Starting phenix.real_space_refine on Tue May 5 17:53:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iaq_35315/05_2026/8iaq_35315.map" } resolution = 3.4 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= 0.002 sd= 0.095 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 26 5.49 5 S 244 5.16 5 C 21116 2.51 5 N 5135 2.21 5 O 5691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s 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: 32212 Number of models: 1 Model: "" Number of chains: 35 Chain: "D" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 328 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 5, 'TRANS': 33} Chain: "J" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1287 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain breaks: 1 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: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3630 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} 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: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 700 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} 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: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} 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: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 859 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "f" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 447 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 839 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "j" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 578 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 6, 'TRANS': 61} Chain: "k" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 618 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "l" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 18, 'TRANS': 137} Chain: "m" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1044 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 11, 'TRANS': 113} 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: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1050 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "p" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1452 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "J" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "L" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "M" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "h" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 93 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "i" 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: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "m" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 6.79, per 1000 atoms: 0.21 Number of scatterers: 32212 At special positions: 0 Unit cell: (185.9, 145.2, 149.6, 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 244 16.00 P 26 15.00 O 5691 8.00 N 5135 7.00 C 21116 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=2.02 Simple disulfide: pdb=" SG CYS e 33 " - pdb=" SG CYS e 66 " distance=2.04 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS p 113 " - pdb=" SG CYS p 125 " distance=2.04 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: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 5 sheets defined 67.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.747A pdb=" N GLN D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'J' and resid 3 through 22 Processing helix chain 'J' and resid 24 through 44 Processing helix chain 'J' and resid 49 through 60 Processing helix chain 'J' and resid 62 through 74 removed outlier: 4.166A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 109 removed outlier: 3.725A pdb=" N LEU J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 removed outlier: 3.520A pdb=" N MET J 144 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 171 removed outlier: 3.777A pdb=" N ALA J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 21 removed outlier: 3.805A pdb=" N LEU K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR K 9 " --> pdb=" O PHE K 5 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.558A 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: 3.812A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.583A 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: 4.418A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 58 removed outlier: 3.609A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 83 through 108 removed outlier: 3.575A 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: 3.547A 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: 3.606A 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: 3.675A 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: 3.534A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.620A 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: 4.063A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 295 removed outlier: 3.837A 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: 3.523A 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: 3.503A 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: 3.531A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 4.758A 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: 5.303A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.438A 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 509 removed outlier: 3.712A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (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: 4.237A pdb=" N LEU L 544 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.594A pdb=" N SER L 567 " --> pdb=" O PRO L 563 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.505A pdb=" N ILE M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU M 68 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.576A 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 172 removed outlier: 3.852A 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: 3.937A pdb=" N LEU M 197 " --> pdb=" O ASN M 193 " (cutoff:3.500A) removed outlier: 3.917A 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: 3.625A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.742A 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: 4.144A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 258 removed outlier: 3.509A pdb=" N ALA M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.505A 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: 3.517A 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: 4.145A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE M 400 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.763A 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: 3.578A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS N 79 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 106 Processing helix chain 'N' and resid 108 through 112 removed outlier: 3.531A pdb=" N PHE N 111 " --> pdb=" O LEU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 3.866A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 135 through 146 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'N' and resid 150 through 172 removed outlier: 3.877A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 194 removed outlier: 3.535A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 222 removed outlier: 3.801A pdb=" N THR N 201 " --> pdb=" O ASN N 197 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU N 203 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.752A 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: 4.195A 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: 3.837A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 317 removed outlier: 4.073A pdb=" N LYS N 312 " --> pdb=" O ASN N 308 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET N 313 " --> pdb=" O ASN N 309 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET N 314 " --> pdb=" O ASN N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 335 removed outlier: 4.323A pdb=" N SER N 327 " --> pdb=" O ASN N 323 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET N 332 " --> pdb=" O THR N 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 333 " --> pdb=" O LEU N 329 " (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 removed outlier: 3.632A pdb=" N LEU N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 45 Processing helix chain 'O' and resid 49 through 53 Processing helix chain 'O' and resid 69 through 81 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 165 Processing helix chain 'O' and resid 166 through 176 removed outlier: 3.965A 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 225 through 229 Processing helix chain 'O' and resid 230 through 243 Processing helix chain 'O' and resid 244 through 251 removed outlier: 3.765A pdb=" N GLU O 251 " --> pdb=" O PRO O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 265 removed outlier: 3.617A pdb=" N ASP O 265 " --> pdb=" O TRP O 261 " (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: 4.568A pdb=" N TYR O 293 " --> pdb=" O TRP O 289 " (cutoff:3.500A) removed outlier: 3.561A 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 80 through 89 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.658A pdb=" N VAL U 116 " --> pdb=" O SER U 112 " (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 5 through 14 removed outlier: 3.899A pdb=" N TYR Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS Y 12 " --> pdb=" O PHE Y 8 " (cutoff:3.500A) removed outlier: 3.631A 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 Processing helix chain 'Y' and resid 88 through 107 removed outlier: 3.814A 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: 3.610A pdb=" N LEU d 62 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.675A 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: 4.272A pdb=" N LYS e 38 " --> pdb=" O HIS e 34 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU e 39 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 52 Processing helix chain 'e' and resid 54 through 56 No H-bonds generated for 'chain 'e' and resid 54 through 56' Processing helix chain 'e' and resid 57 through 67 removed outlier: 3.672A pdb=" N GLU e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 90 removed outlier: 3.527A pdb=" N MET e 73 " --> pdb=" O ARG e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 100 Processing helix chain 'f' and resid 14 through 34 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: 3.824A 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: 5.117A 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: 3.594A 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: 3.691A 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: 4.011A pdb=" N ALA h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 164 removed outlier: 4.070A 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 'i' and resid 10 through 27 removed outlier: 3.769A pdb=" N LEU i 15 " --> pdb=" O ARG i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 69 Processing helix chain 'i' and resid 70 through 89 removed outlier: 3.621A pdb=" N ILE i 77 " --> pdb=" O SER i 73 " (cutoff:3.500A) Proline residue: i 78 - end of helix Processing helix chain 'j' and resid 51 through 76 removed outlier: 3.605A pdb=" N VAL j 55 " --> pdb=" O THR j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 92 removed outlier: 4.188A pdb=" N TRP j 92 " --> pdb=" O PRO j 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 33 through 45 removed outlier: 4.163A pdb=" N THR k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 54 No H-bonds generated for 'chain 'k' and resid 52 through 54' Processing helix chain 'k' and resid 55 through 61 removed outlier: 4.337A pdb=" N TYR k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY k 61 " --> pdb=" O TRP k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 3.513A pdb=" N VAL k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 94 Processing helix chain 'l' and resid 33 through 37 Processing helix chain 'l' and resid 44 through 55 removed outlier: 3.837A 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: 4.181A pdb=" N ASN l 165 " --> pdb=" O TYR l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 24 removed outlier: 3.840A pdb=" N TYR m 23 " --> pdb=" O ASP m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 52 removed outlier: 3.881A pdb=" N LEU m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 74 removed outlier: 3.597A pdb=" N ILE m 66 " --> pdb=" O ASP m 62 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.809A 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: 3.631A pdb=" N ARG n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.863A pdb=" N CYS n 42 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.516A pdb=" N ARG n 65 " --> pdb=" O THR n 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 98 removed outlier: 3.906A 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: 3.672A pdb=" N PHE n 119 " --> pdb=" O TYR n 115 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN n 124 " --> pdb=" O SER n 120 " (cutoff:3.500A) removed outlier: 4.885A 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 3 through 10 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: 3.632A pdb=" N ARG o 65 " --> pdb=" O HIS o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 119 removed outlier: 4.035A pdb=" N LYS o 97 " --> pdb=" O LEU o 93 " (cutoff:3.500A) 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) Processing helix chain 'p' and resid 41 through 59 removed outlier: 3.678A pdb=" N VAL p 45 " --> pdb=" O VAL p 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 113 removed outlier: 3.524A pdb=" N TRP p 92 " --> pdb=" O ALA p 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE p 102 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET p 103 " --> pdb=" O ASP p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 140 removed outlier: 3.734A pdb=" N GLU p 130 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.690A pdb=" N LEU p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) removed outlier: 4.480A 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: 6.267A pdb=" N MET L 78 " --> pdb=" O HIS L 67 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS L 67 " --> pdb=" O MET L 78 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N PHE L 80 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR L 65 " --> 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 59 through 60 removed outlier: 6.591A pdb=" N LYS O 84 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 206 through 207 removed outlier: 6.051A pdb=" N TYR O 206 " --> pdb=" O TYR O 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'h' and resid 97 through 98 removed outlier: 6.019A pdb=" N GLU h 97 " --> pdb=" O TYR p 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 1710 hydrogen bonds defined for protein. 4959 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: 5.84 Time building geometry restraints manager: 4.31 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: 4900 1.29 - 1.43: 8680 1.43 - 1.56: 18931 1.56 - 1.69: 94 1.69 - 1.83: 442 Bond restraints: 33047 Sorted by residual: bond pdb=" O6 EHZ n 201 " pdb=" P1 EHZ n 201 " ideal model delta sigma weight residual 2.378 1.643 0.735 2.00e-02 2.50e+03 1.35e+03 bond pdb=" N PRO O 247 " pdb=" CD PRO O 247 " ideal model delta sigma weight residual 1.473 1.705 -0.232 1.40e-02 5.10e+03 2.75e+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 k 50 " pdb=" CD PRO k 50 " ideal model delta sigma weight residual 1.473 1.281 0.192 1.40e-02 5.10e+03 1.87e+02 bond pdb=" N PRO N 255 " pdb=" CD PRO N 255 " ideal model delta sigma weight residual 1.473 1.284 0.189 1.40e-02 5.10e+03 1.83e+02 ... (remaining 33042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.58: 44029 6.58 - 13.16: 585 13.16 - 19.75: 22 19.75 - 26.33: 0 26.33 - 32.91: 2 Bond angle restraints: 44638 Sorted by residual: angle pdb=" N PRO M 370 " pdb=" CA PRO M 370 " pdb=" C PRO M 370 " ideal model delta sigma weight residual 110.70 128.56 -17.86 1.22e+00 6.72e-01 2.14e+02 angle pdb=" N PRO N 255 " pdb=" CA PRO N 255 " pdb=" C PRO N 255 " ideal model delta sigma weight residual 110.70 128.31 -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 111.07 125.80 -14.73 1.07e+00 8.73e-01 1.90e+02 angle pdb=" N PHE L 522 " pdb=" CA PHE L 522 " pdb=" C PHE L 522 " ideal model delta sigma weight residual 111.14 97.86 13.28 1.08e+00 8.57e-01 1.51e+02 angle pdb=" N VAL J 65 " pdb=" CA VAL J 65 " pdb=" C VAL J 65 " ideal model delta sigma weight residual 110.62 98.34 12.28 1.02e+00 9.61e-01 1.45e+02 ... (remaining 44633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 19394 32.63 - 65.25: 674 65.25 - 97.88: 40 97.88 - 130.51: 5 130.51 - 163.13: 1 Dihedral angle restraints: 20114 sinusoidal: 8823 harmonic: 11291 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 -160.84 74.84 1 1.00e+01 1.00e-02 7.09e+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 93.00 160.86 -67.86 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" C5' ADP O 401 " pdb=" O5' ADP O 401 " pdb=" PA ADP O 401 " pdb=" O2A ADP O 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.87 163.13 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 20111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3786 0.106 - 0.211: 831 0.211 - 0.317: 174 0.317 - 0.423: 34 0.423 - 0.529: 11 Chirality restraints: 4836 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 1.98 0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" CA PRO M 370 " pdb=" N PRO M 370 " pdb=" C PRO M 370 " pdb=" CB PRO M 370 " both_signs ideal model delta sigma weight residual False 2.72 2.22 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA PHE M 151 " pdb=" N PHE M 151 " pdb=" C PHE M 151 " pdb=" CB PHE M 151 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 4833 not shown) Planarity restraints: 5461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR e 92 " -0.027 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C TYR e 92 " 0.094 2.00e-02 2.50e+03 pdb=" O TYR e 92 " -0.035 2.00e-02 2.50e+03 pdb=" N THR e 93 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 47 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLU M 47 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU M 47 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN M 48 " 0.026 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 4.15e-02 1.72e+01 pdb=" C SER l 125 " -0.072 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 ... (remaining 5458 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 675 2.59 - 3.17: 32264 3.17 - 3.75: 51927 3.75 - 4.32: 76343 4.32 - 4.90: 119000 Nonbonded interactions: 280209 Sorted by model distance: nonbonded pdb=" O VAL L 261 " pdb=" CD2 HIS L 264 " model vdw 2.015 3.260 nonbonded pdb=" OE1 GLU L 353 " pdb=" OH TYR n 80 " model vdw 2.032 3.040 nonbonded pdb=" O ASN L 605 " pdb=" OD1 ASN L 605 " model vdw 2.035 3.040 nonbonded pdb=" O GLU n 101 " pdb=" NH2 ARG n 122 " model vdw 2.058 3.120 nonbonded pdb=" O ASN L 579 " pdb=" OD1 ASN L 579 " model vdw 2.061 3.040 ... (remaining 280204 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: 5.570 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.735 33055 Z= 1.001 Angle : 1.893 32.912 44654 Z= 1.342 Chirality : 0.097 0.529 4836 Planarity : 0.007 0.068 5461 Dihedral : 14.781 163.133 12794 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 44.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.33 % Cbeta Deviations : 1.12 % 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: -2.60 (0.12), residues: 3794 helix: -1.29 (0.10), residues: 2393 sheet: -2.64 (0.81), residues: 28 loop : -2.31 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG p 162 TYR 0.036 0.002 TYR l 153 PHE 0.029 0.002 PHE h 171 TRP 0.030 0.002 TRP L 407 HIS 0.008 0.002 HIS l 106 Details of bonding type rmsd covalent geometry : bond 0.01407 (33047) covalent geometry : angle 1.89232 (44638) SS BOND : bond 0.11763 ( 8) SS BOND : angle 2.64654 ( 16) hydrogen bonds : bond 0.22572 ( 1710) hydrogen bonds : angle 8.79553 ( 4959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1409 time to evaluate : 0.838 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 LEU cc_start: 0.9026 (mt) cc_final: 0.8778 (mt) REVERT: L 61 TYR cc_start: 0.8128 (m-80) cc_final: 0.7544 (m-80) REVERT: L 199 GLN cc_start: 0.8725 (mp10) cc_final: 0.7502 (mp10) REVERT: L 208 ASP cc_start: 0.7408 (t0) cc_final: 0.7063 (t70) REVERT: L 294 THR cc_start: 0.8541 (p) cc_final: 0.8309 (p) REVERT: L 543 ASN cc_start: 0.8164 (t0) cc_final: 0.7840 (t0) REVERT: M 88 ASN cc_start: 0.7553 (p0) cc_final: 0.7236 (p0) REVERT: M 271 MET cc_start: 0.7183 (mmp) cc_final: 0.6876 (mmp) REVERT: M 339 SER cc_start: 0.8845 (t) cc_final: 0.8520 (p) REVERT: M 423 MET cc_start: 0.7721 (mmt) cc_final: 0.6845 (mmp) REVERT: M 437 MET cc_start: 0.8220 (mmt) cc_final: 0.8015 (mpp) REVERT: M 459 MET cc_start: 0.8113 (mtp) cc_final: 0.7542 (mtp) REVERT: N 68 MET cc_start: 0.8841 (mmp) cc_final: 0.8637 (mmp) REVERT: N 151 SER cc_start: 0.8678 (p) cc_final: 0.8213 (t) REVERT: N 191 LEU cc_start: 0.8878 (tp) cc_final: 0.8595 (tp) REVERT: N 243 MET cc_start: 0.7551 (mmm) cc_final: 0.6670 (mmt) REVERT: O 93 TYR cc_start: 0.8359 (t80) cc_final: 0.7747 (t80) REVERT: U 101 ASN cc_start: 0.8063 (p0) cc_final: 0.7854 (p0) REVERT: U 111 ASP cc_start: 0.8416 (p0) cc_final: 0.8202 (p0) REVERT: U 152 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8430 (mmtm) REVERT: U 155 TYR cc_start: 0.8740 (p90) cc_final: 0.8537 (p90) REVERT: d 100 ASP cc_start: 0.8059 (m-30) cc_final: 0.7764 (m-30) REVERT: d 107 LYS cc_start: 0.8258 (mmmt) cc_final: 0.8024 (mtmm) REVERT: e 18 PHE cc_start: 0.8217 (p90) cc_final: 0.7969 (p90) REVERT: e 71 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8187 (pttt) REVERT: e 86 LEU cc_start: 0.8660 (mt) cc_final: 0.8416 (mt) REVERT: g 106 TYR cc_start: 0.8856 (m-80) cc_final: 0.8645 (m-10) REVERT: h 72 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7998 (ttpp) REVERT: h 153 GLU cc_start: 0.7527 (tt0) cc_final: 0.7318 (tt0) REVERT: h 170 GLN cc_start: 0.7469 (mm110) cc_final: 0.7254 (mm-40) REVERT: j 91 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6722 (mm110) REVERT: k 22 LEU cc_start: 0.9053 (mt) cc_final: 0.8448 (mt) REVERT: k 81 PHE cc_start: 0.8718 (t80) cc_final: 0.8367 (t80) REVERT: l 67 ASP cc_start: 0.8097 (t0) cc_final: 0.7628 (t0) REVERT: l 129 MET cc_start: 0.8374 (ttm) cc_final: 0.8172 (mtm) REVERT: l 170 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8715 (mtt-85) REVERT: l 173 ASP cc_start: 0.8200 (t0) cc_final: 0.7669 (t0) REVERT: n 56 ASP cc_start: 0.8905 (t0) cc_final: 0.8691 (t0) REVERT: n 85 SER cc_start: 0.9237 (p) cc_final: 0.8901 (m) REVERT: o 14 SER cc_start: 0.8509 (m) cc_final: 0.8225 (p) REVERT: o 26 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8626 (Cg_endo) REVERT: o 43 GLN cc_start: 0.8003 (tt0) cc_final: 0.7694 (tt0) REVERT: o 57 ASP cc_start: 0.5888 (p0) cc_final: 0.5597 (p0) REVERT: o 100 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8272 (mtmt) REVERT: p 81 ASP cc_start: 0.7339 (t0) cc_final: 0.6934 (t0) REVERT: p 146 LEU cc_start: 0.8449 (mt) cc_final: 0.7938 (mp) REVERT: p 149 TYR cc_start: 0.8229 (m-10) cc_final: 0.7938 (m-80) outliers start: 6 outliers final: 0 residues processed: 1413 average time/residue: 0.2109 time to fit residues: 468.7326 Evaluate side-chains 911 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 911 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN D 67 ASN J 85 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN L 2 ASN L 58 ASN L 206 ASN ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 296 ASN L 321 GLN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN M 44 GLN M 89 ASN M 92 GLN M 168 GLN M 169 ASN M 192 ASN M 193 ASN M 213 HIS M 349 GLN M 390 ASN N 87 GLN N 120 GLN N 125 HIS ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 132 GLN O 292 HIS O 306 ASN O 323 GLN Y 108 HIS c 63 ASN d 8 HIS e 7 GLN f 13 HIS g 68 ASN g 84 ASN h 170 GLN i 74 HIS i 83 HIS ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 66 ASN l 31 HIS l 80 ASN l 106 HIS l 165 ASN ** n 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN o 110 GLN p 67 GLN p 91 GLN p 131 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107872 restraints weight = 54102.464| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.90 r_work: 0.3334 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 33055 Z= 0.203 Angle : 0.796 13.659 44654 Z= 0.406 Chirality : 0.047 0.227 4836 Planarity : 0.006 0.063 5461 Dihedral : 14.377 154.619 5145 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 3.57 % Allowed : 14.48 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 3794 helix: 0.20 (0.10), residues: 2455 sheet: -2.09 (0.90), residues: 24 loop : -1.22 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 58 TYR 0.038 0.002 TYR L 422 PHE 0.033 0.002 PHE N 35 TRP 0.023 0.002 TRP J 123 HIS 0.014 0.002 HIS L 264 Details of bonding type rmsd covalent geometry : bond 0.00469 (33047) covalent geometry : angle 0.79353 (44638) SS BOND : bond 0.00684 ( 8) SS BOND : angle 3.66260 ( 16) hydrogen bonds : bond 0.05869 ( 1710) hydrogen bonds : angle 5.27220 ( 4959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 982 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 42 MET cc_start: 0.9192 (ttm) cc_final: 0.8622 (ttm) REVERT: J 85 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5954 (m-40) REVERT: J 91 PHE cc_start: 0.7758 (m-80) cc_final: 0.7509 (m-80) REVERT: J 135 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8954 (tt) REVERT: K 10 MET cc_start: 0.8636 (mtp) cc_final: 0.8269 (mtp) REVERT: K 49 LEU cc_start: 0.9446 (mt) cc_final: 0.9223 (mt) REVERT: L 71 MET cc_start: 0.8529 (mmt) cc_final: 0.8123 (mmt) REVERT: L 84 PHE cc_start: 0.8759 (t80) cc_final: 0.8430 (t80) REVERT: L 199 GLN cc_start: 0.8940 (mp10) cc_final: 0.8667 (mt0) REVERT: L 208 ASP cc_start: 0.7827 (t0) cc_final: 0.7387 (t0) REVERT: L 449 ASP cc_start: 0.9057 (m-30) cc_final: 0.8841 (m-30) REVERT: L 463 PHE cc_start: 0.7988 (m-10) cc_final: 0.7492 (m-10) REVERT: M 10 MET cc_start: 0.8987 (tpp) cc_final: 0.8417 (mmm) REVERT: M 271 MET cc_start: 0.8178 (mmp) cc_final: 0.7692 (mmp) REVERT: M 339 SER cc_start: 0.9238 (t) cc_final: 0.8945 (p) REVERT: M 437 MET cc_start: 0.8832 (mmt) cc_final: 0.8366 (mpp) REVERT: N 243 MET cc_start: 0.8437 (mmm) cc_final: 0.7933 (mmt) REVERT: N 335 MET cc_start: 0.8343 (ptm) cc_final: 0.8137 (ptp) REVERT: O 93 TYR cc_start: 0.8371 (t80) cc_final: 0.7596 (t80) REVERT: O 234 LEU cc_start: 0.8712 (mt) cc_final: 0.8511 (mp) REVERT: O 296 MET cc_start: 0.8034 (mtp) cc_final: 0.7691 (mtp) REVERT: O 300 ASP cc_start: 0.8215 (t0) cc_final: 0.7810 (t0) REVERT: U 122 MET cc_start: 0.9019 (mmt) cc_final: 0.8707 (mmt) REVERT: U 143 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7858 (mt-10) REVERT: Y 22 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8234 (tpt90) REVERT: Y 46 ASN cc_start: 0.9164 (t0) cc_final: 0.8960 (t0) REVERT: Y 83 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8522 (mtm180) REVERT: Y 115 MET cc_start: 0.8781 (mtp) cc_final: 0.8514 (mtp) REVERT: Y 133 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8886 (mm-30) REVERT: Y 137 LEU cc_start: 0.8522 (tt) cc_final: 0.7999 (tp) REVERT: c 38 LYS cc_start: 0.8720 (tttt) cc_final: 0.8115 (tppt) REVERT: c 41 TRP cc_start: 0.8384 (m100) cc_final: 0.8122 (m100) REVERT: d 27 ASN cc_start: 0.8929 (p0) cc_final: 0.8703 (p0) REVERT: e 5 ASP cc_start: 0.8121 (t0) cc_final: 0.7727 (t0) REVERT: e 65 GLU cc_start: 0.8144 (tp30) cc_final: 0.7784 (tp30) REVERT: e 76 MET cc_start: 0.8557 (ttm) cc_final: 0.8058 (tpt) REVERT: f 46 ARG cc_start: 0.8397 (ptt90) cc_final: 0.7948 (ptt90) REVERT: g 62 GLU cc_start: 0.8252 (tt0) cc_final: 0.8008 (tt0) REVERT: g 126 TYR cc_start: 0.8153 (t80) cc_final: 0.7892 (t80) REVERT: h 72 LYS cc_start: 0.8634 (ttpt) cc_final: 0.7259 (tttp) REVERT: h 74 TYR cc_start: 0.8439 (m-10) cc_final: 0.8041 (m-10) REVERT: h 86 ILE cc_start: 0.9280 (mm) cc_final: 0.8921 (mm) REVERT: j 78 ASP cc_start: 0.7837 (m-30) cc_final: 0.7420 (m-30) REVERT: k 22 LEU cc_start: 0.8812 (mt) cc_final: 0.8321 (mt) REVERT: k 58 ARG cc_start: 0.9056 (mmt90) cc_final: 0.8331 (mmt-90) REVERT: l 43 ARG cc_start: 0.8282 (mmt180) cc_final: 0.8028 (mmt180) REVERT: l 53 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8729 (tptm) REVERT: l 129 MET cc_start: 0.8918 (ttm) cc_final: 0.8710 (mtm) REVERT: l 170 ARG cc_start: 0.9012 (ttm-80) cc_final: 0.8721 (mtt-85) REVERT: m 55 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8439 (ptpp) REVERT: m 75 ASN cc_start: 0.8021 (t0) cc_final: 0.7658 (t0) REVERT: m 113 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8549 (tp30) REVERT: n 62 GLN cc_start: 0.9080 (tp40) cc_final: 0.8571 (tp40) REVERT: n 63 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8695 (mp) REVERT: n 85 SER cc_start: 0.9357 (p) cc_final: 0.9150 (m) REVERT: n 141 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8592 (tp40) REVERT: n 144 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7640 (t) REVERT: o 14 SER cc_start: 0.8729 (m) cc_final: 0.8478 (p) REVERT: o 18 ASP cc_start: 0.7722 (t0) cc_final: 0.7346 (t0) REVERT: o 26 PRO cc_start: 0.9127 (Cg_exo) cc_final: 0.8815 (Cg_endo) REVERT: o 43 GLN cc_start: 0.8305 (tt0) cc_final: 0.7751 (tt0) REVERT: o 44 GLN cc_start: 0.7590 (tp40) cc_final: 0.6906 (tp40) REVERT: o 100 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8658 (mtmt) REVERT: o 103 GLU cc_start: 0.8642 (tp30) cc_final: 0.8398 (tp30) REVERT: o 112 LYS cc_start: 0.9211 (tppt) cc_final: 0.9011 (tppt) REVERT: p 6 ASP cc_start: 0.8175 (m-30) cc_final: 0.7903 (m-30) outliers start: 122 outliers final: 61 residues processed: 1043 average time/residue: 0.2001 time to fit residues: 335.6785 Evaluate side-chains 860 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 795 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 273 ILE Chi-restraints excluded: chain L residue 469 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain M residue 458 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 182 GLN Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 136 GLU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain i residue 17 GLU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 113 ILE Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN J 85 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 HIS L 113 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS M 422 HIS N 222 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 HIS O 286 GLN ** O 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 344 ASN Y 108 HIS c 73 ASN d 61 GLN d 97 HIS g 68 ASN ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN n 12 HIS o 54 GLN p 59 ASN p 131 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103844 restraints weight = 55125.871| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.00 r_work: 0.3230 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33055 Z= 0.225 Angle : 0.720 12.304 44654 Z= 0.363 Chirality : 0.045 0.225 4836 Planarity : 0.005 0.064 5461 Dihedral : 13.637 135.055 5145 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 17.05 % Favored : 78.77 % 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: 0.02 (0.13), residues: 3794 helix: 0.56 (0.10), residues: 2459 sheet: -1.59 (1.16), residues: 18 loop : -0.88 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 58 TYR 0.026 0.002 TYR L 422 PHE 0.024 0.002 PHE e 18 TRP 0.020 0.002 TRP L 557 HIS 0.006 0.001 HIS M 319 Details of bonding type rmsd covalent geometry : bond 0.00536 (33047) covalent geometry : angle 0.71640 (44638) SS BOND : bond 0.01062 ( 8) SS BOND : angle 3.74700 ( 16) hydrogen bonds : bond 0.05169 ( 1710) hydrogen bonds : angle 4.83436 ( 4959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 825 time to evaluate : 1.162 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: J 42 MET cc_start: 0.9297 (ttm) cc_final: 0.8923 (ttm) REVERT: J 85 ASN cc_start: 0.5955 (m110) cc_final: 0.5612 (m-40) REVERT: J 135 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8259 (tt) REVERT: K 10 MET cc_start: 0.8783 (mtp) cc_final: 0.8351 (mtm) REVERT: K 49 LEU cc_start: 0.9467 (mt) cc_final: 0.9225 (mt) REVERT: L 53 MET cc_start: 0.9102 (mmm) cc_final: 0.8484 (mmm) REVERT: L 84 PHE cc_start: 0.8744 (t80) cc_final: 0.8470 (t80) REVERT: L 132 THR cc_start: 0.9389 (m) cc_final: 0.9125 (p) REVERT: L 208 ASP cc_start: 0.8100 (t0) cc_final: 0.7561 (t70) REVERT: L 437 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8528 (p90) REVERT: M 10 MET cc_start: 0.9065 (tpp) cc_final: 0.8572 (mmm) REVERT: M 59 ASP cc_start: 0.8810 (p0) cc_final: 0.8291 (p0) REVERT: M 85 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8329 (tptt) REVERT: M 119 TYR cc_start: 0.9095 (t80) cc_final: 0.8863 (t80) REVERT: M 245 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8756 (mmt180) REVERT: M 271 MET cc_start: 0.8253 (mmp) cc_final: 0.7901 (mmp) REVERT: M 339 SER cc_start: 0.9352 (t) cc_final: 0.9033 (p) REVERT: M 437 MET cc_start: 0.9042 (mmt) cc_final: 0.8711 (mpp) REVERT: N 227 ILE cc_start: 0.8066 (pt) cc_final: 0.7753 (mt) REVERT: N 243 MET cc_start: 0.8681 (mmm) cc_final: 0.8193 (mmt) REVERT: O 93 TYR cc_start: 0.8351 (t80) cc_final: 0.7756 (t80) REVERT: O 296 MET cc_start: 0.8158 (mtp) cc_final: 0.7921 (mtp) REVERT: O 300 ASP cc_start: 0.8380 (t0) cc_final: 0.7923 (t0) REVERT: O 326 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8888 (ttp80) REVERT: U 143 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7877 (mt-10) REVERT: Y 22 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8345 (tpt90) REVERT: Y 60 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8022 (ttp80) REVERT: Y 133 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8886 (mm-30) REVERT: c 53 PHE cc_start: 0.8533 (t80) cc_final: 0.8292 (t80) REVERT: c 57 TYR cc_start: 0.8446 (t80) cc_final: 0.7918 (t80) REVERT: c 68 GLU cc_start: 0.8448 (tp30) cc_final: 0.8202 (tp30) REVERT: d 27 ASN cc_start: 0.8999 (p0) cc_final: 0.8680 (p0) REVERT: e 5 ASP cc_start: 0.8322 (t0) cc_final: 0.8057 (m-30) REVERT: e 65 GLU cc_start: 0.8507 (tp30) cc_final: 0.7939 (tp30) REVERT: e 74 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8161 (tpp-160) REVERT: e 82 GLN cc_start: 0.8607 (tp40) cc_final: 0.8210 (tp40) REVERT: f 28 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7847 (mtm-85) REVERT: f 47 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7605 (tm-30) REVERT: g 136 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: h 72 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8533 (ttpp) REVERT: h 74 TYR cc_start: 0.8749 (m-10) cc_final: 0.8214 (m-10) REVERT: h 117 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7241 (mt) REVERT: j 97 LEU cc_start: 0.9503 (mm) cc_final: 0.8992 (tp) REVERT: k 22 LEU cc_start: 0.8818 (mt) cc_final: 0.8482 (mt) REVERT: k 40 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8686 (ttmm) REVERT: l 43 ARG cc_start: 0.8436 (mmt180) cc_final: 0.8083 (mmt180) REVERT: l 53 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8780 (tptp) REVERT: l 77 MET cc_start: 0.9306 (ttp) cc_final: 0.9098 (ttt) REVERT: l 91 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8407 (mt0) REVERT: l 170 ARG cc_start: 0.9069 (ttm-80) cc_final: 0.8547 (mtt90) REVERT: m 75 ASN cc_start: 0.8086 (t0) cc_final: 0.7622 (t0) REVERT: m 77 TYR cc_start: 0.8991 (t80) cc_final: 0.8585 (t80) REVERT: m 125 PHE cc_start: 0.8796 (m-10) cc_final: 0.8509 (m-80) REVERT: m 129 TYR cc_start: 0.7918 (p90) cc_final: 0.7708 (p90) REVERT: n 13 GLN cc_start: 0.8739 (tt0) cc_final: 0.8289 (mp10) REVERT: n 97 TYR cc_start: 0.8575 (m-10) cc_final: 0.8367 (m-10) REVERT: n 144 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7774 (t) REVERT: o 18 ASP cc_start: 0.7711 (t0) cc_final: 0.6768 (t70) REVERT: o 26 PRO cc_start: 0.9220 (Cg_exo) cc_final: 0.8946 (Cg_endo) REVERT: o 44 GLN cc_start: 0.7858 (tp40) cc_final: 0.6975 (tp40) REVERT: o 112 LYS cc_start: 0.9155 (tppt) cc_final: 0.8902 (tppt) REVERT: p 96 PHE cc_start: 0.9102 (t80) cc_final: 0.8899 (t80) REVERT: p 97 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8526 (mtmm) REVERT: p 153 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8112 (mtm-85) outliers start: 143 outliers final: 90 residues processed: 902 average time/residue: 0.2037 time to fit residues: 296.3813 Evaluate side-chains 851 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 755 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 437 PHE Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain M residue 458 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 182 GLN Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain O residue 326 ARG Chi-restraints excluded: chain O residue 344 ASN Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 142 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 112 MET Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 136 GLU Chi-restraints excluded: chain h residue 117 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain h residue 177 GLU Chi-restraints excluded: chain i residue 17 GLU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 122 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 144 THR Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 93 optimal weight: 0.0030 chunk 266 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 227 optimal weight: 0.0040 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 338 optimal weight: 6.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 85 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN O 344 ASN U 101 ASN Y 81 GLN h 90 ASN ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 83 GLN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 HIS n 76 HIS p 59 ASN p 107 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106550 restraints weight = 54497.840| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.00 r_work: 0.3275 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33055 Z= 0.139 Angle : 0.651 12.891 44654 Z= 0.326 Chirality : 0.042 0.247 4836 Planarity : 0.005 0.065 5461 Dihedral : 13.075 127.229 5145 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 3.51 % Allowed : 17.70 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.39 (0.14), residues: 3794 helix: 0.79 (0.10), residues: 2459 sheet: -0.95 (1.30), residues: 18 loop : -0.59 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 71 TYR 0.030 0.001 TYR L 422 PHE 0.023 0.002 PHE e 18 TRP 0.024 0.001 TRP O 353 HIS 0.005 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00309 (33047) covalent geometry : angle 0.64739 (44638) SS BOND : bond 0.00179 ( 8) SS BOND : angle 3.59319 ( 16) hydrogen bonds : bond 0.04531 ( 1710) hydrogen bonds : angle 4.58203 ( 4959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 828 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLN cc_start: 0.9458 (pt0) cc_final: 0.9182 (pt0) REVERT: J 42 MET cc_start: 0.9308 (ttm) cc_final: 0.8851 (ttm) REVERT: J 165 ILE cc_start: 0.9214 (mt) cc_final: 0.9005 (mm) REVERT: K 1 MET cc_start: 0.6429 (mmm) cc_final: 0.6122 (tpt) REVERT: K 49 LEU cc_start: 0.9523 (mt) cc_final: 0.9308 (mt) REVERT: K 57 MET cc_start: 0.9274 (mmm) cc_final: 0.8873 (mmt) REVERT: L 84 PHE cc_start: 0.8639 (t80) cc_final: 0.8253 (t80) REVERT: L 132 THR cc_start: 0.9329 (m) cc_final: 0.9082 (p) REVERT: L 208 ASP cc_start: 0.8103 (t0) cc_final: 0.7695 (p0) REVERT: L 437 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8479 (p90) REVERT: L 523 SER cc_start: 0.8710 (m) cc_final: 0.8258 (t) REVERT: L 547 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7250 (mmtm) REVERT: M 10 MET cc_start: 0.9006 (tpp) cc_final: 0.8518 (mmm) REVERT: M 85 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8426 (tptt) REVERT: M 271 MET cc_start: 0.8251 (mmp) cc_final: 0.7790 (mmp) REVERT: M 339 SER cc_start: 0.9298 (t) cc_final: 0.8995 (p) REVERT: N 227 ILE cc_start: 0.8101 (pt) cc_final: 0.7814 (mt) REVERT: N 298 TYR cc_start: 0.8864 (m-10) cc_final: 0.8541 (m-10) REVERT: N 324 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7675 (mp) REVERT: N 335 MET cc_start: 0.8562 (ptm) cc_final: 0.8319 (ptp) REVERT: O 93 TYR cc_start: 0.8115 (t80) cc_final: 0.7636 (t80) REVERT: O 213 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7840 (tm-30) REVERT: O 296 MET cc_start: 0.8073 (mtp) cc_final: 0.7846 (mtp) REVERT: O 300 ASP cc_start: 0.8284 (t0) cc_final: 0.7815 (t0) REVERT: U 143 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7922 (mt-10) REVERT: U 155 TYR cc_start: 0.9071 (p90) cc_final: 0.8782 (p90) REVERT: Y 22 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8322 (tpt90) REVERT: Y 60 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8038 (ttp80) REVERT: c 38 LYS cc_start: 0.8593 (tttt) cc_final: 0.8010 (tppt) REVERT: c 53 PHE cc_start: 0.8521 (t80) cc_final: 0.8312 (t80) REVERT: c 57 TYR cc_start: 0.8522 (t80) cc_final: 0.8011 (t80) REVERT: d 27 ASN cc_start: 0.8930 (p0) cc_final: 0.8655 (p0) REVERT: e 5 ASP cc_start: 0.8507 (t0) cc_final: 0.8121 (m-30) REVERT: e 24 GLU cc_start: 0.8339 (tp30) cc_final: 0.7939 (mm-30) REVERT: e 65 GLU cc_start: 0.8625 (tp30) cc_final: 0.8096 (tp30) REVERT: e 82 GLN cc_start: 0.8647 (tp40) cc_final: 0.8443 (tp40) REVERT: f 28 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.8014 (mtm-85) REVERT: f 47 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7605 (tm-30) REVERT: g 85 MET cc_start: 0.8748 (tmm) cc_final: 0.8522 (tmm) REVERT: g 119 GLU cc_start: 0.8903 (tp30) cc_final: 0.8671 (tp30) REVERT: g 136 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: h 74 TYR cc_start: 0.8709 (m-10) cc_final: 0.8116 (m-80) REVERT: i 96 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8125 (p) REVERT: j 91 GLN cc_start: 0.9091 (tp40) cc_final: 0.8648 (mm110) REVERT: k 30 ILE cc_start: 0.9295 (tp) cc_final: 0.9003 (tp) REVERT: k 40 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8663 (ttmm) REVERT: k 81 PHE cc_start: 0.9216 (t80) cc_final: 0.8995 (t80) REVERT: l 53 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8865 (tptp) REVERT: l 70 MET cc_start: 0.9127 (tpp) cc_final: 0.8885 (mmt) REVERT: l 91 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8380 (mt0) REVERT: l 170 ARG cc_start: 0.9038 (ttm-80) cc_final: 0.8751 (mtt-85) REVERT: m 77 TYR cc_start: 0.8903 (t80) cc_final: 0.8574 (t80) REVERT: m 113 GLU cc_start: 0.8757 (tp30) cc_final: 0.8507 (tp30) REVERT: m 125 PHE cc_start: 0.8710 (m-10) cc_final: 0.8418 (m-80) REVERT: n 13 GLN cc_start: 0.8736 (tt0) cc_final: 0.8281 (mp10) REVERT: n 20 TYR cc_start: 0.9163 (t80) cc_final: 0.8945 (t80) REVERT: n 59 ARG cc_start: 0.8303 (tpt-90) cc_final: 0.7944 (tpt170) REVERT: n 63 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8534 (mp) REVERT: o 18 ASP cc_start: 0.7376 (t0) cc_final: 0.6270 (t0) REVERT: o 20 GLU cc_start: 0.7427 (pm20) cc_final: 0.7170 (pm20) REVERT: o 21 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8215 (ptpp) REVERT: o 26 PRO cc_start: 0.9260 (Cg_exo) cc_final: 0.9017 (Cg_endo) REVERT: o 44 GLN cc_start: 0.7924 (tp40) cc_final: 0.7104 (tp40) REVERT: o 65 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8655 (mmm-85) REVERT: o 103 GLU cc_start: 0.8657 (tp30) cc_final: 0.8443 (tp30) REVERT: o 112 LYS cc_start: 0.9213 (tppt) cc_final: 0.8925 (tppt) REVERT: p 97 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8359 (mtmm) REVERT: p 153 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8108 (mtm-85) outliers start: 120 outliers final: 64 residues processed: 901 average time/residue: 0.1982 time to fit residues: 288.8522 Evaluate side-chains 829 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 759 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 437 PHE Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 142 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 136 GLU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain h residue 177 GLU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain p residue 103 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 220 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 328 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 334 optimal weight: 0.0470 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 323 HIS M 89 ASN M 415 GLN N 222 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 GLN ** O 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN c 73 ASN g 68 ASN g 113 GLN h 90 ASN l 80 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN o 110 GLN p 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102764 restraints weight = 54408.614| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.90 r_work: 0.3250 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33055 Z= 0.155 Angle : 0.640 11.724 44654 Z= 0.318 Chirality : 0.042 0.186 4836 Planarity : 0.005 0.065 5461 Dihedral : 12.683 113.368 5145 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 4.04 % Allowed : 17.49 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3794 helix: 0.92 (0.10), residues: 2468 sheet: -0.75 (1.36), residues: 18 loop : -0.46 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG i 121 TYR 0.028 0.001 TYR O 241 PHE 0.024 0.002 PHE J 91 TRP 0.027 0.001 TRP O 353 HIS 0.007 0.001 HIS L 323 Details of bonding type rmsd covalent geometry : bond 0.00363 (33047) covalent geometry : angle 0.63986 (44638) SS BOND : bond 0.00177 ( 8) SS BOND : angle 1.03772 ( 16) hydrogen bonds : bond 0.04405 ( 1710) hydrogen bonds : angle 4.48487 ( 4959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 784 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 42 MET cc_start: 0.9336 (ttm) cc_final: 0.8875 (ttm) REVERT: J 54 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7529 (mmt) REVERT: J 134 MET cc_start: 0.5600 (mtt) cc_final: 0.5208 (tpt) REVERT: J 165 ILE cc_start: 0.9252 (mt) cc_final: 0.8894 (mm) REVERT: K 49 LEU cc_start: 0.9512 (mt) cc_final: 0.9305 (mt) REVERT: K 57 MET cc_start: 0.9281 (mmm) cc_final: 0.8920 (mmt) REVERT: L 84 PHE cc_start: 0.8618 (t80) cc_final: 0.8253 (t80) REVERT: L 132 THR cc_start: 0.9350 (m) cc_final: 0.9127 (p) REVERT: L 208 ASP cc_start: 0.8166 (t0) cc_final: 0.7692 (p0) REVERT: L 397 GLU cc_start: 0.7838 (pt0) cc_final: 0.7508 (pm20) REVERT: L 476 SER cc_start: 0.8348 (m) cc_final: 0.8037 (p) REVERT: L 513 MET cc_start: 0.7514 (ttp) cc_final: 0.7195 (mtm) REVERT: L 523 SER cc_start: 0.8692 (m) cc_final: 0.8337 (t) REVERT: L 547 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7436 (mmtm) REVERT: M 10 MET cc_start: 0.9004 (tpp) cc_final: 0.8533 (mmm) REVERT: M 85 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8460 (tptt) REVERT: M 141 GLU cc_start: 0.8451 (mp0) cc_final: 0.8235 (mp0) REVERT: M 187 ASP cc_start: 0.8531 (t0) cc_final: 0.8285 (t0) REVERT: M 271 MET cc_start: 0.8314 (mmp) cc_final: 0.7944 (mmp) REVERT: M 339 SER cc_start: 0.9288 (t) cc_final: 0.8982 (p) REVERT: N 237 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8853 (p) REVERT: N 335 MET cc_start: 0.8790 (ptm) cc_final: 0.8491 (ptp) REVERT: O 93 TYR cc_start: 0.8157 (t80) cc_final: 0.7841 (t80) REVERT: O 182 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: O 213 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7798 (tm-30) REVERT: O 236 ASP cc_start: 0.8698 (m-30) cc_final: 0.8498 (m-30) REVERT: O 300 ASP cc_start: 0.8298 (t0) cc_final: 0.7877 (t0) REVERT: U 143 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7953 (mt-10) REVERT: U 155 TYR cc_start: 0.9029 (p90) cc_final: 0.8724 (p90) REVERT: Y 22 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8353 (tpt90) REVERT: c 57 TYR cc_start: 0.8590 (t80) cc_final: 0.8034 (t80) REVERT: c 68 GLU cc_start: 0.8249 (tp30) cc_final: 0.7968 (tp30) REVERT: d 27 ASN cc_start: 0.8909 (p0) cc_final: 0.8662 (p0) REVERT: e 5 ASP cc_start: 0.8599 (t0) cc_final: 0.8172 (m-30) REVERT: e 24 GLU cc_start: 0.8379 (tp30) cc_final: 0.7909 (mm-30) REVERT: e 65 GLU cc_start: 0.8627 (tp30) cc_final: 0.8155 (tp30) REVERT: e 82 GLN cc_start: 0.8697 (tp40) cc_final: 0.8460 (tp40) REVERT: f 28 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7925 (mtm-85) REVERT: f 47 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7577 (tm-30) REVERT: g 119 GLU cc_start: 0.8874 (tp30) cc_final: 0.8650 (tp30) REVERT: g 136 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: h 74 TYR cc_start: 0.8722 (m-10) cc_final: 0.8201 (m-80) REVERT: h 86 ILE cc_start: 0.9373 (mm) cc_final: 0.9127 (mm) REVERT: i 96 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (p) REVERT: j 62 SER cc_start: 0.8988 (m) cc_final: 0.8622 (m) REVERT: k 40 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8696 (ttmm) REVERT: l 170 ARG cc_start: 0.9072 (ttm-80) cc_final: 0.8761 (mtt-85) REVERT: m 113 GLU cc_start: 0.8694 (tp30) cc_final: 0.8440 (tp30) REVERT: n 13 GLN cc_start: 0.8762 (tt0) cc_final: 0.8317 (mp10) REVERT: o 18 ASP cc_start: 0.7549 (t0) cc_final: 0.6409 (t70) REVERT: o 21 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8293 (ptpp) REVERT: o 26 PRO cc_start: 0.9356 (Cg_exo) cc_final: 0.9102 (Cg_endo) REVERT: o 44 GLN cc_start: 0.8077 (tp40) cc_final: 0.7257 (tp40) REVERT: o 103 GLU cc_start: 0.8639 (tp30) cc_final: 0.8383 (tp30) REVERT: p 143 TYR cc_start: 0.8362 (m-10) cc_final: 0.8018 (m-10) REVERT: p 153 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8087 (mtm-85) outliers start: 138 outliers final: 82 residues processed: 868 average time/residue: 0.1940 time to fit residues: 273.5408 Evaluate side-chains 831 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 743 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain M residue 458 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 182 GLN Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 142 LYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain g residue 136 GLU Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 177 GLU Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 123 PHE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 59 GLU Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 52 THR Chi-restraints excluded: chain p residue 103 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 317 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 308 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 362 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 56 HIS L 207 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN g 72 HIS h 90 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 141 GLN p 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105168 restraints weight = 54845.557| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.98 r_work: 0.3255 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33055 Z= 0.141 Angle : 0.636 14.314 44654 Z= 0.315 Chirality : 0.041 0.192 4836 Planarity : 0.005 0.065 5461 Dihedral : 12.380 111.212 5145 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 3.74 % Allowed : 18.16 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.75 (0.14), residues: 3794 helix: 1.04 (0.10), residues: 2471 sheet: -0.77 (1.33), residues: 18 loop : -0.41 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 121 TYR 0.026 0.001 TYR L 422 PHE 0.026 0.002 PHE J 91 TRP 0.029 0.001 TRP O 353 HIS 0.004 0.001 HIS l 84 Details of bonding type rmsd covalent geometry : bond 0.00329 (33047) covalent geometry : angle 0.63396 (44638) SS BOND : bond 0.00577 ( 8) SS BOND : angle 2.43920 ( 16) hydrogen bonds : bond 0.04239 ( 1710) hydrogen bonds : angle 4.40943 ( 4959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 773 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 42 MET cc_start: 0.9334 (ttm) cc_final: 0.8874 (ttm) REVERT: J 54 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: J 134 MET cc_start: 0.5812 (mtt) cc_final: 0.5376 (tpt) REVERT: J 165 ILE cc_start: 0.9246 (mt) cc_final: 0.8922 (mm) REVERT: K 10 MET cc_start: 0.8928 (mtp) cc_final: 0.8631 (mtm) REVERT: K 20 LEU cc_start: 0.9179 (mt) cc_final: 0.8856 (mt) REVERT: K 49 LEU cc_start: 0.9523 (mt) cc_final: 0.9318 (mt) REVERT: K 57 MET cc_start: 0.9299 (mmm) cc_final: 0.8953 (mmt) REVERT: L 84 PHE cc_start: 0.8647 (t80) cc_final: 0.8302 (t80) REVERT: L 132 THR cc_start: 0.9313 (m) cc_final: 0.9099 (p) REVERT: L 208 ASP cc_start: 0.8196 (t0) cc_final: 0.7721 (t70) REVERT: L 476 SER cc_start: 0.8298 (m) cc_final: 0.7973 (p) REVERT: L 523 SER cc_start: 0.8705 (m) cc_final: 0.8348 (t) REVERT: L 547 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7537 (mmtm) REVERT: M 10 MET cc_start: 0.9036 (tpp) cc_final: 0.8565 (mmm) REVERT: M 85 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8424 (tptt) REVERT: M 119 TYR cc_start: 0.9098 (t80) cc_final: 0.8830 (t80) REVERT: M 140 THR cc_start: 0.9115 (m) cc_final: 0.8755 (t) REVERT: M 141 GLU cc_start: 0.8468 (mp0) cc_final: 0.8049 (mp0) REVERT: M 187 ASP cc_start: 0.8564 (t0) cc_final: 0.8307 (t0) REVERT: M 271 MET cc_start: 0.8323 (mmp) cc_final: 0.7962 (mmp) REVERT: M 310 MET cc_start: 0.8704 (ppp) cc_final: 0.8443 (ppp) REVERT: M 339 SER cc_start: 0.9331 (t) cc_final: 0.9018 (p) REVERT: M 423 MET cc_start: 0.7836 (mmp) cc_final: 0.6589 (mmt) REVERT: N 22 SER cc_start: 0.9280 (t) cc_final: 0.9046 (p) REVERT: N 97 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8154 (ttp) REVERT: N 227 ILE cc_start: 0.8137 (pt) cc_final: 0.7850 (mt) REVERT: N 237 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8856 (p) REVERT: N 298 TYR cc_start: 0.8872 (m-10) cc_final: 0.8642 (m-10) REVERT: O 93 TYR cc_start: 0.8028 (t80) cc_final: 0.7812 (t80) REVERT: O 213 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7784 (tm-30) REVERT: O 236 ASP cc_start: 0.8781 (m-30) cc_final: 0.8539 (m-30) REVERT: O 238 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7873 (tp30) REVERT: O 300 ASP cc_start: 0.8254 (t0) cc_final: 0.7789 (t0) REVERT: U 155 TYR cc_start: 0.9006 (p90) cc_final: 0.8702 (p90) REVERT: Y 4 VAL cc_start: 0.7316 (m) cc_final: 0.6933 (t) REVERT: Y 22 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8289 (tpt90) REVERT: Y 133 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8540 (mt-10) REVERT: c 57 TYR cc_start: 0.8602 (t80) cc_final: 0.8046 (t80) REVERT: c 68 GLU cc_start: 0.8268 (tp30) cc_final: 0.7952 (tp30) REVERT: d 27 ASN cc_start: 0.8876 (p0) cc_final: 0.8643 (p0) REVERT: e 5 ASP cc_start: 0.8529 (t0) cc_final: 0.8141 (m-30) REVERT: e 24 GLU cc_start: 0.8423 (tp30) cc_final: 0.7831 (mm-30) REVERT: e 65 GLU cc_start: 0.8756 (tp30) cc_final: 0.8288 (tp30) REVERT: e 74 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7879 (tpt170) REVERT: f 28 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7922 (mtm-85) REVERT: f 47 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7633 (tm-30) REVERT: g 119 GLU cc_start: 0.8883 (tp30) cc_final: 0.8623 (tp30) REVERT: g 136 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8518 (mp0) REVERT: h 74 TYR cc_start: 0.8744 (m-10) cc_final: 0.8266 (m-80) REVERT: j 62 SER cc_start: 0.8975 (m) cc_final: 0.8599 (m) REVERT: j 91 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8669 (mm110) REVERT: j 97 LEU cc_start: 0.9273 (mm) cc_final: 0.8936 (tp) REVERT: k 40 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8716 (ttmm) REVERT: k 60 MET cc_start: 0.8921 (tpp) cc_final: 0.8095 (tpp) REVERT: l 170 ARG cc_start: 0.9093 (ttm-80) cc_final: 0.8758 (mtt-85) REVERT: m 113 GLU cc_start: 0.8691 (tp30) cc_final: 0.8426 (tp30) REVERT: n 13 GLN cc_start: 0.8787 (tt0) cc_final: 0.8298 (mp10) REVERT: n 58 MET cc_start: 0.8866 (mtp) cc_final: 0.8487 (mtm) REVERT: o 18 ASP cc_start: 0.7516 (t0) cc_final: 0.6134 (t70) REVERT: o 20 GLU cc_start: 0.7403 (pm20) cc_final: 0.7127 (pm20) REVERT: o 21 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8338 (ptpp) REVERT: o 26 PRO cc_start: 0.9382 (Cg_exo) cc_final: 0.9142 (Cg_endo) REVERT: o 44 GLN cc_start: 0.8083 (tp40) cc_final: 0.7201 (tp40) REVERT: o 112 LYS cc_start: 0.9171 (tppt) cc_final: 0.8933 (tppt) REVERT: p 143 TYR cc_start: 0.8425 (m-10) cc_final: 0.8048 (m-10) REVERT: p 153 ARG cc_start: 0.8666 (mtm110) cc_final: 0.8384 (mtm-85) outliers start: 128 outliers final: 86 residues processed: 848 average time/residue: 0.1924 time to fit residues: 265.5849 Evaluate side-chains 822 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 732 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 210 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 111 SER Chi-restraints excluded: chain O residue 182 GLN Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 TYR Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain h residue 177 GLU Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 123 PHE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 50 GLU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 57 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 230 HIS L 361 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 GLN e 34 HIS h 90 ASN h 154 GLN l 84 HIS ** 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 = 0.3548 r_free = 0.3548 target = 0.115819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098595 restraints weight = 54755.997| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.92 r_work: 0.3185 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33055 Z= 0.213 Angle : 0.690 11.375 44654 Z= 0.342 Chirality : 0.044 0.197 4836 Planarity : 0.005 0.063 5461 Dihedral : 12.242 111.325 5145 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 4.12 % Allowed : 18.16 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3794 helix: 1.08 (0.10), residues: 2460 sheet: -0.70 (1.32), residues: 18 loop : -0.47 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 71 TYR 0.027 0.002 TYR h 105 PHE 0.025 0.002 PHE L 124 TRP 0.031 0.001 TRP O 353 HIS 0.009 0.001 HIS i 83 Details of bonding type rmsd covalent geometry : bond 0.00509 (33047) covalent geometry : angle 0.68981 (44638) SS BOND : bond 0.01151 ( 8) SS BOND : angle 1.28272 ( 16) hydrogen bonds : bond 0.04443 ( 1710) hydrogen bonds : angle 4.44621 ( 4959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 747 time to evaluate : 1.059 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: J 42 MET cc_start: 0.9328 (ttm) cc_final: 0.8895 (ttm) REVERT: J 54 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7441 (mmt) REVERT: J 91 PHE cc_start: 0.7736 (m-80) cc_final: 0.7268 (m-80) REVERT: K 49 LEU cc_start: 0.9506 (mt) cc_final: 0.9261 (mt) REVERT: K 57 MET cc_start: 0.9303 (mmm) cc_final: 0.8966 (mmt) REVERT: L 59 MET cc_start: 0.8251 (ptp) cc_final: 0.8032 (ptp) REVERT: L 84 PHE cc_start: 0.8640 (t80) cc_final: 0.8277 (t80) REVERT: L 476 SER cc_start: 0.8340 (m) cc_final: 0.8110 (p) REVERT: L 523 SER cc_start: 0.8733 (m) cc_final: 0.8417 (t) REVERT: M 10 MET cc_start: 0.9083 (tpp) cc_final: 0.8630 (mmm) REVERT: M 85 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8479 (tptt) REVERT: M 140 THR cc_start: 0.9132 (m) cc_final: 0.8883 (t) REVERT: M 141 GLU cc_start: 0.8512 (mp0) cc_final: 0.8139 (mp0) REVERT: M 187 ASP cc_start: 0.8589 (t0) cc_final: 0.8324 (t0) REVERT: M 271 MET cc_start: 0.8443 (mmp) cc_final: 0.8102 (mmp) REVERT: N 22 SER cc_start: 0.9266 (t) cc_final: 0.9016 (p) REVERT: N 97 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8177 (ttp) REVERT: N 164 MET cc_start: 0.9059 (mmt) cc_final: 0.8822 (mmt) REVERT: N 237 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8892 (p) REVERT: O 213 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7789 (tm-30) REVERT: O 236 ASP cc_start: 0.8729 (m-30) cc_final: 0.8473 (m-30) REVERT: O 249 MET cc_start: 0.6751 (mmm) cc_final: 0.6523 (mmm) REVERT: O 300 ASP cc_start: 0.8361 (t0) cc_final: 0.7959 (t0) REVERT: U 155 TYR cc_start: 0.9055 (p90) cc_final: 0.8725 (p90) REVERT: Y 19 GLN cc_start: 0.7798 (mt0) cc_final: 0.7327 (mm-40) REVERT: Y 22 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8278 (tpt90) REVERT: Y 133 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8520 (mt-10) REVERT: c 53 PHE cc_start: 0.8542 (t80) cc_final: 0.8285 (t80) REVERT: c 57 TYR cc_start: 0.8628 (t80) cc_final: 0.8187 (t80) REVERT: c 68 GLU cc_start: 0.8331 (tp30) cc_final: 0.8010 (tp30) REVERT: d 27 ASN cc_start: 0.8937 (p0) cc_final: 0.8667 (p0) REVERT: e 24 GLU cc_start: 0.8385 (tp30) cc_final: 0.7785 (mm-30) REVERT: e 65 GLU cc_start: 0.8848 (tp30) cc_final: 0.8384 (tp30) REVERT: f 28 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7978 (mtm-85) REVERT: f 47 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7703 (tm-30) REVERT: g 113 GLN cc_start: 0.8346 (pt0) cc_final: 0.8075 (mt0) REVERT: h 74 TYR cc_start: 0.8879 (m-10) cc_final: 0.8490 (m-80) REVERT: i 96 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8198 (p) REVERT: k 40 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8711 (ttmm) REVERT: k 60 MET cc_start: 0.8982 (tpp) cc_final: 0.8029 (tpp) REVERT: l 36 MET cc_start: 0.8466 (ptm) cc_final: 0.8166 (ptt) REVERT: l 68 ASP cc_start: 0.8582 (p0) cc_final: 0.7752 (t0) REVERT: l 170 ARG cc_start: 0.9153 (ttm-80) cc_final: 0.8769 (mtt90) REVERT: m 113 GLU cc_start: 0.8731 (tp30) cc_final: 0.8516 (tp30) REVERT: n 13 GLN cc_start: 0.8810 (tt0) cc_final: 0.8358 (mp10) REVERT: n 58 MET cc_start: 0.8895 (mtp) cc_final: 0.8499 (mtm) REVERT: n 101 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: o 18 ASP cc_start: 0.7653 (t0) cc_final: 0.6450 (t70) REVERT: o 21 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8401 (ptpp) REVERT: o 26 PRO cc_start: 0.9433 (Cg_exo) cc_final: 0.9193 (Cg_endo) REVERT: o 44 GLN cc_start: 0.8066 (tp40) cc_final: 0.7386 (tp40) REVERT: o 112 LYS cc_start: 0.9181 (tppt) cc_final: 0.8957 (tppt) REVERT: p 97 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8386 (mtmm) REVERT: p 143 TYR cc_start: 0.8736 (m-10) cc_final: 0.8404 (m-10) outliers start: 141 outliers final: 103 residues processed: 831 average time/residue: 0.1959 time to fit residues: 264.7727 Evaluate side-chains 828 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 720 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 PHE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 210 ILE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 333 SER Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 241 TYR Chi-restraints excluded: chain O residue 251 GLU Chi-restraints excluded: chain O residue 261 TRP Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 20 CYS Chi-restraints excluded: chain c residue 66 VAL Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain h residue 177 GLU Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 123 PHE Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 59 GLU Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain n residue 50 GLU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 52 THR Chi-restraints excluded: chain p residue 77 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 322 optimal weight: 0.8980 chunk 327 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 361 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 ASN ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103441 restraints weight = 55071.677| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.02 r_work: 0.3226 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33055 Z= 0.142 Angle : 0.654 12.831 44654 Z= 0.322 Chirality : 0.042 0.190 4836 Planarity : 0.005 0.066 5461 Dihedral : 11.921 106.668 5145 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 3.57 % Allowed : 19.60 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3794 helix: 1.22 (0.11), residues: 2448 sheet: -0.60 (1.29), residues: 18 loop : -0.37 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 121 TYR 0.042 0.001 TYR M 119 PHE 0.024 0.002 PHE L 124 TRP 0.033 0.001 TRP O 353 HIS 0.006 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00334 (33047) covalent geometry : angle 0.65336 (44638) SS BOND : bond 0.00206 ( 8) SS BOND : angle 1.00156 ( 16) hydrogen bonds : bond 0.04165 ( 1710) hydrogen bonds : angle 4.35997 ( 4959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 757 time to evaluate : 1.208 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: D 45 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8533 (mm-30) REVERT: J 42 MET cc_start: 0.9320 (ttm) cc_final: 0.8940 (ttm) REVERT: J 98 MET cc_start: 0.7380 (ppp) cc_final: 0.7021 (ptt) REVERT: J 134 MET cc_start: 0.5995 (mtt) cc_final: 0.5643 (tpt) REVERT: K 49 LEU cc_start: 0.9520 (mt) cc_final: 0.9313 (mt) REVERT: K 57 MET cc_start: 0.9281 (mmm) cc_final: 0.8958 (mmt) REVERT: L 59 MET cc_start: 0.8207 (ptp) cc_final: 0.7980 (ptp) REVERT: L 84 PHE cc_start: 0.8637 (t80) cc_final: 0.8325 (t80) REVERT: L 476 SER cc_start: 0.8259 (m) cc_final: 0.7989 (p) REVERT: L 523 SER cc_start: 0.8709 (m) cc_final: 0.8396 (t) REVERT: L 547 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7561 (mmtm) REVERT: L 548 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8955 (m) REVERT: M 10 MET cc_start: 0.9051 (tpp) cc_final: 0.8592 (mmm) REVERT: M 85 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8435 (tptt) REVERT: M 140 THR cc_start: 0.9092 (m) cc_final: 0.8857 (t) REVERT: M 141 GLU cc_start: 0.8504 (mp0) cc_final: 0.8156 (mp0) REVERT: M 187 ASP cc_start: 0.8607 (t0) cc_final: 0.8335 (t0) REVERT: M 271 MET cc_start: 0.8483 (mmp) cc_final: 0.8097 (mmp) REVERT: M 423 MET cc_start: 0.7888 (mmp) cc_final: 0.6722 (mmt) REVERT: N 22 SER cc_start: 0.9265 (t) cc_final: 0.9006 (p) REVERT: N 43 MET cc_start: 0.8907 (mmm) cc_final: 0.8618 (tpt) REVERT: N 237 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (p) REVERT: O 213 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7827 (tm-30) REVERT: O 236 ASP cc_start: 0.8759 (m-30) cc_final: 0.8508 (m-30) REVERT: O 249 MET cc_start: 0.6681 (mmm) cc_final: 0.5916 (mmm) REVERT: O 300 ASP cc_start: 0.8353 (t0) cc_final: 0.7894 (t0) REVERT: U 155 TYR cc_start: 0.9032 (p90) cc_final: 0.8796 (p90) REVERT: Y 19 GLN cc_start: 0.7681 (mt0) cc_final: 0.7194 (mm-40) REVERT: Y 22 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8301 (tpt90) REVERT: Y 133 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8604 (mt-10) REVERT: c 57 TYR cc_start: 0.8622 (t80) cc_final: 0.8080 (t80) REVERT: c 68 GLU cc_start: 0.8306 (tp30) cc_final: 0.7848 (tp30) REVERT: e 24 GLU cc_start: 0.8380 (tp30) cc_final: 0.7877 (mm-30) REVERT: e 65 GLU cc_start: 0.8871 (tp30) cc_final: 0.8371 (tp30) REVERT: e 74 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: f 28 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7980 (mtm-85) REVERT: g 75 ASP cc_start: 0.8721 (t0) cc_final: 0.8450 (t0) REVERT: g 113 GLN cc_start: 0.8308 (pt0) cc_final: 0.8012 (mt0) REVERT: g 130 ASN cc_start: 0.8815 (m-40) cc_final: 0.8579 (m-40) REVERT: g 144 LYS cc_start: 0.8881 (mttm) cc_final: 0.8559 (mttm) REVERT: h 74 TYR cc_start: 0.8840 (m-10) cc_final: 0.8500 (m-80) REVERT: i 96 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (p) REVERT: k 40 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8689 (ttmm) REVERT: l 68 ASP cc_start: 0.8556 (p0) cc_final: 0.7658 (t0) REVERT: l 165 ASN cc_start: 0.9106 (t0) cc_final: 0.8878 (t0) REVERT: l 170 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8641 (mtt90) REVERT: m 113 GLU cc_start: 0.8757 (tp30) cc_final: 0.8516 (tp30) REVERT: n 13 GLN cc_start: 0.8781 (tt0) cc_final: 0.8317 (mp10) REVERT: n 58 MET cc_start: 0.8874 (mtp) cc_final: 0.8466 (mtm) REVERT: n 94 TYR cc_start: 0.8738 (m-80) cc_final: 0.8488 (m-80) REVERT: n 101 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: o 18 ASP cc_start: 0.7568 (t0) cc_final: 0.6317 (t0) REVERT: o 20 GLU cc_start: 0.7499 (pm20) cc_final: 0.7248 (pm20) REVERT: o 21 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8334 (ptpp) REVERT: o 44 GLN cc_start: 0.8103 (tp40) cc_final: 0.7284 (tp-100) REVERT: o 76 ASN cc_start: 0.8498 (t0) cc_final: 0.8263 (t0) REVERT: o 112 LYS cc_start: 0.9218 (tppt) cc_final: 0.8973 (tppt) REVERT: p 108 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8089 (mt-10) REVERT: p 143 TYR cc_start: 0.8688 (m-10) cc_final: 0.8356 (m-10) outliers start: 122 outliers final: 85 residues processed: 834 average time/residue: 0.1953 time to fit residues: 264.7474 Evaluate side-chains 816 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 726 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 PHE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 210 ILE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 241 TYR Chi-restraints excluded: chain O residue 251 GLU Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 20 CYS Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 51 MET Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 59 GLU Chi-restraints excluded: chain k residue 88 LEU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain n residue 50 GLU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain p residue 77 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 364 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 296 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 248 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 361 ASN M 89 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 ASN h 154 GLN l 56 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102476 restraints weight = 54244.553| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.93 r_work: 0.3245 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33055 Z= 0.137 Angle : 0.652 11.624 44654 Z= 0.321 Chirality : 0.042 0.191 4836 Planarity : 0.005 0.064 5461 Dihedral : 11.642 107.298 5145 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.92 % Allowed : 20.12 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3794 helix: 1.26 (0.10), residues: 2460 sheet: -0.58 (1.28), residues: 18 loop : -0.38 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 19 TYR 0.035 0.001 TYR O 93 PHE 0.023 0.001 PHE L 124 TRP 0.033 0.001 TRP O 353 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00322 (33047) covalent geometry : angle 0.65224 (44638) SS BOND : bond 0.00128 ( 8) SS BOND : angle 0.96366 ( 16) hydrogen bonds : bond 0.04080 ( 1710) hydrogen bonds : angle 4.32071 ( 4959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 749 time to evaluate : 1.253 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: J 42 MET cc_start: 0.9318 (ttm) cc_final: 0.8931 (ttm) REVERT: J 54 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7301 (mmt) REVERT: J 98 MET cc_start: 0.7583 (ppp) cc_final: 0.7059 (ptt) REVERT: J 134 MET cc_start: 0.6174 (mtt) cc_final: 0.5829 (tpt) REVERT: K 57 MET cc_start: 0.9274 (mmm) cc_final: 0.8961 (mmt) REVERT: L 53 MET cc_start: 0.9042 (mtt) cc_final: 0.8783 (ttm) REVERT: L 59 MET cc_start: 0.8133 (ptp) cc_final: 0.7906 (ptp) REVERT: L 84 PHE cc_start: 0.8661 (t80) cc_final: 0.8407 (t80) REVERT: L 476 SER cc_start: 0.8136 (m) cc_final: 0.7877 (p) REVERT: L 523 SER cc_start: 0.8611 (m) cc_final: 0.8325 (t) REVERT: L 547 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7603 (mmtm) REVERT: L 548 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8868 (m) REVERT: M 10 MET cc_start: 0.8992 (tpp) cc_final: 0.8552 (mmm) REVERT: M 95 TYR cc_start: 0.9157 (t80) cc_final: 0.8891 (t80) REVERT: M 140 THR cc_start: 0.9018 (m) cc_final: 0.8725 (t) REVERT: M 141 GLU cc_start: 0.8486 (mp0) cc_final: 0.8133 (mp0) REVERT: M 187 ASP cc_start: 0.8566 (t0) cc_final: 0.8300 (t0) REVERT: M 271 MET cc_start: 0.8464 (mmp) cc_final: 0.8073 (mmp) REVERT: M 399 ASN cc_start: 0.8427 (t0) cc_final: 0.8187 (t0) REVERT: M 423 MET cc_start: 0.7858 (mmp) cc_final: 0.6671 (mmt) REVERT: N 22 SER cc_start: 0.9186 (t) cc_final: 0.8935 (p) REVERT: N 97 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: N 126 MET cc_start: 0.6799 (mmp) cc_final: 0.6439 (mmp) REVERT: N 164 MET cc_start: 0.9023 (mmt) cc_final: 0.8805 (mmt) REVERT: N 237 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8840 (p) REVERT: O 213 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7821 (tm-30) REVERT: O 236 ASP cc_start: 0.8814 (m-30) cc_final: 0.8560 (m-30) REVERT: O 249 MET cc_start: 0.6677 (mmm) cc_final: 0.5939 (mmm) REVERT: O 300 ASP cc_start: 0.8364 (t0) cc_final: 0.7893 (t0) REVERT: U 155 TYR cc_start: 0.8963 (p90) cc_final: 0.8740 (p90) REVERT: Y 22 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8383 (tpt90) REVERT: Y 133 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8583 (mt-10) REVERT: c 57 TYR cc_start: 0.8662 (t80) cc_final: 0.8138 (t80) REVERT: c 68 GLU cc_start: 0.8142 (tp30) cc_final: 0.7832 (tp30) REVERT: e 24 GLU cc_start: 0.8385 (tp30) cc_final: 0.7990 (mm-30) REVERT: e 65 GLU cc_start: 0.8859 (tp30) cc_final: 0.8378 (tp30) REVERT: e 73 MET cc_start: 0.8541 (mtt) cc_final: 0.8331 (mtt) REVERT: e 74 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: f 28 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7991 (mtm-85) REVERT: f 47 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7567 (tm-30) REVERT: g 113 GLN cc_start: 0.8251 (pt0) cc_final: 0.8026 (mt0) REVERT: g 114 GLU cc_start: 0.9166 (tp30) cc_final: 0.8936 (tp30) REVERT: g 130 ASN cc_start: 0.8802 (m-40) cc_final: 0.8563 (m-40) REVERT: h 74 TYR cc_start: 0.8747 (m-10) cc_final: 0.8416 (m-80) REVERT: i 96 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8137 (p) REVERT: k 40 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8691 (ttmm) REVERT: l 32 MET cc_start: 0.7941 (mmm) cc_final: 0.7701 (tpp) REVERT: l 34 LYS cc_start: 0.8680 (pttp) cc_final: 0.8311 (mmmt) REVERT: l 68 ASP cc_start: 0.8516 (p0) cc_final: 0.7617 (t0) REVERT: l 118 ASP cc_start: 0.7889 (t0) cc_final: 0.7362 (t70) REVERT: l 170 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8636 (mtt90) REVERT: m 28 GLU cc_start: 0.8667 (pm20) cc_final: 0.8440 (pm20) REVERT: m 113 GLU cc_start: 0.8770 (tp30) cc_final: 0.8378 (tp30) REVERT: n 13 GLN cc_start: 0.8746 (tt0) cc_final: 0.8325 (mp10) REVERT: n 58 MET cc_start: 0.8869 (mtp) cc_final: 0.8480 (mtm) REVERT: n 94 TYR cc_start: 0.8770 (m-80) cc_final: 0.8534 (m-80) REVERT: n 101 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: o 18 ASP cc_start: 0.7624 (t0) cc_final: 0.6231 (t70) REVERT: o 20 GLU cc_start: 0.7432 (pm20) cc_final: 0.7188 (pm20) REVERT: o 21 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8399 (ptpp) REVERT: o 44 GLN cc_start: 0.8080 (tp40) cc_final: 0.7551 (tp40) REVERT: o 48 ASP cc_start: 0.8519 (m-30) cc_final: 0.8038 (m-30) REVERT: o 76 ASN cc_start: 0.8466 (t0) cc_final: 0.8214 (t0) REVERT: o 103 GLU cc_start: 0.8532 (tp30) cc_final: 0.8124 (tm-30) REVERT: p 108 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8017 (mt-10) REVERT: p 143 TYR cc_start: 0.8667 (m-10) cc_final: 0.8326 (m-10) outliers start: 100 outliers final: 77 residues processed: 811 average time/residue: 0.1914 time to fit residues: 251.6943 Evaluate side-chains 807 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 723 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 56 PHE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 210 ILE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 241 TYR Chi-restraints excluded: chain O residue 251 GLU Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 20 CYS Chi-restraints excluded: chain c residue 32 ARG Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 51 MET Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 59 GLU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain n residue 50 GLU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 360 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN K 92 ASN L 361 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 GLN h 90 ASN j 57 GLN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099868 restraints weight = 54943.410| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.92 r_work: 0.3184 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33055 Z= 0.181 Angle : 0.684 12.146 44654 Z= 0.337 Chirality : 0.044 0.215 4836 Planarity : 0.005 0.064 5461 Dihedral : 11.580 107.094 5145 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.84 % Allowed : 20.47 % Favored : 76.69 % 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: 0.96 (0.14), residues: 3794 helix: 1.24 (0.10), residues: 2455 sheet: -0.65 (1.27), residues: 18 loop : -0.38 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 121 TYR 0.023 0.002 TYR J 69 PHE 0.027 0.002 PHE L 124 TRP 0.033 0.001 TRP O 353 HIS 0.008 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00435 (33047) covalent geometry : angle 0.68368 (44638) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.95015 ( 16) hydrogen bonds : bond 0.04234 ( 1710) hydrogen bonds : angle 4.38332 ( 4959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7588 Ramachandran restraints generated. 3794 Oldfield, 0 Emsley, 3794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 730 time to evaluate : 1.208 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: J 42 MET cc_start: 0.9295 (ttm) cc_final: 0.8910 (ttm) REVERT: J 54 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7426 (mmt) REVERT: J 91 PHE cc_start: 0.7913 (m-80) cc_final: 0.7568 (m-80) REVERT: J 98 MET cc_start: 0.7629 (ppp) cc_final: 0.7137 (ptt) REVERT: J 134 MET cc_start: 0.5720 (mtt) cc_final: 0.5291 (mmt) REVERT: K 21 MET cc_start: 0.8679 (mtp) cc_final: 0.8123 (mmt) REVERT: K 57 MET cc_start: 0.9296 (mmm) cc_final: 0.9006 (mmt) REVERT: L 53 MET cc_start: 0.9044 (mtt) cc_final: 0.8760 (ttm) REVERT: L 59 MET cc_start: 0.8118 (ptp) cc_final: 0.7895 (ptp) REVERT: L 71 MET cc_start: 0.8074 (tpp) cc_final: 0.7806 (tpp) REVERT: L 84 PHE cc_start: 0.8701 (t80) cc_final: 0.8422 (t80) REVERT: L 193 MET cc_start: 0.7998 (tpp) cc_final: 0.7585 (mmp) REVERT: L 476 SER cc_start: 0.8207 (m) cc_final: 0.7946 (p) REVERT: L 523 SER cc_start: 0.8722 (m) cc_final: 0.8449 (t) REVERT: L 547 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7607 (mmtm) REVERT: L 548 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8961 (m) REVERT: M 10 MET cc_start: 0.8997 (tpp) cc_final: 0.8558 (mmm) REVERT: M 95 TYR cc_start: 0.9192 (t80) cc_final: 0.8957 (t80) REVERT: M 140 THR cc_start: 0.9035 (m) cc_final: 0.8798 (t) REVERT: M 141 GLU cc_start: 0.8457 (mp0) cc_final: 0.8126 (mp0) REVERT: M 187 ASP cc_start: 0.8525 (t0) cc_final: 0.8243 (t0) REVERT: M 271 MET cc_start: 0.8505 (mmp) cc_final: 0.8147 (mmp) REVERT: M 423 MET cc_start: 0.7909 (mmp) cc_final: 0.6832 (mmt) REVERT: N 22 SER cc_start: 0.9184 (t) cc_final: 0.8818 (p) REVERT: N 97 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8050 (ttp) REVERT: O 213 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7813 (tm-30) REVERT: O 236 ASP cc_start: 0.8788 (m-30) cc_final: 0.8563 (m-30) REVERT: O 249 MET cc_start: 0.6801 (mmm) cc_final: 0.5934 (mmm) REVERT: O 265 ASP cc_start: 0.8305 (t0) cc_final: 0.8003 (t0) REVERT: O 300 ASP cc_start: 0.8393 (t0) cc_final: 0.7922 (t0) REVERT: Y 19 GLN cc_start: 0.7683 (mt0) cc_final: 0.7174 (mm-40) REVERT: Y 22 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8354 (tpt90) REVERT: Y 133 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8627 (mt-10) REVERT: c 53 PHE cc_start: 0.8519 (t80) cc_final: 0.8254 (t80) REVERT: c 57 TYR cc_start: 0.8686 (t80) cc_final: 0.8250 (t80) REVERT: c 68 GLU cc_start: 0.8102 (tp30) cc_final: 0.7880 (tp30) REVERT: d 2 MET cc_start: 0.8356 (mmm) cc_final: 0.7815 (mtt) REVERT: e 24 GLU cc_start: 0.8384 (tp30) cc_final: 0.7984 (mm-30) REVERT: e 73 MET cc_start: 0.8577 (mtt) cc_final: 0.8367 (mtt) REVERT: e 74 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: f 28 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7990 (mtm-85) REVERT: f 47 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7637 (tm-30) REVERT: g 113 GLN cc_start: 0.8284 (pt0) cc_final: 0.8061 (mt0) REVERT: g 130 ASN cc_start: 0.8810 (m-40) cc_final: 0.8560 (m-40) REVERT: h 74 TYR cc_start: 0.8823 (m-10) cc_final: 0.8535 (m-80) REVERT: h 153 GLU cc_start: 0.8228 (tt0) cc_final: 0.7949 (tt0) REVERT: i 96 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8168 (p) REVERT: k 78 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8046 (ttpp) REVERT: l 36 MET cc_start: 0.8345 (ptm) cc_final: 0.8051 (ptt) REVERT: l 68 ASP cc_start: 0.8562 (p0) cc_final: 0.7664 (t0) REVERT: l 118 ASP cc_start: 0.7917 (t0) cc_final: 0.7405 (t70) REVERT: l 170 ARG cc_start: 0.9244 (ttm-80) cc_final: 0.8554 (ttm-80) REVERT: m 113 GLU cc_start: 0.8672 (tp30) cc_final: 0.8373 (tp30) REVERT: n 13 GLN cc_start: 0.8778 (tt0) cc_final: 0.8352 (mp10) REVERT: n 58 MET cc_start: 0.8916 (mtp) cc_final: 0.8488 (mtm) REVERT: n 101 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: n 106 TYR cc_start: 0.8964 (m-80) cc_final: 0.8739 (m-80) REVERT: o 18 ASP cc_start: 0.7702 (t0) cc_final: 0.6312 (t70) REVERT: o 20 GLU cc_start: 0.7456 (pm20) cc_final: 0.7202 (pm20) REVERT: o 21 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8471 (ptpp) REVERT: o 40 VAL cc_start: 0.8748 (t) cc_final: 0.8400 (t) REVERT: o 44 GLN cc_start: 0.8164 (tp40) cc_final: 0.7865 (tp40) REVERT: o 48 ASP cc_start: 0.8541 (m-30) cc_final: 0.8217 (m-30) REVERT: o 76 ASN cc_start: 0.8584 (t0) cc_final: 0.8361 (t0) REVERT: o 103 GLU cc_start: 0.8577 (tp30) cc_final: 0.8175 (tm-30) REVERT: p 108 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8070 (mt-10) outliers start: 97 outliers final: 82 residues processed: 792 average time/residue: 0.1993 time to fit residues: 255.7579 Evaluate side-chains 801 residues out of total 3419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 713 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 355 ASP Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 183 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 448 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 210 ILE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 241 TYR Chi-restraints excluded: chain O residue 251 GLU Chi-restraints excluded: chain O residue 304 VAL Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 134 ASP Chi-restraints excluded: chain U residue 151 LYS Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 20 CYS Chi-restraints excluded: chain c residue 32 ARG Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 51 MET Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain h residue 106 ILE Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 51 THR Chi-restraints excluded: chain j residue 59 GLU Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain n residue 50 GLU Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain n residue 110 SER Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 52 THR Chi-restraints excluded: chain p residue 77 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 327 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 321 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN K 92 ASN L 361 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 GLN h 90 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102131 restraints weight = 54440.061| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.91 r_work: 0.3223 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33055 Z= 0.141 Angle : 0.660 12.309 44654 Z= 0.326 Chirality : 0.042 0.196 4836 Planarity : 0.005 0.064 5461 Dihedral : 11.402 105.361 5145 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 2.75 % Allowed : 20.65 % Favored : 76.60 % 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: 1.06 (0.14), residues: 3794 helix: 1.33 (0.11), residues: 2453 sheet: -0.60 (1.29), residues: 18 loop : -0.37 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 121 TYR 0.050 0.002 TYR M 119 PHE 0.025 0.002 PHE L 124 TRP 0.033 0.001 TRP O 353 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00333 (33047) covalent geometry : angle 0.66002 (44638) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.92453 ( 16) hydrogen bonds : bond 0.04102 ( 1710) hydrogen bonds : angle 4.32968 ( 4959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8843.27 seconds wall clock time: 152 minutes 16.44 seconds (9136.44 seconds total)