: f 10 HIS cc_start: 0.7377 (m-70) cc_final: 0.6955 (m-70) REVERT: f 28 ARG cc_start: 0.7460 (ptp-170) cc_final: 0.7174 (mtm110) REVERT: f 53 GLU cc_start: 0.8545 (tt0) cc_final: 0.8320 (tt0) REVERT: g 77 ASP cc_start: 0.8969 (p0) cc_final: 0.8644 (p0) REVERT: g 84 ASN cc_start: 0.8932 (t0) cc_final: 0.8537 (t0) REVERT: g 141 ASP cc_start: 0.8448 (t0) cc_final: 0.8232 (t0) REVERT: h 90 ASN cc_start: 0.9242 (m-40) cc_final: 0.9015 (m110) REVERT: h 132 ASN cc_start: 0.8012 (m-40) cc_final: 0.7795 (t0) REVERT: h 184 LYS cc_start: 0.4822 (pttt) cc_final: 0.4593 (ttpt) REVERT: i 17 GLU cc_start: 0.8781 (tp30) cc_final: 0.8484 (tt0) REVERT: i 24 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8394 (tptt) REVERT: i 108 ASP cc_start: 0.7551 (t0) cc_final: 0.7160 (t0) REVERT: i 112 GLU cc_start: 0.8677 (mp0) cc_final: 0.8358 (mp0) REVERT: i 120 MET cc_start: 0.8721 (mtp) cc_final: 0.8130 (mtm) REVERT: j 57 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7955 (mm-40) REVERT: j 88 ASP cc_start: 0.8445 (t70) cc_final: 0.7853 (t70) REVERT: j 91 GLN cc_start: 0.8428 (mm110) cc_final: 0.7941 (mm110) REVERT: j 96 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8402 (mt-10) REVERT: k 27 GLN cc_start: 0.8829 (tt0) cc_final: 0.8622 (tt0) REVERT: l 32 MET cc_start: 0.7863 (mmt) cc_final: 0.7603 (mmp) REVERT: l 36 MET cc_start: 0.8425 (ttm) cc_final: 0.7645 (ttp) REVERT: l 43 ARG cc_start: 0.7948 (mmt-90) cc_final: 0.7700 (mmt-90) REVERT: l 67 ASP cc_start: 0.8465 (t0) cc_final: 0.8018 (t0) REVERT: l 70 MET cc_start: 0.9124 (tpp) cc_final: 0.8876 (mmt) REVERT: l 120 SER cc_start: 0.9135 (t) cc_final: 0.8834 (m) REVERT: l 153 TYR cc_start: 0.8955 (p90) cc_final: 0.8653 (p90) REVERT: l 164 ASN cc_start: 0.8306 (m-40) cc_final: 0.8045 (m-40) REVERT: m 26 SER cc_start: 0.8503 (m) cc_final: 0.8283 (t) REVERT: m 75 ASN cc_start: 0.7827 (t0) cc_final: 0.7400 (t0) REVERT: m 120 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8911 (mtpp) REVERT: m 129 TYR cc_start: 0.7816 (p90) cc_final: 0.7505 (p90) REVERT: n 80 TYR cc_start: 0.7933 (t80) cc_final: 0.7678 (t80) REVERT: n 141 GLN cc_start: 0.8779 (tt0) cc_final: 0.8519 (tt0) REVERT: o 14 SER cc_start: 0.8814 (m) cc_final: 0.8533 (t) REVERT: o 74 PHE cc_start: 0.8742 (t80) cc_final: 0.8100 (t80) REVERT: o 119 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6858 (tp30) REVERT: p 81 ASP cc_start: 0.8307 (t0) cc_final: 0.8002 (t0) REVERT: p 95 ASP cc_start: 0.8447 (m-30) cc_final: 0.8168 (m-30) REVERT: p 119 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7824 (mm-30) REVERT: p 137 LYS cc_start: 0.8260 (tptp) cc_final: 0.7648 (tppt) REVERT: p 141 ASP cc_start: 0.8536 (m-30) cc_final: 0.8271 (m-30) outliers start: 95 outliers final: 48 residues processed: 1056 average time/residue: 0.1854 time to fit residues: 315.6567 Evaluate side-chains 920 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 865 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 422 HIS Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain U residue 136 GLU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 13 GLN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain j residue 57 GLN Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 96 GLU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 142 GLU Chi-restraints excluded: chain o residue 31 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 329 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN L 2 ASN L 67 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 GLN L 200 GLN L 230 HIS ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 HIS ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 422 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 ASN O 182 GLN O 186 HIS d 59 HIS d 117 HIS f 45 GLN k 39 GLN l 31 HIS l 80 ASN ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 GLN n 169 HIS ** o 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102971 restraints weight = 49755.793| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.3126 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32662 Z= 0.225 Angle : 0.731 12.366 44149 Z= 0.369 Chirality : 0.046 0.310 4797 Planarity : 0.006 0.068 5412 Dihedral : 12.484 123.359 4969 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 3.63 % Allowed : 15.68 % Favored : 80.70 % 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: 0.01 (0.14), residues: 3763 helix: 0.59 (0.10), residues: 2448 sheet: -1.87 (1.00), residues: 31 loop : -0.95 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 278 TYR 0.040 0.002 TYR L 422 PHE 0.036 0.002 PHE e 18 TRP 0.018 0.001 TRP L 557 HIS 0.028 0.002 HIS M 422 Details of bonding type rmsd covalent geometry : bond 0.00529 (32654) covalent geometry : angle 0.73020 (44133) SS BOND : bond 0.00675 ( 8) SS BOND : angle 1.34307 ( 16) hydrogen bonds : bond 0.05280 ( 1697) hydrogen bonds : angle 4.75724 ( 4935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 960 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8321 (tpp) cc_final: 0.8077 (mmm) REVERT: K 24 SER cc_start: 0.9385 (m) cc_final: 0.8987 (p) REVERT: K 66 PHE cc_start: 0.8460 (m-80) cc_final: 0.8187 (m-80) REVERT: K 96 LEU cc_start: 0.8430 (mt) cc_final: 0.8116 (mp) REVERT: L 24 SER cc_start: 0.8332 (t) cc_final: 0.8029 (p) REVERT: L 26 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8459 (tt) REVERT: L 422 TYR cc_start: 0.9122 (p90) cc_final: 0.8564 (p90) REVERT: L 493 ILE cc_start: 0.8713 (tp) cc_final: 0.8425 (tp) REVERT: L 510 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7535 (mptt) REVERT: L 523 SER cc_start: 0.8404 (m) cc_final: 0.7788 (t) REVERT: L 598 ILE cc_start: 0.8687 (mt) cc_final: 0.8401 (mm) REVERT: M 59 ASP cc_start: 0.8369 (p0) cc_final: 0.7952 (p0) REVERT: M 155 ILE cc_start: 0.8917 (pt) cc_final: 0.8687 (pt) REVERT: M 157 SER cc_start: 0.8502 (m) cc_final: 0.8262 (p) REVERT: M 245 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8222 (mmt180) REVERT: M 271 MET cc_start: 0.8557 (mmm) cc_final: 0.8192 (mtp) REVERT: M 278 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8284 (mtp180) REVERT: M 308 SER cc_start: 0.9154 (m) cc_final: 0.8703 (p) REVERT: M 366 ASN cc_start: 0.9290 (t0) cc_final: 0.8782 (t0) REVERT: M 421 ASN cc_start: 0.7646 (p0) cc_final: 0.7033 (m-40) REVERT: N 91 ASN cc_start: 0.8228 (t0) cc_final: 0.7960 (t0) REVERT: N 175 MET cc_start: 0.8533 (tpp) cc_final: 0.8122 (mmt) REVERT: N 190 MET cc_start: 0.8564 (mtm) cc_final: 0.8056 (mtm) REVERT: N 225 MET cc_start: 0.8522 (mpp) cc_final: 0.8182 (mmm) REVERT: N 243 MET cc_start: 0.8247 (mmm) cc_final: 0.7898 (mmt) REVERT: N 271 MET cc_start: 0.9317 (mmm) cc_final: 0.9022 (mmm) REVERT: N 314 MET cc_start: 0.8387 (ttp) cc_final: 0.8184 (ttp) REVERT: O 62 VAL cc_start: 0.8011 (t) cc_final: 0.7663 (p) REVERT: O 92 GLN cc_start: 0.7739 (mp10) cc_final: 0.7220 (mt0) REVERT: O 113 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7586 (p) REVERT: O 125 ASP cc_start: 0.7966 (p0) cc_final: 0.7678 (p0) REVERT: O 149 HIS cc_start: 0.7495 (t-170) cc_final: 0.7188 (t-170) REVERT: O 195 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7961 (tp) REVERT: O 208 ASP cc_start: 0.7635 (t70) cc_final: 0.7142 (p0) REVERT: O 215 GLN cc_start: 0.8363 (mt0) cc_final: 0.7914 (mt0) REVERT: O 231 SER cc_start: 0.8943 (p) cc_final: 0.8580 (t) REVERT: O 258 TYR cc_start: 0.8138 (m-80) cc_final: 0.7872 (m-80) REVERT: O 306 ASN cc_start: 0.8934 (t0) cc_final: 0.8710 (t0) REVERT: U 101 ASN cc_start: 0.8643 (m-40) cc_final: 0.8197 (m-40) REVERT: U 151 LYS cc_start: 0.8845 (tptm) cc_final: 0.8638 (tttp) REVERT: Y 6 ARG cc_start: 0.5987 (mtm-85) cc_final: 0.5167 (ptp90) REVERT: Y 15 PRO cc_start: 0.8091 (Cg_exo) cc_final: 0.7540 (Cg_endo) REVERT: Y 18 THR cc_start: 0.7820 (m) cc_final: 0.7435 (p) REVERT: Y 46 ASN cc_start: 0.8921 (t0) cc_final: 0.8571 (t0) REVERT: Y 53 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7775 (mt-10) REVERT: Y 60 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7068 (ttp80) REVERT: Y 81 GLN cc_start: 0.8649 (tp40) cc_final: 0.8393 (tp40) REVERT: Y 83 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: Y 88 ASP cc_start: 0.8612 (t0) cc_final: 0.8223 (t0) REVERT: Y 133 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8325 (mt-10) REVERT: c 31 VAL cc_start: 0.8519 (t) cc_final: 0.8214 (m) REVERT: c 65 ASP cc_start: 0.9093 (m-30) cc_final: 0.8749 (m-30) REVERT: c 69 TYR cc_start: 0.8150 (t80) cc_final: 0.7635 (t80) REVERT: d 19 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8534 (mmm-85) REVERT: d 25 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7546 (mmtt) REVERT: d 90 MET cc_start: 0.8433 (ttp) cc_final: 0.8224 (ttm) REVERT: e 19 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7715 (ttm) REVERT: e 28 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8729 (mmmt) REVERT: e 37 GLU cc_start: 0.7735 (tm-30) cc_final: 0.6665 (tm-30) REVERT: e 82 GLN cc_start: 0.8383 (tp40) cc_final: 0.7700 (tt0) REVERT: f 10 HIS cc_start: 0.7447 (m-70) cc_final: 0.7033 (m-70) REVERT: f 28 ARG cc_start: 0.7526 (ptp-170) cc_final: 0.7305 (mtm110) REVERT: g 77 ASP cc_start: 0.8892 (p0) cc_final: 0.8539 (p0) REVERT: g 139 TYR cc_start: 0.7217 (t80) cc_final: 0.6665 (t80) REVERT: g 144 LYS cc_start: 0.8753 (mttt) cc_final: 0.8456 (mtpt) REVERT: h 74 TYR cc_start: 0.8682 (m-10) cc_final: 0.8463 (m-80) REVERT: h 86 ILE cc_start: 0.9112 (mm) cc_final: 0.8825 (mt) REVERT: h 90 ASN cc_start: 0.9145 (m-40) cc_final: 0.8882 (m-40) REVERT: h 132 ASN cc_start: 0.8313 (m-40) cc_final: 0.8033 (t0) REVERT: h 139 ILE cc_start: 0.8978 (mt) cc_final: 0.8761 (mt) REVERT: i 13 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8514 (mt0) REVERT: i 17 GLU cc_start: 0.8851 (tp30) cc_final: 0.8492 (tt0) REVERT: i 24 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8439 (tptt) REVERT: i 88 TYR cc_start: 0.8966 (m-80) cc_final: 0.8591 (m-80) REVERT: i 95 TYR cc_start: 0.9125 (m-10) cc_final: 0.8903 (m-10) REVERT: i 108 ASP cc_start: 0.7674 (t0) cc_final: 0.7341 (t0) REVERT: i 112 GLU cc_start: 0.8808 (mp0) cc_final: 0.8488 (mp0) REVERT: i 120 MET cc_start: 0.8675 (mtp) cc_final: 0.8239 (mtm) REVERT: j 78 ASP cc_start: 0.8229 (p0) cc_final: 0.7423 (m-30) REVERT: j 88 ASP cc_start: 0.8505 (t70) cc_final: 0.7937 (t70) REVERT: j 91 GLN cc_start: 0.8592 (mm110) cc_final: 0.8065 (mm110) REVERT: j 96 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8412 (mt-10) REVERT: k 30 ILE cc_start: 0.8880 (tp) cc_final: 0.8639 (tp) REVERT: k 39 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7791 (tp40) REVERT: k 48 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7605 (tpt170) REVERT: k 81 PHE cc_start: 0.8781 (t80) cc_final: 0.8496 (t80) REVERT: l 60 GLU cc_start: 0.8527 (mp0) cc_final: 0.8266 (mp0) REVERT: l 93 ASP cc_start: 0.9164 (m-30) cc_final: 0.8951 (m-30) REVERT: l 120 SER cc_start: 0.9112 (t) cc_final: 0.8666 (m) REVERT: l 164 ASN cc_start: 0.8247 (m-40) cc_final: 0.7957 (m-40) REVERT: m 62 ASP cc_start: 0.8658 (t0) cc_final: 0.8313 (t0) REVERT: m 75 ASN cc_start: 0.8282 (t0) cc_final: 0.7733 (t0) REVERT: m 100 PHE cc_start: 0.8682 (t80) cc_final: 0.8475 (t80) REVERT: n 114 MET cc_start: 0.8898 (ptt) cc_final: 0.8546 (ptt) REVERT: n 124 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8391 (mt0) REVERT: o 8 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7641 (ttp-170) REVERT: o 14 SER cc_start: 0.8667 (m) cc_final: 0.8440 (t) REVERT: o 16 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6180 (tt0) REVERT: o 18 ASP cc_start: 0.7763 (t70) cc_final: 0.7416 (t70) REVERT: o 20 GLU cc_start: 0.8371 (mp0) cc_final: 0.7926 (mp0) REVERT: o 25 PHE cc_start: 0.7871 (m-80) cc_final: 0.7655 (m-10) REVERT: o 52 THR cc_start: 0.9006 (m) cc_final: 0.8636 (p) REVERT: o 74 PHE cc_start: 0.8782 (t80) cc_final: 0.8101 (t80) REVERT: o 119 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6761 (mm-30) REVERT: p 12 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8157 (tm-30) REVERT: p 28 ASN cc_start: 0.8714 (t0) cc_final: 0.8485 (t0) REVERT: p 58 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8086 (mttt) REVERT: p 81 ASP cc_start: 0.8548 (t0) cc_final: 0.8239 (t0) REVERT: p 95 ASP cc_start: 0.8613 (m-30) cc_final: 0.7886 (m-30) REVERT: p 137 LYS cc_start: 0.8355 (tptp) cc_final: 0.7904 (tppt) REVERT: p 141 ASP cc_start: 0.8784 (m-30) cc_final: 0.8520 (m-30) outliers start: 123 outliers final: 72 residues processed: 1014 average time/residue: 0.1887 time to fit residues: 307.0453 Evaluate side-chains 948 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 867 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 139 MET Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 38 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 19 MET Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 13 GLN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 39 GLN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 96 GLU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 142 GLU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 27 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 305 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN L 207 ASN ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 170 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 142 GLN O 329 ASN f 45 GLN l 80 ASN ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 165 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103367 restraints weight = 49280.266| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32662 Z= 0.151 Angle : 0.648 11.518 44149 Z= 0.324 Chirality : 0.043 0.303 4797 Planarity : 0.005 0.066 5412 Dihedral : 12.030 120.949 4969 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 3.54 % Allowed : 17.65 % Favored : 78.81 % 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: 0.32 (0.14), residues: 3763 helix: 0.81 (0.10), residues: 2443 sheet: -1.67 (1.03), residues: 31 loop : -0.78 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 153 TYR 0.033 0.001 TYR L 422 PHE 0.029 0.002 PHE X 169 TRP 0.018 0.001 TRP L 66 HIS 0.005 0.001 HIS N 186 Details of bonding type rmsd covalent geometry : bond 0.00344 (32654) covalent geometry : angle 0.64748 (44133) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.02628 ( 16) hydrogen bonds : bond 0.04642 ( 1697) hydrogen bonds : angle 4.49547 ( 4935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 930 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8349 (tpp) cc_final: 0.8125 (mmm) REVERT: J 64 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8369 (mp) REVERT: J 77 GLU cc_start: 0.7502 (mp0) cc_final: 0.7296 (mp0) REVERT: J 152 MET cc_start: 0.8995 (tpp) cc_final: 0.8691 (tpp) REVERT: K 96 LEU cc_start: 0.8437 (mt) cc_final: 0.8170 (mp) REVERT: L 26 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8494 (tt) REVERT: L 199 GLN cc_start: 0.9207 (mp10) cc_final: 0.8245 (mp10) REVERT: L 493 ILE cc_start: 0.8607 (tp) cc_final: 0.8325 (tp) REVERT: L 510 LYS cc_start: 0.7773 (ptmt) cc_final: 0.7504 (mptt) REVERT: L 523 SER cc_start: 0.8368 (m) cc_final: 0.7776 (t) REVERT: L 598 ILE cc_start: 0.8663 (mt) cc_final: 0.8365 (mm) REVERT: M 271 MET cc_start: 0.8466 (mmm) cc_final: 0.7967 (mtp) REVERT: M 308 SER cc_start: 0.9189 (m) cc_final: 0.8709 (p) REVERT: M 366 ASN cc_start: 0.9270 (t0) cc_final: 0.8750 (t0) REVERT: M 421 ASN cc_start: 0.7555 (p0) cc_final: 0.6918 (m-40) REVERT: M 423 MET cc_start: 0.8034 (mmt) cc_final: 0.7813 (mmt) REVERT: N 2 ASN cc_start: 0.7012 (t0) cc_final: 0.6808 (t0) REVERT: N 68 MET cc_start: 0.9034 (mmt) cc_final: 0.8807 (mmp) REVERT: N 91 ASN cc_start: 0.8078 (t0) cc_final: 0.7815 (t0) REVERT: N 175 MET cc_start: 0.8417 (tpp) cc_final: 0.8215 (mmt) REVERT: N 225 MET cc_start: 0.8577 (mpp) cc_final: 0.8207 (mmm) REVERT: N 271 MET cc_start: 0.9289 (mmm) cc_final: 0.8994 (mmm) REVERT: N 293 TYR cc_start: 0.8340 (m-10) cc_final: 0.8110 (m-80) REVERT: N 296 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8520 (tt) REVERT: N 314 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: O 56 TYR cc_start: 0.7062 (m-80) cc_final: 0.6851 (m-80) REVERT: O 63 ASP cc_start: 0.7922 (t0) cc_final: 0.7683 (t0) REVERT: O 92 GLN cc_start: 0.7669 (mp10) cc_final: 0.7114 (mt0) REVERT: O 113 SER cc_start: 0.8325 (m) cc_final: 0.7705 (p) REVERT: O 149 HIS cc_start: 0.7489 (t-170) cc_final: 0.7166 (t-170) REVERT: O 195 LEU cc_start: 0.8149 (tt) cc_final: 0.7899 (tp) REVERT: O 208 ASP cc_start: 0.7703 (t70) cc_final: 0.7290 (p0) REVERT: O 215 GLN cc_start: 0.8476 (mt0) cc_final: 0.8102 (mt0) REVERT: O 231 SER cc_start: 0.8950 (p) cc_final: 0.8738 (p) REVERT: O 306 ASN cc_start: 0.8885 (t0) cc_final: 0.8680 (t0) REVERT: U 101 ASN cc_start: 0.8495 (m-40) cc_final: 0.8109 (m-40) REVERT: X 170 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.7974 (m-90) REVERT: Y 6 ARG cc_start: 0.6032 (mtm-85) cc_final: 0.5200 (ptp90) REVERT: Y 18 THR cc_start: 0.7787 (m) cc_final: 0.7462 (p) REVERT: Y 46 ASN cc_start: 0.8911 (t0) cc_final: 0.8490 (t0) REVERT: Y 53 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7700 (mt-10) REVERT: Y 60 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7295 (ttp80) REVERT: Y 88 ASP cc_start: 0.8582 (t0) cc_final: 0.8246 (t0) REVERT: Y 133 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8347 (mt-10) REVERT: c 31 VAL cc_start: 0.8671 (t) cc_final: 0.8382 (m) REVERT: c 65 ASP cc_start: 0.9074 (m-30) cc_final: 0.8759 (m-30) REVERT: c 67 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8683 (mm) REVERT: c 69 TYR cc_start: 0.8094 (t80) cc_final: 0.7358 (t80) REVERT: d 25 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7528 (mmtt) REVERT: d 34 MET cc_start: 0.8879 (mmm) cc_final: 0.8584 (mmm) REVERT: d 70 PHE cc_start: 0.9188 (t80) cc_final: 0.8952 (t80) REVERT: e 82 GLN cc_start: 0.8339 (tp40) cc_final: 0.7599 (tt0) REVERT: f 5 GLN cc_start: 0.7888 (mp10) cc_final: 0.7514 (mp10) REVERT: f 10 HIS cc_start: 0.7425 (m-70) cc_final: 0.6915 (m-70) REVERT: f 28 ARG cc_start: 0.7395 (ptp-170) cc_final: 0.7135 (mtp85) REVERT: g 77 ASP cc_start: 0.8815 (p0) cc_final: 0.8426 (p0) REVERT: g 144 LYS cc_start: 0.8755 (mttt) cc_final: 0.8538 (mtpt) REVERT: h 86 ILE cc_start: 0.9051 (mm) cc_final: 0.8758 (mt) REVERT: h 90 ASN cc_start: 0.9102 (m-40) cc_final: 0.8852 (m-40) REVERT: h 139 ILE cc_start: 0.8893 (mt) cc_final: 0.8688 (mt) REVERT: h 143 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7974 (mm-30) REVERT: h 182 SER cc_start: 0.8594 (m) cc_final: 0.8129 (t) REVERT: i 17 GLU cc_start: 0.8839 (tp30) cc_final: 0.8533 (tm-30) REVERT: i 24 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8294 (tptt) REVERT: i 88 TYR cc_start: 0.8954 (m-80) cc_final: 0.8541 (m-80) REVERT: i 95 TYR cc_start: 0.9011 (m-10) cc_final: 0.8700 (m-10) REVERT: i 108 ASP cc_start: 0.7870 (t0) cc_final: 0.7625 (t0) REVERT: i 112 GLU cc_start: 0.8841 (mp0) cc_final: 0.8532 (mp0) REVERT: i 120 MET cc_start: 0.8616 (mtp) cc_final: 0.8283 (mtm) REVERT: j 78 ASP cc_start: 0.8179 (p0) cc_final: 0.7461 (m-30) REVERT: j 88 ASP cc_start: 0.8451 (t70) cc_final: 0.7812 (t70) REVERT: j 91 GLN cc_start: 0.8618 (mm110) cc_final: 0.8053 (mm110) REVERT: j 95 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8229 (tm-30) REVERT: j 96 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8327 (mt-10) REVERT: k 30 ILE cc_start: 0.8840 (tp) cc_final: 0.8552 (tp) REVERT: k 48 ARG cc_start: 0.8134 (tpt90) cc_final: 0.7448 (tpt90) REVERT: k 60 MET cc_start: 0.9058 (tpp) cc_final: 0.8710 (tpp) REVERT: l 30 PHE cc_start: 0.7697 (t80) cc_final: 0.7465 (t80) REVERT: l 36 MET cc_start: 0.8456 (ttm) cc_final: 0.7560 (ttp) REVERT: l 60 GLU cc_start: 0.8464 (mp0) cc_final: 0.8177 (mp0) REVERT: l 120 SER cc_start: 0.9038 (t) cc_final: 0.8638 (m) REVERT: l 164 ASN cc_start: 0.8209 (m-40) cc_final: 0.7914 (m-40) REVERT: m 75 ASN cc_start: 0.8273 (t0) cc_final: 0.7682 (t0) REVERT: m 100 PHE cc_start: 0.8646 (t80) cc_final: 0.8417 (t80) REVERT: m 124 LYS cc_start: 0.8525 (tptt) cc_final: 0.8031 (ptmm) REVERT: n 114 MET cc_start: 0.8861 (ptt) cc_final: 0.8591 (ptt) REVERT: n 124 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8367 (mt0) REVERT: o 14 SER cc_start: 0.8641 (m) cc_final: 0.8422 (t) REVERT: o 16 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6218 (tt0) REVERT: o 25 PHE cc_start: 0.7750 (m-80) cc_final: 0.7377 (m-10) REVERT: o 119 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6791 (mm-30) REVERT: p 12 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8120 (tm-30) REVERT: p 58 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8287 (mttt) REVERT: p 81 ASP cc_start: 0.8560 (t0) cc_final: 0.8203 (t0) REVERT: p 137 LYS cc_start: 0.8321 (tptp) cc_final: 0.7892 (tppt) REVERT: p 141 ASP cc_start: 0.8810 (m-30) cc_final: 0.8554 (m-30) outliers start: 120 outliers final: 68 residues processed: 986 average time/residue: 0.1773 time to fit residues: 285.1233 Evaluate side-chains 930 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 856 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 207 ASN Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 170 TRP Chi-restraints excluded: chain c residue 38 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 149 ILE Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 88 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN L 200 GLN ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN N 204 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN O 292 HIS O 329 ASN e 34 HIS f 45 GLN h 132 ASN l 80 ASN l 84 HIS ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN p 107 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101870 restraints weight = 49774.107| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.28 r_work: 0.3112 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32662 Z= 0.156 Angle : 0.643 11.465 44149 Z= 0.320 Chirality : 0.043 0.270 4797 Planarity : 0.005 0.065 5412 Dihedral : 11.785 124.073 4969 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 3.60 % Allowed : 18.36 % Favored : 78.04 % 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: 0.44 (0.14), residues: 3763 helix: 0.93 (0.10), residues: 2441 sheet: -1.60 (1.04), residues: 31 loop : -0.77 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 83 TYR 0.029 0.002 TYR L 422 PHE 0.025 0.002 PHE X 169 TRP 0.012 0.001 TRP L 66 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00364 (32654) covalent geometry : angle 0.64280 (44133) SS BOND : bond 0.00291 ( 8) SS BOND : angle 0.91018 ( 16) hydrogen bonds : bond 0.04491 ( 1697) hydrogen bonds : angle 4.40567 ( 4935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 891 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8330 (tpp) cc_final: 0.8119 (mmm) REVERT: J 19 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8437 (mp) REVERT: J 64 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8289 (mp) REVERT: J 144 MET cc_start: 0.9014 (ttm) cc_final: 0.7986 (ttm) REVERT: J 152 MET cc_start: 0.8976 (tpp) cc_final: 0.8325 (tpp) REVERT: K 64 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7730 (mp) REVERT: K 96 LEU cc_start: 0.8397 (mt) cc_final: 0.7999 (mp) REVERT: L 26 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8454 (tt) REVERT: L 199 GLN cc_start: 0.9256 (mp10) cc_final: 0.8344 (mp10) REVERT: L 202 MET cc_start: 0.9003 (mmp) cc_final: 0.8705 (mmt) REVERT: L 338 MET cc_start: 0.8852 (tpp) cc_final: 0.8623 (ttt) REVERT: L 493 ILE cc_start: 0.8583 (tp) cc_final: 0.8291 (tp) REVERT: L 510 LYS cc_start: 0.7660 (ptmt) cc_final: 0.7362 (mmtt) REVERT: L 523 SER cc_start: 0.8305 (m) cc_final: 0.7718 (t) REVERT: L 598 ILE cc_start: 0.8643 (mt) cc_final: 0.8348 (mm) REVERT: M 59 ASP cc_start: 0.8682 (p0) cc_final: 0.8360 (p0) REVERT: M 245 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8232 (mmt180) REVERT: M 271 MET cc_start: 0.8457 (mmm) cc_final: 0.8217 (mmm) REVERT: M 302 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9047 (mmm) REVERT: M 308 SER cc_start: 0.9197 (m) cc_final: 0.8690 (p) REVERT: M 366 ASN cc_start: 0.9294 (t0) cc_final: 0.8804 (t0) REVERT: M 410 MET cc_start: 0.8820 (ttm) cc_final: 0.8527 (ttp) REVERT: M 421 ASN cc_start: 0.7572 (p0) cc_final: 0.6982 (m-40) REVERT: N 2 ASN cc_start: 0.7089 (t0) cc_final: 0.6848 (t0) REVERT: N 91 ASN cc_start: 0.7864 (t0) cc_final: 0.7563 (t0) REVERT: N 190 MET cc_start: 0.8347 (mtm) cc_final: 0.8052 (mtm) REVERT: N 225 MET cc_start: 0.8546 (mpp) cc_final: 0.8155 (mmm) REVERT: N 243 MET cc_start: 0.8250 (mmm) cc_final: 0.7555 (mmm) REVERT: N 271 MET cc_start: 0.9274 (mmm) cc_final: 0.8994 (mmm) REVERT: N 293 TYR cc_start: 0.8330 (m-10) cc_final: 0.8069 (m-80) REVERT: N 296 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8470 (tt) REVERT: N 314 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: O 92 GLN cc_start: 0.7517 (mp10) cc_final: 0.7013 (mt0) REVERT: O 149 HIS cc_start: 0.7471 (t-170) cc_final: 0.7097 (t-170) REVERT: O 176 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: O 202 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7036 (m170) REVERT: O 208 ASP cc_start: 0.7694 (t70) cc_final: 0.7109 (p0) REVERT: O 215 GLN cc_start: 0.8488 (mt0) cc_final: 0.8111 (mt0) REVERT: O 231 SER cc_start: 0.8941 (p) cc_final: 0.8720 (p) REVERT: U 101 ASN cc_start: 0.8494 (m-40) cc_final: 0.8099 (m-40) REVERT: X 170 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.7898 (m-90) REVERT: Y 6 ARG cc_start: 0.6022 (mtm-85) cc_final: 0.5177 (ptp90) REVERT: Y 13 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: Y 15 PRO cc_start: 0.8087 (Cg_exo) cc_final: 0.7596 (Cg_endo) REVERT: Y 18 THR cc_start: 0.7540 (m) cc_final: 0.7082 (p) REVERT: Y 46 ASN cc_start: 0.8951 (t0) cc_final: 0.8629 (t0) REVERT: Y 53 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7731 (mt-10) REVERT: Y 60 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7270 (ttp80) REVERT: Y 88 ASP cc_start: 0.8638 (t0) cc_final: 0.8239 (t0) REVERT: Y 133 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8293 (mt-10) REVERT: c 31 VAL cc_start: 0.8652 (t) cc_final: 0.8364 (m) REVERT: c 65 ASP cc_start: 0.9045 (m-30) cc_final: 0.8732 (m-30) REVERT: c 69 TYR cc_start: 0.8070 (t80) cc_final: 0.7307 (t80) REVERT: d 2 MET cc_start: 0.6299 (tpp) cc_final: 0.5848 (tpp) REVERT: d 25 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7505 (mmtt) REVERT: d 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8543 (mmm) REVERT: d 70 PHE cc_start: 0.9172 (t80) cc_final: 0.8971 (t80) REVERT: e 37 GLU cc_start: 0.8480 (tt0) cc_final: 0.8164 (tt0) REVERT: e 82 GLN cc_start: 0.8334 (tp40) cc_final: 0.7639 (tt0) REVERT: f 28 ARG cc_start: 0.7315 (ptp-170) cc_final: 0.7065 (mtp85) REVERT: f 33 LYS cc_start: 0.8253 (tptt) cc_final: 0.7717 (ttpt) REVERT: g 77 ASP cc_start: 0.8814 (p0) cc_final: 0.8393 (p0) REVERT: g 144 LYS cc_start: 0.8808 (mttt) cc_final: 0.8546 (mtpt) REVERT: h 86 ILE cc_start: 0.9017 (mm) cc_final: 0.8731 (mt) REVERT: h 90 ASN cc_start: 0.9123 (m-40) cc_final: 0.8803 (m-40) REVERT: h 139 ILE cc_start: 0.8920 (mt) cc_final: 0.8700 (mt) REVERT: h 182 SER cc_start: 0.8581 (m) cc_final: 0.8099 (t) REVERT: i 17 GLU cc_start: 0.8881 (tp30) cc_final: 0.8572 (tm-30) REVERT: i 24 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8212 (tptt) REVERT: i 88 TYR cc_start: 0.8956 (m-80) cc_final: 0.8496 (m-80) REVERT: i 95 TYR cc_start: 0.9007 (m-10) cc_final: 0.8662 (m-10) REVERT: i 108 ASP cc_start: 0.7686 (t0) cc_final: 0.7412 (t0) REVERT: j 78 ASP cc_start: 0.8300 (p0) cc_final: 0.7557 (m-30) REVERT: j 88 ASP cc_start: 0.8478 (t70) cc_final: 0.7828 (t70) REVERT: j 91 GLN cc_start: 0.8576 (mm110) cc_final: 0.7990 (mm110) REVERT: j 95 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8284 (tm-30) REVERT: j 96 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8299 (mt-10) REVERT: k 30 ILE cc_start: 0.8658 (tp) cc_final: 0.8402 (tp) REVERT: k 39 GLN cc_start: 0.8319 (tp40) cc_final: 0.7783 (tp40) REVERT: k 48 ARG cc_start: 0.7993 (tpt90) cc_final: 0.7510 (tpt90) REVERT: k 60 MET cc_start: 0.9127 (tpp) cc_final: 0.8742 (tpp) REVERT: l 36 MET cc_start: 0.8437 (ttm) cc_final: 0.7637 (ttp) REVERT: l 60 GLU cc_start: 0.8428 (mp0) cc_final: 0.8185 (mp0) REVERT: l 85 GLU cc_start: 0.8046 (pt0) cc_final: 0.7757 (pt0) REVERT: l 120 SER cc_start: 0.9043 (t) cc_final: 0.8593 (m) REVERT: l 164 ASN cc_start: 0.8216 (m-40) cc_final: 0.7930 (m-40) REVERT: m 62 ASP cc_start: 0.8642 (t0) cc_final: 0.8313 (t0) REVERT: m 75 ASN cc_start: 0.8476 (t0) cc_final: 0.7873 (t0) REVERT: m 100 PHE cc_start: 0.8675 (t80) cc_final: 0.8424 (t80) REVERT: m 124 LYS cc_start: 0.8482 (tptt) cc_final: 0.7981 (ptmm) REVERT: n 44 MET cc_start: 0.8469 (tpp) cc_final: 0.7986 (tpp) REVERT: n 124 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8444 (mt0) REVERT: o 8 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7620 (ttp-170) REVERT: o 14 SER cc_start: 0.8627 (m) cc_final: 0.8425 (t) REVERT: o 16 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6146 (tt0) REVERT: o 20 GLU cc_start: 0.8577 (mp0) cc_final: 0.8321 (mp0) REVERT: o 25 PHE cc_start: 0.7797 (m-80) cc_final: 0.7445 (m-80) REVERT: o 29 LEU cc_start: 0.8050 (tp) cc_final: 0.7833 (tp) REVERT: o 119 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6743 (mm-30) REVERT: p 12 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8173 (tm-30) REVERT: p 58 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8320 (mttt) REVERT: p 81 ASP cc_start: 0.8493 (t0) cc_final: 0.8278 (t0) REVERT: p 127 LYS cc_start: 0.9054 (tppp) cc_final: 0.8798 (ttmm) REVERT: p 137 LYS cc_start: 0.8298 (tptp) cc_final: 0.7852 (tppt) outliers start: 122 outliers final: 79 residues processed: 955 average time/residue: 0.1824 time to fit residues: 284.6326 Evaluate side-chains 933 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 842 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 207 ASN Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 202 HIS Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 170 TRP Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 38 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 149 ILE Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 128 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN L 207 ASN L 270 ASN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN O 329 ASN d 61 GLN f 45 GLN i 74 HIS l 80 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102153 restraints weight = 49448.608| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3115 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32662 Z= 0.149 Angle : 0.631 11.211 44149 Z= 0.313 Chirality : 0.042 0.274 4797 Planarity : 0.005 0.064 5412 Dihedral : 11.581 124.970 4969 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 3.71 % Allowed : 18.66 % Favored : 77.63 % 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: 0.54 (0.14), residues: 3763 helix: 0.98 (0.10), residues: 2462 sheet: -1.64 (1.00), residues: 31 loop : -0.73 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 171 TYR 0.026 0.001 TYR L 422 PHE 0.023 0.001 PHE N 292 TRP 0.010 0.001 TRP L 557 HIS 0.008 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00349 (32654) covalent geometry : angle 0.63064 (44133) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.88314 ( 16) hydrogen bonds : bond 0.04360 ( 1697) hydrogen bonds : angle 4.34307 ( 4935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 883 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8334 (tpp) cc_final: 0.8128 (mmm) REVERT: J 19 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8502 (mp) REVERT: J 49 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.8002 (m) REVERT: J 64 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8206 (mp) REVERT: J 144 MET cc_start: 0.9057 (ttm) cc_final: 0.7763 (ttm) REVERT: J 152 MET cc_start: 0.8956 (tpp) cc_final: 0.8054 (tpp) REVERT: K 64 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7730 (mp) REVERT: K 96 LEU cc_start: 0.8355 (mt) cc_final: 0.7953 (mp) REVERT: L 202 MET cc_start: 0.9040 (mmp) cc_final: 0.8818 (mmt) REVERT: L 262 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.7940 (mmp80) REVERT: L 493 ILE cc_start: 0.8569 (tp) cc_final: 0.8264 (tp) REVERT: L 510 LYS cc_start: 0.7679 (ptmt) cc_final: 0.7385 (mptt) REVERT: L 513 MET cc_start: 0.6740 (tmm) cc_final: 0.6500 (tmm) REVERT: L 523 SER cc_start: 0.8257 (m) cc_final: 0.7718 (t) REVERT: L 544 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8455 (tt) REVERT: L 598 ILE cc_start: 0.8640 (mt) cc_final: 0.8354 (mm) REVERT: M 59 ASP cc_start: 0.8641 (p0) cc_final: 0.8331 (p0) REVERT: M 207 MET cc_start: 0.8656 (ttp) cc_final: 0.8314 (ttm) REVERT: M 245 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8181 (mmt180) REVERT: M 271 MET cc_start: 0.8460 (mmm) cc_final: 0.8243 (mmm) REVERT: M 302 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8993 (mmm) REVERT: M 410 MET cc_start: 0.8834 (ttm) cc_final: 0.8582 (ttp) REVERT: M 421 ASN cc_start: 0.7726 (p0) cc_final: 0.7063 (m-40) REVERT: N 2 ASN cc_start: 0.7155 (t0) cc_final: 0.6927 (t0) REVERT: N 91 ASN cc_start: 0.7798 (t0) cc_final: 0.6991 (m-40) REVERT: N 190 MET cc_start: 0.8388 (mtm) cc_final: 0.8032 (mtm) REVERT: N 225 MET cc_start: 0.8547 (mpp) cc_final: 0.8171 (mmm) REVERT: N 271 MET cc_start: 0.9268 (mmm) cc_final: 0.8977 (mmm) REVERT: N 314 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: O 92 GLN cc_start: 0.7534 (mp10) cc_final: 0.7030 (mt0) REVERT: O 158 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6671 (m) REVERT: O 176 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: O 208 ASP cc_start: 0.7787 (t70) cc_final: 0.7185 (p0) REVERT: O 215 GLN cc_start: 0.8495 (mt0) cc_final: 0.8105 (mt0) REVERT: O 231 SER cc_start: 0.8938 (p) cc_final: 0.8706 (p) REVERT: O 236 ASP cc_start: 0.7565 (m-30) cc_final: 0.7008 (m-30) REVERT: U 101 ASN cc_start: 0.8445 (m-40) cc_final: 0.8181 (m110) REVERT: Y 6 ARG cc_start: 0.6019 (mtm-85) cc_final: 0.5196 (ptp90) REVERT: Y 13 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: Y 15 PRO cc_start: 0.8025 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: Y 18 THR cc_start: 0.7447 (m) cc_final: 0.7010 (p) REVERT: Y 46 ASN cc_start: 0.9012 (t0) cc_final: 0.8726 (t0) REVERT: Y 53 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7724 (mt-10) REVERT: Y 60 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7257 (ttp80) REVERT: Y 88 ASP cc_start: 0.8627 (t0) cc_final: 0.8241 (t0) REVERT: Y 133 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8290 (mt-10) REVERT: c 31 VAL cc_start: 0.8671 (t) cc_final: 0.8395 (m) REVERT: c 65 ASP cc_start: 0.9050 (m-30) cc_final: 0.8726 (m-30) REVERT: c 68 GLU cc_start: 0.8120 (tp30) cc_final: 0.7357 (tm-30) REVERT: c 69 TYR cc_start: 0.8048 (t80) cc_final: 0.7301 (t80) REVERT: d 2 MET cc_start: 0.6489 (tpp) cc_final: 0.6102 (tpp) REVERT: d 25 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7557 (mmtt) REVERT: d 34 MET cc_start: 0.8886 (mmm) cc_final: 0.8525 (mmm) REVERT: d 70 PHE cc_start: 0.9198 (t80) cc_final: 0.8993 (t80) REVERT: e 28 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8707 (mmmt) REVERT: e 37 GLU cc_start: 0.8433 (tt0) cc_final: 0.8081 (tt0) REVERT: e 74 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6766 (tmm160) REVERT: e 82 GLN cc_start: 0.8421 (tp40) cc_final: 0.7749 (tt0) REVERT: f 28 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7098 (mtp85) REVERT: f 33 LYS cc_start: 0.8039 (tptt) cc_final: 0.7437 (ttpt) REVERT: f 47 GLU cc_start: 0.8793 (tp30) cc_final: 0.8562 (tp30) REVERT: g 77 ASP cc_start: 0.8819 (p0) cc_final: 0.8396 (p0) REVERT: g 144 LYS cc_start: 0.8809 (mttt) cc_final: 0.8558 (mtpt) REVERT: h 86 ILE cc_start: 0.9014 (mm) cc_final: 0.8721 (mt) REVERT: h 90 ASN cc_start: 0.9130 (m-40) cc_final: 0.8801 (m110) REVERT: h 182 SER cc_start: 0.8626 (m) cc_final: 0.8012 (t) REVERT: i 17 GLU cc_start: 0.8883 (tp30) cc_final: 0.8610 (tm-30) REVERT: i 24 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8128 (tptt) REVERT: i 87 LYS cc_start: 0.9083 (tttp) cc_final: 0.8881 (tttt) REVERT: i 108 ASP cc_start: 0.7636 (t0) cc_final: 0.7367 (t0) REVERT: j 76 ASP cc_start: 0.8420 (m-30) cc_final: 0.7986 (m-30) REVERT: j 78 ASP cc_start: 0.8251 (p0) cc_final: 0.7557 (m-30) REVERT: j 88 ASP cc_start: 0.8426 (t70) cc_final: 0.7789 (t70) REVERT: j 91 GLN cc_start: 0.8554 (mm110) cc_final: 0.7976 (mm110) REVERT: j 95 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8438 (tm-30) REVERT: j 96 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8364 (mt-10) REVERT: k 30 ILE cc_start: 0.8612 (tp) cc_final: 0.8330 (tp) REVERT: k 39 GLN cc_start: 0.8286 (tp40) cc_final: 0.7361 (tp40) REVERT: k 60 MET cc_start: 0.9129 (tpp) cc_final: 0.8759 (tpp) REVERT: l 36 MET cc_start: 0.8480 (ttm) cc_final: 0.7643 (ttp) REVERT: l 85 GLU cc_start: 0.8001 (pt0) cc_final: 0.7730 (pt0) REVERT: l 120 SER cc_start: 0.9035 (t) cc_final: 0.8576 (m) REVERT: l 164 ASN cc_start: 0.8219 (m-40) cc_final: 0.7934 (m-40) REVERT: m 62 ASP cc_start: 0.8606 (t0) cc_final: 0.8283 (t0) REVERT: m 75 ASN cc_start: 0.8547 (t0) cc_final: 0.7924 (t0) REVERT: m 98 LEU cc_start: 0.9152 (mt) cc_final: 0.8941 (mm) REVERT: m 100 PHE cc_start: 0.8701 (t80) cc_final: 0.8439 (t80) REVERT: m 124 LYS cc_start: 0.8465 (tptt) cc_final: 0.7983 (ptmm) REVERT: n 44 MET cc_start: 0.8505 (tpp) cc_final: 0.8036 (tpp) REVERT: n 124 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8510 (mt0) REVERT: n 149 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7666 (pt) REVERT: o 7 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7746 (ttm-80) REVERT: o 8 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7644 (ttp-170) REVERT: o 14 SER cc_start: 0.8602 (m) cc_final: 0.8372 (p) REVERT: o 16 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6400 (tt0) REVERT: o 20 GLU cc_start: 0.8621 (mp0) cc_final: 0.8304 (mp0) REVERT: o 25 PHE cc_start: 0.7758 (m-80) cc_final: 0.7374 (m-80) REVERT: o 29 LEU cc_start: 0.8087 (tp) cc_final: 0.7874 (tp) REVERT: o 84 GLN cc_start: 0.9034 (tp40) cc_final: 0.8633 (tp-100) REVERT: o 119 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6747 (mm-30) REVERT: p 12 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8155 (tm-30) REVERT: p 53 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8092 (mm-30) REVERT: p 58 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8443 (mttt) REVERT: p 81 ASP cc_start: 0.8517 (t0) cc_final: 0.8168 (t0) outliers start: 126 outliers final: 77 residues processed: 951 average time/residue: 0.1803 time to fit residues: 279.7777 Evaluate side-chains 940 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 848 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 314 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 38 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 137 SER Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 142 GLU Chi-restraints excluded: chain n residue 149 ILE Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain o residue 110 GLN Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 295 optimal weight: 0.1980 chunk 365 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN O 329 ASN d 61 GLN i 13 GLN k 39 GLN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103024 restraints weight = 49347.736| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.27 r_work: 0.3127 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32662 Z= 0.137 Angle : 0.625 10.909 44149 Z= 0.310 Chirality : 0.042 0.315 4797 Planarity : 0.005 0.065 5412 Dihedral : 11.384 125.057 4968 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 3.48 % Allowed : 19.51 % Favored : 77.01 % 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 (0.14), residues: 3763 helix: 1.09 (0.10), residues: 2456 sheet: -1.65 (0.90), residues: 35 loop : -0.71 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG d 55 TYR 0.024 0.001 TYR L 422 PHE 0.021 0.001 PHE N 292 TRP 0.011 0.001 TRP X 170 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00318 (32654) covalent geometry : angle 0.62503 (44133) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.82897 ( 16) hydrogen bonds : bond 0.04215 ( 1697) hydrogen bonds : angle 4.28882 ( 4935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 874 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8308 (tpp) cc_final: 0.8006 (mmm) REVERT: J 19 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8459 (mp) REVERT: J 144 MET cc_start: 0.9055 (ttm) cc_final: 0.7745 (ttm) REVERT: J 152 MET cc_start: 0.8993 (tpp) cc_final: 0.8008 (tpp) REVERT: K 64 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (mp) REVERT: K 96 LEU cc_start: 0.8328 (mt) cc_final: 0.7935 (mp) REVERT: L 493 ILE cc_start: 0.8535 (tp) cc_final: 0.8238 (tp) REVERT: L 510 LYS cc_start: 0.7640 (ptmt) cc_final: 0.7348 (mptt) REVERT: L 513 MET cc_start: 0.6746 (tmm) cc_final: 0.6487 (tmm) REVERT: L 523 SER cc_start: 0.8134 (m) cc_final: 0.7688 (t) REVERT: L 544 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8398 (tt) REVERT: L 598 ILE cc_start: 0.8586 (mt) cc_final: 0.8326 (mm) REVERT: M 59 ASP cc_start: 0.8581 (p0) cc_final: 0.8300 (p0) REVERT: M 165 ILE cc_start: 0.8968 (mm) cc_final: 0.8730 (mp) REVERT: M 245 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.8087 (mmt180) REVERT: M 271 MET cc_start: 0.8354 (mmm) cc_final: 0.8146 (mmm) REVERT: M 302 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8951 (mmm) REVERT: M 307 TRP cc_start: 0.8501 (m-10) cc_final: 0.8240 (m-10) REVERT: M 410 MET cc_start: 0.8835 (ttm) cc_final: 0.8632 (ttp) REVERT: M 421 ASN cc_start: 0.7994 (p0) cc_final: 0.7219 (m-40) REVERT: M 423 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7331 (mtt) REVERT: M 437 MET cc_start: 0.9238 (mpp) cc_final: 0.8866 (mpp) REVERT: N 2 ASN cc_start: 0.7105 (t0) cc_final: 0.6871 (t0) REVERT: N 91 ASN cc_start: 0.7764 (t0) cc_final: 0.6958 (m-40) REVERT: N 175 MET cc_start: 0.8559 (tpp) cc_final: 0.8208 (tpp) REVERT: N 190 MET cc_start: 0.8478 (mtm) cc_final: 0.8083 (mtm) REVERT: N 225 MET cc_start: 0.8589 (mpp) cc_final: 0.8166 (mmm) REVERT: N 271 MET cc_start: 0.9243 (mmm) cc_final: 0.8985 (mmm) REVERT: N 296 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (tt) REVERT: N 314 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (ttm) REVERT: O 92 GLN cc_start: 0.7494 (mp10) cc_final: 0.6944 (mt0) REVERT: O 149 HIS cc_start: 0.7293 (t-170) cc_final: 0.6848 (t-170) REVERT: O 208 ASP cc_start: 0.7822 (t70) cc_final: 0.7086 (p0) REVERT: O 215 GLN cc_start: 0.8493 (mt0) cc_final: 0.8098 (mt0) REVERT: O 231 SER cc_start: 0.8971 (p) cc_final: 0.8716 (p) REVERT: O 236 ASP cc_start: 0.7572 (m-30) cc_final: 0.7070 (m-30) REVERT: Y 6 ARG cc_start: 0.5993 (mtm-85) cc_final: 0.5725 (ppt170) REVERT: Y 13 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: Y 46 ASN cc_start: 0.8934 (t0) cc_final: 0.8699 (t0) REVERT: Y 53 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7700 (mt-10) REVERT: Y 60 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7191 (ttp80) REVERT: Y 88 ASP cc_start: 0.8629 (t0) cc_final: 0.8211 (t0) REVERT: Y 133 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8283 (mt-10) REVERT: c 31 VAL cc_start: 0.8637 (t) cc_final: 0.8371 (m) REVERT: c 65 ASP cc_start: 0.9056 (m-30) cc_final: 0.8714 (m-30) REVERT: c 68 GLU cc_start: 0.8109 (tp30) cc_final: 0.7348 (tm-30) REVERT: c 69 TYR cc_start: 0.8006 (t80) cc_final: 0.7262 (t80) REVERT: d 2 MET cc_start: 0.6571 (tpp) cc_final: 0.6185 (tpp) REVERT: d 25 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7410 (mmtt) REVERT: d 34 MET cc_start: 0.8849 (mmm) cc_final: 0.8476 (mmm) REVERT: d 70 PHE cc_start: 0.9187 (t80) cc_final: 0.8969 (t80) REVERT: e 28 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8719 (mmmt) REVERT: e 37 GLU cc_start: 0.8457 (tt0) cc_final: 0.8088 (tt0) REVERT: e 62 ASP cc_start: 0.8146 (m-30) cc_final: 0.7655 (m-30) REVERT: e 74 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6765 (tmm160) REVERT: e 82 GLN cc_start: 0.8469 (tp40) cc_final: 0.7693 (tt0) REVERT: f 5 GLN cc_start: 0.7638 (mp10) cc_final: 0.6934 (mp10) REVERT: f 33 LYS cc_start: 0.8190 (tptt) cc_final: 0.7572 (ttpt) REVERT: f 47 GLU cc_start: 0.8803 (tp30) cc_final: 0.8568 (tp30) REVERT: g 77 ASP cc_start: 0.8838 (p0) cc_final: 0.8412 (p0) REVERT: g 135 MET cc_start: 0.8893 (ttm) cc_final: 0.8618 (mtp) REVERT: g 144 LYS cc_start: 0.8801 (mttt) cc_final: 0.8517 (mtpt) REVERT: h 55 PHE cc_start: 0.9182 (t80) cc_final: 0.8964 (t80) REVERT: h 86 ILE cc_start: 0.8957 (mm) cc_final: 0.8669 (mt) REVERT: h 90 ASN cc_start: 0.9097 (m-40) cc_final: 0.8766 (m110) REVERT: h 182 SER cc_start: 0.8618 (m) cc_final: 0.8024 (t) REVERT: i 17 GLU cc_start: 0.8871 (tp30) cc_final: 0.8586 (tm-30) REVERT: i 87 LYS cc_start: 0.9034 (tttp) cc_final: 0.8727 (ttpp) REVERT: i 108 ASP cc_start: 0.7666 (t0) cc_final: 0.7378 (t0) REVERT: j 76 ASP cc_start: 0.8425 (m-30) cc_final: 0.7992 (m-30) REVERT: j 78 ASP cc_start: 0.8201 (p0) cc_final: 0.7540 (m-30) REVERT: j 88 ASP cc_start: 0.8368 (t70) cc_final: 0.7740 (t70) REVERT: j 91 GLN cc_start: 0.8569 (mm110) cc_final: 0.8005 (mm110) REVERT: j 95 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8444 (tm-30) REVERT: j 96 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8218 (mt-10) REVERT: k 30 ILE cc_start: 0.8585 (tp) cc_final: 0.8244 (tp) REVERT: k 48 ARG cc_start: 0.8324 (tpt90) cc_final: 0.7687 (tpm170) REVERT: k 60 MET cc_start: 0.9068 (tpp) cc_final: 0.8762 (tpp) REVERT: l 36 MET cc_start: 0.8441 (ttm) cc_final: 0.7608 (ttp) REVERT: l 85 GLU cc_start: 0.8079 (pt0) cc_final: 0.7873 (pt0) REVERT: l 164 ASN cc_start: 0.8261 (m-40) cc_final: 0.7974 (m-40) REVERT: m 50 GLN cc_start: 0.8758 (tt0) cc_final: 0.8476 (tt0) REVERT: m 75 ASN cc_start: 0.8559 (t0) cc_final: 0.7951 (t0) REVERT: m 100 PHE cc_start: 0.8724 (t80) cc_final: 0.8434 (t80) REVERT: m 124 LYS cc_start: 0.8462 (tptt) cc_final: 0.7954 (ptmm) REVERT: n 17 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8308 (mp) REVERT: n 44 MET cc_start: 0.8459 (tpp) cc_final: 0.8004 (tpp) REVERT: n 124 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8523 (mt0) REVERT: o 7 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7743 (ttm-80) REVERT: o 8 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: o 14 SER cc_start: 0.8586 (m) cc_final: 0.8368 (p) REVERT: o 16 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6355 (tt0) REVERT: o 20 GLU cc_start: 0.8581 (mp0) cc_final: 0.8241 (mp0) REVERT: o 29 LEU cc_start: 0.8043 (tp) cc_final: 0.7832 (tp) REVERT: o 84 GLN cc_start: 0.9002 (tp40) cc_final: 0.8622 (tp-100) REVERT: o 119 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6775 (mm-30) REVERT: p 12 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8075 (tm-30) REVERT: p 53 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8087 (mm-30) REVERT: p 58 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8452 (mttt) REVERT: p 81 ASP cc_start: 0.8528 (t0) cc_final: 0.8154 (t0) outliers start: 118 outliers final: 71 residues processed: 940 average time/residue: 0.1820 time to fit residues: 279.6523 Evaluate side-chains 921 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 838 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 423 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 198 TYR Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain c residue 38 LYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 137 SER Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain o residue 110 GLN Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 342 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 292 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 ASN O 176 GLN O 329 ASN l 100 ASN l 115 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101860 restraints weight = 49754.612| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.27 r_work: 0.3110 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32662 Z= 0.155 Angle : 0.650 13.438 44149 Z= 0.319 Chirality : 0.043 0.329 4797 Planarity : 0.005 0.064 5412 Dihedral : 11.300 125.948 4968 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 19.95 % Favored : 76.75 % 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: 0.68 (0.14), residues: 3763 helix: 1.11 (0.10), residues: 2455 sheet: -1.60 (0.89), residues: 34 loop : -0.69 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG l 114 TYR 0.028 0.001 TYR O 164 PHE 0.022 0.001 PHE N 292 TRP 0.009 0.001 TRP j 71 HIS 0.008 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00370 (32654) covalent geometry : angle 0.64873 (44133) SS BOND : bond 0.00313 ( 8) SS BOND : angle 2.21817 ( 16) hydrogen bonds : bond 0.04257 ( 1697) hydrogen bonds : angle 4.29500 ( 4935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 862 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8220 (tpp) cc_final: 0.7962 (mmm) REVERT: J 19 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8460 (mp) REVERT: J 64 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8189 (mp) REVERT: J 144 MET cc_start: 0.9100 (ttm) cc_final: 0.7787 (ttm) REVERT: J 152 MET cc_start: 0.8998 (tpp) cc_final: 0.7965 (tpp) REVERT: K 64 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7744 (mp) REVERT: K 96 LEU cc_start: 0.8340 (mt) cc_final: 0.7945 (mp) REVERT: L 262 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8819 (mtp85) REVERT: L 338 MET cc_start: 0.8747 (tpp) cc_final: 0.8489 (ttt) REVERT: L 459 PHE cc_start: 0.8268 (m-10) cc_final: 0.7917 (m-10) REVERT: L 493 ILE cc_start: 0.8554 (tp) cc_final: 0.8257 (tp) REVERT: L 510 LYS cc_start: 0.7596 (ptmt) cc_final: 0.7364 (mptt) REVERT: L 513 MET cc_start: 0.6721 (tmm) cc_final: 0.6429 (tmm) REVERT: L 523 SER cc_start: 0.8125 (m) cc_final: 0.7693 (t) REVERT: L 544 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8498 (tt) REVERT: L 598 ILE cc_start: 0.8584 (mt) cc_final: 0.8348 (mm) REVERT: M 59 ASP cc_start: 0.8595 (p0) cc_final: 0.8337 (p0) REVERT: M 165 ILE cc_start: 0.8987 (mm) cc_final: 0.8731 (mp) REVERT: M 245 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.8028 (mmt180) REVERT: M 302 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8952 (mmm) REVERT: M 410 MET cc_start: 0.8803 (ttm) cc_final: 0.8597 (ttp) REVERT: M 421 ASN cc_start: 0.7943 (p0) cc_final: 0.7173 (m-40) REVERT: N 2 ASN cc_start: 0.7153 (t0) cc_final: 0.6896 (t0) REVERT: N 91 ASN cc_start: 0.7763 (t0) cc_final: 0.6955 (m-40) REVERT: N 175 MET cc_start: 0.8559 (tpp) cc_final: 0.8210 (tpp) REVERT: N 190 MET cc_start: 0.8476 (mtm) cc_final: 0.8154 (mtm) REVERT: N 225 MET cc_start: 0.8611 (mpp) cc_final: 0.8330 (mpp) REVERT: N 271 MET cc_start: 0.9232 (mmm) cc_final: 0.8960 (mmm) REVERT: N 296 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (tt) REVERT: N 314 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8086 (ttm) REVERT: N 332 MET cc_start: 0.8680 (mmm) cc_final: 0.7622 (mtp) REVERT: N 335 MET cc_start: 0.8913 (mtp) cc_final: 0.8236 (ttm) REVERT: O 92 GLN cc_start: 0.7523 (mp10) cc_final: 0.6963 (mt0) REVERT: O 208 ASP cc_start: 0.7859 (t70) cc_final: 0.7125 (p0) REVERT: O 215 GLN cc_start: 0.8486 (mt0) cc_final: 0.8088 (mt0) REVERT: O 231 SER cc_start: 0.8974 (p) cc_final: 0.8739 (p) REVERT: X 166 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8293 (mtt90) REVERT: Y 6 ARG cc_start: 0.5990 (mtm-85) cc_final: 0.5727 (ppt170) REVERT: Y 46 ASN cc_start: 0.8924 (t0) cc_final: 0.8701 (t0) REVERT: Y 53 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7693 (mt-10) REVERT: Y 60 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7313 (ttp80) REVERT: Y 88 ASP cc_start: 0.8658 (t0) cc_final: 0.8256 (t0) REVERT: Y 133 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8273 (mt-10) REVERT: c 31 VAL cc_start: 0.8650 (t) cc_final: 0.8388 (m) REVERT: c 65 ASP cc_start: 0.9050 (m-30) cc_final: 0.8679 (m-30) REVERT: c 68 GLU cc_start: 0.8115 (tp30) cc_final: 0.7362 (tm-30) REVERT: c 69 TYR cc_start: 0.8087 (t80) cc_final: 0.7387 (t80) REVERT: d 2 MET cc_start: 0.6546 (tpp) cc_final: 0.6213 (tpp) REVERT: d 25 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7419 (mmtt) REVERT: e 19 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7576 (ttm) REVERT: e 28 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8717 (mmmt) REVERT: e 37 GLU cc_start: 0.8476 (tt0) cc_final: 0.8077 (tt0) REVERT: e 62 ASP cc_start: 0.8208 (m-30) cc_final: 0.7682 (m-30) REVERT: e 74 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6745 (tmm160) REVERT: e 82 GLN cc_start: 0.8490 (tp40) cc_final: 0.7701 (tt0) REVERT: f 5 GLN cc_start: 0.7581 (mp10) cc_final: 0.6888 (mp10) REVERT: f 33 LYS cc_start: 0.8176 (tptt) cc_final: 0.7583 (ttpt) REVERT: f 47 GLU cc_start: 0.8796 (tp30) cc_final: 0.8549 (tp30) REVERT: f 57 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8655 (ttmm) REVERT: g 77 ASP cc_start: 0.8834 (p0) cc_final: 0.8398 (p0) REVERT: g 135 MET cc_start: 0.8978 (ttm) cc_final: 0.8764 (mtp) REVERT: g 144 LYS cc_start: 0.8826 (mttt) cc_final: 0.8457 (mtpt) REVERT: h 52 LYS cc_start: 0.7126 (tppp) cc_final: 0.6906 (ttmt) REVERT: h 55 PHE cc_start: 0.9202 (t80) cc_final: 0.8992 (t80) REVERT: h 86 ILE cc_start: 0.8944 (mm) cc_final: 0.8596 (mt) REVERT: h 90 ASN cc_start: 0.9096 (m-40) cc_final: 0.8759 (m110) REVERT: h 182 SER cc_start: 0.8678 (m) cc_final: 0.8113 (t) REVERT: i 17 GLU cc_start: 0.8893 (tp30) cc_final: 0.8598 (tm-30) REVERT: i 87 LYS cc_start: 0.9024 (tttp) cc_final: 0.8696 (ttpp) REVERT: i 108 ASP cc_start: 0.7782 (t0) cc_final: 0.7504 (t0) REVERT: j 76 ASP cc_start: 0.8464 (m-30) cc_final: 0.8032 (m-30) REVERT: j 78 ASP cc_start: 0.8183 (p0) cc_final: 0.7596 (m-30) REVERT: j 88 ASP cc_start: 0.8400 (t70) cc_final: 0.7780 (t70) REVERT: j 91 GLN cc_start: 0.8623 (mm110) cc_final: 0.8067 (mm110) REVERT: j 95 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8440 (tm-30) REVERT: k 30 ILE cc_start: 0.8573 (tp) cc_final: 0.8241 (tp) REVERT: k 48 ARG cc_start: 0.8241 (tpt90) cc_final: 0.7919 (tpm170) REVERT: k 60 MET cc_start: 0.9078 (tpp) cc_final: 0.8837 (tpp) REVERT: l 36 MET cc_start: 0.8399 (ttm) cc_final: 0.7576 (ttp) REVERT: l 85 GLU cc_start: 0.8123 (pt0) cc_final: 0.7920 (pt0) REVERT: l 164 ASN cc_start: 0.8269 (m-40) cc_final: 0.7988 (m-40) REVERT: m 50 GLN cc_start: 0.8791 (tt0) cc_final: 0.8537 (tt0) REVERT: m 75 ASN cc_start: 0.8554 (t0) cc_final: 0.8027 (t0) REVERT: m 100 PHE cc_start: 0.8757 (t80) cc_final: 0.8406 (t80) REVERT: m 124 LYS cc_start: 0.8500 (tptt) cc_final: 0.7954 (ptmm) REVERT: n 17 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8286 (mp) REVERT: n 44 MET cc_start: 0.8486 (tpp) cc_final: 0.8050 (tpp) REVERT: n 124 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8559 (mt0) REVERT: o 8 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7598 (ttp-170) REVERT: o 16 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6347 (tt0) REVERT: o 20 GLU cc_start: 0.8608 (mp0) cc_final: 0.8264 (mp0) REVERT: o 29 LEU cc_start: 0.7948 (tp) cc_final: 0.7566 (tp) REVERT: o 33 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7719 (pm20) REVERT: o 76 ASN cc_start: 0.8741 (t0) cc_final: 0.8537 (t0) REVERT: o 84 GLN cc_start: 0.9022 (tp40) cc_final: 0.8633 (tp-100) REVERT: p 12 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7976 (tm-30) REVERT: p 53 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8092 (mm-30) REVERT: p 58 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8518 (mttt) REVERT: p 81 ASP cc_start: 0.8591 (t0) cc_final: 0.8165 (t0) outliers start: 112 outliers final: 75 residues processed: 918 average time/residue: 0.1794 time to fit residues: 269.9672 Evaluate side-chains 940 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 852 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 127 ASN Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 198 TYR Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 19 MET Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 137 SER Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain l residue 32 MET Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain o residue 110 GLN Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 303 optimal weight: 0.7980 chunk 250 optimal weight: 7.9990 chunk 328 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN N 274 ASN O 127 ASN O 176 GLN O 329 ASN g 68 ASN l 115 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102531 restraints weight = 49497.740| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.26 r_work: 0.3120 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32662 Z= 0.145 Angle : 0.655 12.242 44149 Z= 0.321 Chirality : 0.043 0.422 4797 Planarity : 0.005 0.065 5412 Dihedral : 11.195 125.584 4968 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 2.77 % Allowed : 20.95 % Favored : 76.27 % 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 (0.14), residues: 3763 helix: 1.14 (0.10), residues: 2462 sheet: -1.60 (0.89), residues: 34 loop : -0.64 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 171 TYR 0.036 0.001 TYR O 164 PHE 0.022 0.001 PHE N 292 TRP 0.010 0.001 TRP n 102 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00344 (32654) covalent geometry : angle 0.65448 (44133) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.91348 ( 16) hydrogen bonds : bond 0.04195 ( 1697) hydrogen bonds : angle 4.28067 ( 4935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 863 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8261 (tpp) cc_final: 0.8016 (mmm) REVERT: J 63 MET cc_start: 0.6438 (ttp) cc_final: 0.5561 (tpp) REVERT: J 64 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8292 (mp) REVERT: J 144 MET cc_start: 0.9114 (ttm) cc_final: 0.8815 (ttm) REVERT: K 64 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7825 (mp) REVERT: K 96 LEU cc_start: 0.8381 (mt) cc_final: 0.7990 (mp) REVERT: L 59 MET cc_start: 0.7973 (mtm) cc_final: 0.7454 (ptt) REVERT: L 262 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8827 (mtp85) REVERT: L 286 LEU cc_start: 0.8929 (tp) cc_final: 0.8596 (tp) REVERT: L 338 MET cc_start: 0.8760 (tpp) cc_final: 0.8517 (ttt) REVERT: L 493 ILE cc_start: 0.8583 (tp) cc_final: 0.8294 (tp) REVERT: L 510 LYS cc_start: 0.7634 (ptmt) cc_final: 0.7410 (mptt) REVERT: L 513 MET cc_start: 0.6771 (tmm) cc_final: 0.6489 (tmm) REVERT: L 523 SER cc_start: 0.8134 (m) cc_final: 0.7719 (t) REVERT: L 544 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8503 (tt) REVERT: L 598 ILE cc_start: 0.8571 (mt) cc_final: 0.8345 (mm) REVERT: M 59 ASP cc_start: 0.8519 (p0) cc_final: 0.8301 (p0) REVERT: M 165 ILE cc_start: 0.9008 (mm) cc_final: 0.8746 (mp) REVERT: M 245 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8082 (mmt180) REVERT: M 271 MET cc_start: 0.8404 (mmm) cc_final: 0.8197 (mtp) REVERT: M 302 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8949 (mmm) REVERT: M 408 MET cc_start: 0.9256 (mmt) cc_final: 0.8958 (mmm) REVERT: M 421 ASN cc_start: 0.7875 (p0) cc_final: 0.7104 (m-40) REVERT: N 2 ASN cc_start: 0.7181 (t0) cc_final: 0.6930 (t0) REVERT: N 91 ASN cc_start: 0.7803 (t0) cc_final: 0.6994 (m-40) REVERT: N 175 MET cc_start: 0.8611 (tpp) cc_final: 0.8284 (tpp) REVERT: N 190 MET cc_start: 0.8469 (mtm) cc_final: 0.8147 (mtm) REVERT: N 225 MET cc_start: 0.8645 (mpp) cc_final: 0.8373 (mpp) REVERT: N 271 MET cc_start: 0.9202 (mmm) cc_final: 0.8936 (mmm) REVERT: N 296 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (tt) REVERT: N 314 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: N 335 MET cc_start: 0.8937 (mtp) cc_final: 0.8295 (ttm) REVERT: O 63 ASP cc_start: 0.8041 (t0) cc_final: 0.7819 (t0) REVERT: O 92 GLN cc_start: 0.7555 (mp10) cc_final: 0.7024 (mt0) REVERT: O 149 HIS cc_start: 0.7440 (t-170) cc_final: 0.7061 (t-170) REVERT: O 158 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6670 (m) REVERT: O 208 ASP cc_start: 0.7876 (t70) cc_final: 0.7095 (p0) REVERT: O 215 GLN cc_start: 0.8494 (mt0) cc_final: 0.8088 (mt0) REVERT: O 231 SER cc_start: 0.8994 (p) cc_final: 0.8752 (p) REVERT: O 236 ASP cc_start: 0.7472 (m-30) cc_final: 0.7049 (m-30) REVERT: U 120 MET cc_start: 0.8665 (mtp) cc_final: 0.8448 (mtm) REVERT: U 139 MET cc_start: 0.9006 (tpp) cc_final: 0.8580 (mmt) REVERT: Y 6 ARG cc_start: 0.5998 (mtm-85) cc_final: 0.5776 (ppt170) REVERT: Y 46 ASN cc_start: 0.8932 (t0) cc_final: 0.8730 (t0) REVERT: Y 53 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7757 (mt-10) REVERT: Y 60 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7360 (ttp80) REVERT: Y 63 PHE cc_start: 0.8100 (t80) cc_final: 0.7719 (t80) REVERT: Y 88 ASP cc_start: 0.8661 (t0) cc_final: 0.8266 (t0) REVERT: Y 133 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8272 (mt-10) REVERT: c 31 VAL cc_start: 0.8691 (t) cc_final: 0.8439 (m) REVERT: c 65 ASP cc_start: 0.9019 (m-30) cc_final: 0.8668 (m-30) REVERT: c 68 GLU cc_start: 0.8109 (tp30) cc_final: 0.7366 (tm-30) REVERT: c 69 TYR cc_start: 0.8106 (t80) cc_final: 0.7412 (t80) REVERT: d 2 MET cc_start: 0.6656 (tpp) cc_final: 0.6333 (tpp) REVERT: d 25 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7468 (mmtt) REVERT: d 34 MET cc_start: 0.8827 (mmm) cc_final: 0.8506 (mmm) REVERT: e 19 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7606 (ttm) REVERT: e 28 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8635 (mmmt) REVERT: e 37 GLU cc_start: 0.8428 (tt0) cc_final: 0.8071 (tt0) REVERT: e 62 ASP cc_start: 0.8209 (m-30) cc_final: 0.7677 (m-30) REVERT: e 74 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6698 (tmm160) REVERT: e 82 GLN cc_start: 0.8517 (tp40) cc_final: 0.7726 (tt0) REVERT: f 5 GLN cc_start: 0.7568 (mp10) cc_final: 0.6903 (mp10) REVERT: f 33 LYS cc_start: 0.8213 (tptt) cc_final: 0.7625 (ttpt) REVERT: f 47 GLU cc_start: 0.8794 (tp30) cc_final: 0.8533 (tp30) REVERT: f 57 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8667 (ttmm) REVERT: g 62 GLU cc_start: 0.8477 (pt0) cc_final: 0.8242 (pt0) REVERT: g 77 ASP cc_start: 0.8797 (p0) cc_final: 0.8388 (p0) REVERT: g 144 LYS cc_start: 0.8743 (mttt) cc_final: 0.8489 (mtpt) REVERT: h 52 LYS cc_start: 0.7042 (tppp) cc_final: 0.6765 (ttmt) REVERT: h 86 ILE cc_start: 0.8971 (mm) cc_final: 0.8645 (mt) REVERT: h 90 ASN cc_start: 0.9123 (m-40) cc_final: 0.8799 (m110) REVERT: h 182 SER cc_start: 0.8686 (m) cc_final: 0.8112 (t) REVERT: i 17 GLU cc_start: 0.8880 (tp30) cc_final: 0.8618 (tm-30) REVERT: i 87 LYS cc_start: 0.9025 (tttp) cc_final: 0.8714 (ttpp) REVERT: i 108 ASP cc_start: 0.7897 (t0) cc_final: 0.7605 (t0) REVERT: j 76 ASP cc_start: 0.8336 (m-30) cc_final: 0.7955 (m-30) REVERT: j 78 ASP cc_start: 0.8171 (p0) cc_final: 0.7627 (m-30) REVERT: j 88 ASP cc_start: 0.8427 (t70) cc_final: 0.7832 (t70) REVERT: j 91 GLN cc_start: 0.8629 (mm110) cc_final: 0.8083 (mm110) REVERT: j 95 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8401 (tm-30) REVERT: k 30 ILE cc_start: 0.8571 (tp) cc_final: 0.8255 (tp) REVERT: l 36 MET cc_start: 0.8411 (ttm) cc_final: 0.7627 (ttp) REVERT: l 164 ASN cc_start: 0.8263 (m-40) cc_final: 0.8019 (m-40) REVERT: m 50 GLN cc_start: 0.8766 (tt0) cc_final: 0.8526 (tt0) REVERT: m 75 ASN cc_start: 0.8571 (t0) cc_final: 0.8048 (t0) REVERT: m 100 PHE cc_start: 0.8809 (t80) cc_final: 0.8489 (t80) REVERT: m 124 LYS cc_start: 0.8495 (tptt) cc_final: 0.8005 (ptmm) REVERT: n 17 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8304 (mp) REVERT: n 44 MET cc_start: 0.8489 (tpp) cc_final: 0.8040 (tpp) REVERT: n 124 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8587 (mt0) REVERT: o 8 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7671 (ttp-170) REVERT: o 29 LEU cc_start: 0.7978 (tp) cc_final: 0.7586 (tp) REVERT: o 76 ASN cc_start: 0.8750 (t0) cc_final: 0.8510 (t0) REVERT: o 84 GLN cc_start: 0.9052 (tp40) cc_final: 0.8673 (tp-100) REVERT: p 12 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7926 (tm-30) REVERT: p 58 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8503 (mttt) REVERT: p 104 ASN cc_start: 0.8702 (m-40) cc_final: 0.8431 (m-40) outliers start: 94 outliers final: 71 residues processed: 911 average time/residue: 0.1800 time to fit residues: 268.4099 Evaluate side-chains 920 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 836 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 198 TYR Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 19 MET Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain l residue 32 MET Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 8 ARG Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain o residue 110 GLN Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 117 optimal weight: 0.0060 chunk 142 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 288 optimal weight: 0.0010 chunk 11 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 506 ASN ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 309 ASN N 317 GLN O 127 ASN O 176 GLN O 329 ASN g 68 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104700 restraints weight = 49361.845| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.26 r_work: 0.3150 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32662 Z= 0.132 Angle : 0.657 13.875 44149 Z= 0.322 Chirality : 0.043 0.444 4797 Planarity : 0.005 0.066 5412 Dihedral : 10.949 124.664 4968 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 2.53 % Allowed : 21.13 % Favored : 76.33 % 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: 0.82 (0.14), residues: 3763 helix: 1.20 (0.10), residues: 2460 sheet: -1.46 (0.91), residues: 34 loop : -0.61 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 171 TYR 0.031 0.001 TYR O 164 PHE 0.021 0.001 PHE N 292 TRP 0.017 0.001 TRP p 43 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00306 (32654) covalent geometry : angle 0.65625 (44133) SS BOND : bond 0.00233 ( 8) SS BOND : angle 1.61425 ( 16) hydrogen bonds : bond 0.04080 ( 1697) hydrogen bonds : angle 4.24151 ( 4935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 867 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 MET cc_start: 0.8221 (tpp) cc_final: 0.8015 (mmm) REVERT: J 6 PHE cc_start: 0.8233 (t80) cc_final: 0.8029 (t80) REVERT: J 63 MET cc_start: 0.6403 (ttp) cc_final: 0.5567 (tpp) REVERT: J 64 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8298 (mp) REVERT: J 144 MET cc_start: 0.9072 (ttm) cc_final: 0.8777 (ttm) REVERT: K 96 LEU cc_start: 0.8363 (mt) cc_final: 0.7978 (mp) REVERT: L 230 HIS cc_start: 0.8579 (p-80) cc_final: 0.8209 (p-80) REVERT: L 262 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8840 (mtp85) REVERT: L 286 LEU cc_start: 0.8872 (tp) cc_final: 0.8612 (tp) REVERT: L 459 PHE cc_start: 0.8206 (m-10) cc_final: 0.7853 (m-10) REVERT: L 493 ILE cc_start: 0.8538 (tp) cc_final: 0.8235 (tp) REVERT: L 507 LEU cc_start: 0.8946 (mp) cc_final: 0.8612 (mp) REVERT: L 513 MET cc_start: 0.6744 (tmm) cc_final: 0.6472 (tmm) REVERT: L 523 SER cc_start: 0.8053 (m) cc_final: 0.7644 (t) REVERT: L 544 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8428 (tt) REVERT: M 59 ASP cc_start: 0.8396 (p0) cc_final: 0.8108 (p0) REVERT: M 302 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: M 421 ASN cc_start: 0.7771 (p0) cc_final: 0.6966 (m-40) REVERT: N 2 ASN cc_start: 0.7112 (t0) cc_final: 0.6859 (t0) REVERT: N 91 ASN cc_start: 0.7802 (t0) cc_final: 0.6945 (m-40) REVERT: N 175 MET cc_start: 0.8535 (tpp) cc_final: 0.8208 (tpp) REVERT: N 190 MET cc_start: 0.8440 (mtm) cc_final: 0.8077 (mtm) REVERT: N 225 MET cc_start: 0.8646 (mpp) cc_final: 0.8386 (mpp) REVERT: N 271 MET cc_start: 0.9166 (mmm) cc_final: 0.8897 (mmm) REVERT: N 296 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (tt) REVERT: N 323 ASN cc_start: 0.7283 (t0) cc_final: 0.6742 (t0) REVERT: N 332 MET cc_start: 0.8545 (mmm) cc_final: 0.7591 (mtp) REVERT: N 335 MET cc_start: 0.8988 (mtp) cc_final: 0.8433 (ttm) REVERT: O 92 GLN cc_start: 0.7532 (mp10) cc_final: 0.6992 (mt0) REVERT: O 149 HIS cc_start: 0.7390 (t-170) cc_final: 0.7033 (t-170) REVERT: O 215 GLN cc_start: 0.8501 (mt0) cc_final: 0.8078 (mt0) REVERT: O 231 SER cc_start: 0.8982 (p) cc_final: 0.8743 (p) REVERT: O 236 ASP cc_start: 0.7291 (m-30) cc_final: 0.6874 (m-30) REVERT: U 139 MET cc_start: 0.8935 (tpp) cc_final: 0.8542 (mmt) REVERT: Y 6 ARG cc_start: 0.5975 (mtm-85) cc_final: 0.5743 (ppt170) REVERT: Y 53 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7784 (mt-10) REVERT: Y 60 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7313 (ttp80) REVERT: Y 63 PHE cc_start: 0.8037 (t80) cc_final: 0.7680 (t80) REVERT: Y 88 ASP cc_start: 0.8651 (t0) cc_final: 0.8225 (t0) REVERT: Y 133 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8384 (mm-30) REVERT: c 31 VAL cc_start: 0.8677 (t) cc_final: 0.8436 (m) REVERT: c 65 ASP cc_start: 0.9031 (m-30) cc_final: 0.8668 (m-30) REVERT: c 68 GLU cc_start: 0.8063 (tp30) cc_final: 0.7343 (tm-30) REVERT: c 69 TYR cc_start: 0.8029 (t80) cc_final: 0.7295 (t80) REVERT: d 2 MET cc_start: 0.6557 (tpp) cc_final: 0.6243 (tpp) REVERT: d 25 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7426 (mmtt) REVERT: d 34 MET cc_start: 0.8716 (mmm) cc_final: 0.8435 (mmm) REVERT: e 28 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8732 (mmmt) REVERT: e 37 GLU cc_start: 0.8463 (tt0) cc_final: 0.8107 (tt0) REVERT: e 62 ASP cc_start: 0.8166 (m-30) cc_final: 0.7671 (m-30) REVERT: e 74 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6809 (tmm160) REVERT: e 82 GLN cc_start: 0.8476 (tp40) cc_final: 0.7695 (tt0) REVERT: f 5 GLN cc_start: 0.7528 (mp10) cc_final: 0.6880 (mp10) REVERT: f 33 LYS cc_start: 0.8158 (tptt) cc_final: 0.7583 (ttpt) REVERT: f 47 GLU cc_start: 0.8801 (tp30) cc_final: 0.8538 (tp30) REVERT: f 57 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8664 (ttmm) REVERT: g 77 ASP cc_start: 0.8790 (p0) cc_final: 0.8372 (p0) REVERT: g 130 ASN cc_start: 0.8587 (m-40) cc_final: 0.8176 (m-40) REVERT: g 144 LYS cc_start: 0.8860 (mttt) cc_final: 0.8416 (mtpt) REVERT: h 52 LYS cc_start: 0.6803 (tppp) cc_final: 0.6435 (ttmt) REVERT: h 86 ILE cc_start: 0.8938 (mm) cc_final: 0.8610 (mt) REVERT: h 90 ASN cc_start: 0.9078 (m-40) cc_final: 0.8722 (m110) REVERT: h 169 TYR cc_start: 0.8900 (m-10) cc_final: 0.8640 (m-10) REVERT: h 182 SER cc_start: 0.8695 (m) cc_final: 0.8188 (t) REVERT: i 17 GLU cc_start: 0.8861 (tp30) cc_final: 0.8596 (tm-30) REVERT: i 27 GLU cc_start: 0.8553 (tt0) cc_final: 0.8044 (tt0) REVERT: i 87 LYS cc_start: 0.8979 (tttp) cc_final: 0.8659 (ttpp) REVERT: j 76 ASP cc_start: 0.8328 (m-30) cc_final: 0.7952 (m-30) REVERT: j 78 ASP cc_start: 0.8094 (p0) cc_final: 0.7596 (m-30) REVERT: j 88 ASP cc_start: 0.8354 (t70) cc_final: 0.7745 (t70) REVERT: j 91 GLN cc_start: 0.8466 (mm110) cc_final: 0.7926 (mm110) REVERT: j 95 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8349 (tm-30) REVERT: j 96 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8229 (mt-10) REVERT: k 30 ILE cc_start: 0.8481 (tp) cc_final: 0.8169 (tp) REVERT: l 36 MET cc_start: 0.8412 (ttm) cc_final: 0.7750 (ttp) REVERT: l 81 ARG cc_start: 0.8781 (mmt90) cc_final: 0.8463 (mmt90) REVERT: l 164 ASN cc_start: 0.8168 (m-40) cc_final: 0.7950 (m-40) REVERT: m 50 GLN cc_start: 0.8756 (tt0) cc_final: 0.8521 (tt0) REVERT: m 75 ASN cc_start: 0.8530 (t0) cc_final: 0.8028 (t0) REVERT: m 124 LYS cc_start: 0.8507 (tptt) cc_final: 0.7951 (ptmm) REVERT: n 44 MET cc_start: 0.8475 (tpp) cc_final: 0.8026 (tpp) REVERT: n 124 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8557 (mt0) REVERT: n 167 TRP cc_start: 0.8910 (p-90) cc_final: 0.8454 (p-90) REVERT: n 176 GLU cc_start: 0.8330 (tt0) cc_final: 0.8118 (pp20) REVERT: o 29 LEU cc_start: 0.7904 (tp) cc_final: 0.7538 (tp) REVERT: o 76 ASN cc_start: 0.8656 (t0) cc_final: 0.8425 (t0) REVERT: p 12 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7911 (tm-30) REVERT: p 58 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8524 (mttt) REVERT: p 81 ASP cc_start: 0.8478 (t0) cc_final: 0.8070 (t0) REVERT: p 104 ASN cc_start: 0.8684 (m-40) cc_final: 0.8469 (m-40) outliers start: 86 outliers final: 57 residues processed: 907 average time/residue: 0.1763 time to fit residues: 262.6951 Evaluate side-chains 896 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 832 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 127 ASN Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 198 TYR Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain Y residue 132 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 74 ARG Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 113 THR Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 128 HIS Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain l residue 110 ASP Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 31 PHE Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 224 optimal weight: 4.9990 chunk 312 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN O 175 ASN O 176 GLN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102564 restraints weight = 49654.990| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.28 r_work: 0.3118 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32662 Z= 0.160 Angle : 0.677 15.159 44149 Z= 0.332 Chirality : 0.043 0.407 4797 Planarity : 0.005 0.066 5412 Dihedral : 10.893 125.414 4968 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 2.21 % Allowed : 21.90 % Favored : 75.89 % 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: 0.81 (0.14), residues: 3763 helix: 1.20 (0.10), residues: 2462 sheet: -1.46 (0.92), residues: 34 loop : -0.63 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 171 TYR 0.030 0.001 TYR O 129 PHE 0.022 0.002 PHE N 292 TRP 0.014 0.001 TRP c 55 HIS 0.009 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00384 (32654) covalent geometry : angle 0.67651 (44133) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.67391 ( 16) hydrogen bonds : bond 0.04170 ( 1697) hydrogen bonds : angle 4.26615 ( 4935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9569.48 seconds wall clock time: 164 minutes 9.49 seconds (9849.49 seconds total)