Starting phenix.real_space_refine on Mon Jul 6 00:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibb_35338/07_2026/8ibb_35338.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.088 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 25 5.49 5 S 243 5.16 5 C 20887 2.51 5 N 5096 2.21 5 O 5629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31880 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: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1193 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 2 Chain: "K" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 4798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4798 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Chain: "M" Number of atoms: 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: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1030 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "c" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 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: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 842 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} 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: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 773 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 11, 'TRANS': 80} Chain breaks: 1 Chain: "j" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 587 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "k" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 578 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} 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: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1534 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1019 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "p" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1438 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 343 Unusual residues: {'3PE': 3, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Chain: "M" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "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: "j" 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: "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: 6.29, per 1000 atoms: 0.20 Number of scatterers: 31880 At special positions: 0 Unit cell: (184.8, 140.8, 147.4, 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 243 16.00 P 25 15.00 O 5629 8.00 N 5096 7.00 C 20887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS Y 20 " - pdb=" SG CYS Y 77 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 97 " - pdb=" SG CYS Y 117 " distance=2.36 Simple disulfide: pdb=" SG CYS e 33 " - pdb=" SG CYS e 66 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 5 sheets defined 67.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.748A pdb=" N GLN D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'J' and resid 3 through 21 removed outlier: 3.813A pdb=" N LEU J 8 " --> pdb=" O TYR J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 44 removed outlier: 4.203A pdb=" N LEU J 30 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 Processing helix chain 'J' and resid 62 through 74 Processing helix chain 'J' and resid 85 through 109 Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 148 through 171 removed outlier: 4.067A pdb=" N MET J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL J 153 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 21 removed outlier: 3.803A 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: 3.519A pdb=" N MET K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.559A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 85 removed outlier: 3.811A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.583A 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: 4.114A 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: 4.417A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 58 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 83 through 108 removed outlier: 3.576A 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: 3.677A 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: 4.374A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 270 removed outlier: 4.062A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 295 removed outlier: 3.837A 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: 3.504A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 Processing helix chain 'L' and resid 361 through 366 Processing helix chain 'L' and resid 366 through 381 Processing helix chain 'L' and resid 386 through 402 removed outlier: 3.530A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.789A 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: 4.759A 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: 5.301A 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 510 removed outlier: 3.693A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS L 510 " --> pdb=" O ASN L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 525 removed outlier: 3.837A pdb=" N SER L 523 " --> pdb=" O TYR L 519 " (cutoff:3.500A) 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: 3.837A pdb=" N SER L 545 " --> pdb=" O SER L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 561 Processing helix chain 'L' and resid 562 through 579 removed outlier: 3.683A pdb=" N THR L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER L 567 " --> pdb=" O PRO L 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 605 removed outlier: 3.500A 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: 3.506A pdb=" N ILE M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.695A 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: 3.575A 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: 3.543A 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: 3.936A 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: 3.627A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.744A 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: 3.816A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 258 removed outlier: 3.510A pdb=" N ALA M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.505A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.674A 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 removed outlier: 3.500A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) 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: 4.144A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE M 400 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.554A pdb=" N THR N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 removed outlier: 3.531A 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: 3.577A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS N 79 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 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: 3.534A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.558A pdb=" N LEU N 203 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.752A 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: 4.130A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 301 removed outlier: 3.836A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 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: 3.670A 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 48 through 53 removed outlier: 3.822A pdb=" N LEU O 53 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 82 Processing helix chain 'O' and resid 92 through 98 Processing helix chain 'O' and resid 113 through 120 Processing helix chain 'O' and resid 126 through 153 Processing helix chain 'O' and resid 162 through 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 removed outlier: 3.797A pdb=" N LYS O 221 " --> pdb=" O ARG O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 228 Processing helix chain 'O' and resid 230 through 243 Processing helix chain 'O' and resid 244 through 253 removed outlier: 3.704A pdb=" N GLU O 251 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET O 252 " --> pdb=" O LYS O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 276 Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 287 through 299 removed outlier: 4.568A 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: 3.652A 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: 3.659A 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: 3.520A pdb=" N ALA U 149 " --> pdb=" O VAL U 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.899A pdb=" N TYR Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS Y 12 " --> pdb=" O PHE Y 8 " (cutoff:3.500A) removed outlier: 3.632A 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: 4.212A pdb=" N TYR Y 92 " --> pdb=" O ASP Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 134 Processing helix chain 'c' and resid 40 through 73 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 28 through 49 Processing helix chain 'd' and resid 57 through 97 removed outlier: 3.609A pdb=" N LEU d 62 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG d 78 " --> pdb=" O PHE d 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 11 Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 33 through 42 removed outlier: 4.272A pdb=" N LYS e 38 " --> pdb=" O HIS e 34 " (cutoff:3.500A) removed outlier: 4.372A 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: 3.671A pdb=" N GLU e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 89 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 removed outlier: 3.845A pdb=" N GLY e 100 " --> pdb=" O HIS e 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 32 removed outlier: 3.842A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 86 Processing helix chain 'g' and resid 87 through 93 Processing helix chain 'g' and resid 98 through 106 Processing helix chain 'g' and resid 109 through 111 No H-bonds generated for 'chain 'g' and resid 109 through 111' Processing helix chain 'g' and resid 112 through 131 removed outlier: 3.824A pdb=" N ARG g 117 " --> pdb=" O GLN g 113 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG g 118 " --> pdb=" O GLU g 114 " (cutoff:3.500A) removed outlier: 3.978A 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: 5.115A pdb=" N LEU h 68 " --> pdb=" O ASP h 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE h 73 " --> pdb=" O ARG h 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET h 76 " --> pdb=" O LYS h 72 " (cutoff:3.500A) removed outlier: 3.952A 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: 4.012A pdb=" N ALA h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 164 removed outlier: 4.071A pdb=" N ASN h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.572A 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 70 through 89 removed outlier: 3.562A pdb=" N HIS i 74 " --> pdb=" O PHE i 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Proline residue: i 78 - end of helix removed outlier: 3.584A pdb=" N PHE i 81 " --> pdb=" O ILE i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 76 removed outlier: 3.603A pdb=" N VAL j 55 " --> pdb=" O THR j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 92 removed outlier: 4.187A pdb=" N TRP j 92 " --> pdb=" O PRO j 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 98 removed outlier: 3.521A pdb=" N LEU j 97 " --> pdb=" O THR j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 33 through 45 removed outlier: 4.162A 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: 4.336A pdb=" N TYR k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY k 61 " --> pdb=" O TRP k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 3.513A pdb=" N VAL k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 90 Processing helix chain 'l' and resid 33 through 37 Processing helix chain 'l' and resid 44 through 55 removed outlier: 3.837A 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 23 Processing helix chain 'm' and resid 28 through 52 removed outlier: 3.882A pdb=" N VAL m 34 " --> pdb=" O ARG m 30 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU m 37 " --> pdb=" O GLN m 33 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER m 38 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN m 50 " --> pdb=" O GLU m 46 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 74 removed outlier: 3.596A pdb=" N ILE m 66 " --> pdb=" O ASP m 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP m 68 " --> pdb=" O ALA m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 Processing helix chain 'm' and resid 95 through 101 Processing helix chain 'm' and resid 101 through 119 removed outlier: 3.810A 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: 3.525A pdb=" N MET n 44 " --> pdb=" O PHE n 40 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.635A pdb=" N GLU n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.709A pdb=" N PHE n 119 " --> pdb=" O TYR n 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN n 124 " --> pdb=" O SER n 120 " (cutoff:3.500A) removed outlier: 4.885A 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 18 through 22 removed outlier: 3.907A pdb=" N ILE o 22 " --> pdb=" O PRO o 19 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 49 Processing helix chain 'o' and resid 52 through 56 Processing helix chain 'o' and resid 59 through 72 removed outlier: 3.623A pdb=" N ARG o 65 " --> pdb=" O HIS o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 120 removed outlier: 4.036A pdb=" N LYS o 97 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 41 removed outlier: 3.740A pdb=" N TYR p 32 " --> pdb=" O ASN p 28 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU p 33 " --> pdb=" O PRO p 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU p 39 " --> pdb=" O LYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 59 removed outlier: 4.253A pdb=" N ASN p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 113 removed outlier: 3.523A pdb=" N TRP p 92 " --> pdb=" O ALA p 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE p 102 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET p 103 " --> pdb=" O ASP p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 140 removed outlier: 3.733A pdb=" N GLU p 130 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN p 131 " --> pdb=" O LYS p 127 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA p 138 " --> pdb=" O LYS p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 174 removed outlier: 3.757A pdb=" N ARG p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) removed outlier: 4.480A 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: 6.268A 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: 6.427A 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 208 removed outlier: 6.231A 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: 5.968A pdb=" N GLU h 97 " --> pdb=" O TYR p 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 1691 hydrogen bonds defined for protein. 4905 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: 5.54 Time building geometry restraints manager: 4.02 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: 4845 1.29 - 1.42: 8519 1.42 - 1.56: 18806 1.56 - 1.69: 97 1.69 - 1.82: 439 Bond restraints: 32706 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 d 115 " pdb=" CD PRO d 115 " ideal model delta sigma weight residual 1.473 1.276 0.197 1.40e-02 5.10e+03 1.99e+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 1.91e+02 bond pdb=" N PRO k 50 " pdb=" CD PRO k 50 " ideal model delta sigma weight residual 1.473 1.282 0.191 1.40e-02 5.10e+03 1.86e+02 bond pdb=" N PRO N 255 " pdb=" CD PRO N 255 " ideal model delta sigma weight residual 1.473 1.283 0.190 1.40e-02 5.10e+03 1.84e+02 ... (remaining 32701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 43566 6.55 - 13.10: 595 13.10 - 19.65: 23 19.65 - 26.20: 0 26.20 - 32.75: 2 Bond angle restraints: 44186 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 110.70 128.48 -17.78 1.22e+00 6.72e-01 2.12e+02 angle pdb=" N PRO N 255 " pdb=" CA PRO N 255 " pdb=" C PRO N 255 " ideal model delta sigma weight residual 110.70 128.37 -17.67 1.22e+00 6.72e-01 2.10e+02 angle pdb=" N TYR O 118 " pdb=" CA TYR O 118 " pdb=" C TYR O 118 " ideal model delta sigma weight residual 111.07 125.87 -14.80 1.07e+00 8.73e-01 1.91e+02 angle pdb=" N ILE M 424 " pdb=" CA ILE M 424 " pdb=" C ILE M 424 " ideal model delta sigma weight residual 109.30 94.03 15.27 1.31e+00 5.83e-01 1.36e+02 angle pdb=" N GLN i 14 " pdb=" CA GLN i 14 " pdb=" C GLN i 14 " ideal model delta sigma weight residual 111.28 123.90 -12.62 1.09e+00 8.42e-01 1.34e+02 ... (remaining 44181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 19372 32.33 - 64.66: 541 64.66 - 96.98: 38 96.98 - 129.31: 4 129.31 - 161.64: 3 Dihedral angle restraints: 19958 sinusoidal: 8761 harmonic: 11197 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 93.00 160.93 -67.93 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" C5' ADP O 402 " pdb=" O5' ADP O 402 " pdb=" PA ADP O 402 " pdb=" O2A ADP O 402 " ideal model delta sinusoidal sigma weight residual 300.00 158.73 141.27 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 19955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3690 0.106 - 0.212: 877 0.212 - 0.318: 183 0.318 - 0.424: 35 0.424 - 0.530: 11 Chirality restraints: 4796 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 7.02e+00 chirality pdb=" CA LEU d 113 " pdb=" N LEU d 113 " pdb=" C LEU d 113 " pdb=" CB LEU d 113 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" CA TRP L 557 " pdb=" N TRP L 557 " pdb=" C TRP L 557 " pdb=" CB TRP L 557 " 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 4793 not shown) Planarity restraints: 5411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER l 125 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C SER l 125 " -0.071 2.00e-02 2.50e+03 pdb=" O SER l 125 " 0.027 2.00e-02 2.50e+03 pdb=" N TRP l 126 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE i 105 " -0.067 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO i 106 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO i 106 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO i 106 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 546 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU L 546 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU L 546 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS L 547 " -0.022 2.00e-02 2.50e+03 ... (remaining 5408 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 505 2.57 - 3.15: 30648 3.15 - 3.73: 51058 3.73 - 4.32: 75774 4.32 - 4.90: 118862 Nonbonded interactions: 276847 Sorted by model distance: nonbonded pdb=" OD1 ASN L 572 " pdb=" OA4 CDL L 705 " model vdw 1.982 3.040 nonbonded pdb=" O VAL L 261 " pdb=" CD2 HIS L 264 " model vdw 2.015 3.260 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 2.062 3.040 ... (remaining 276842 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.015 0.752 32715 Z= 1.064 Angle : 1.923 42.450 44202 Z= 1.351 Chirality : 0.100 0.530 4796 Planarity : 0.007 0.098 5411 Dihedral : 13.932 161.640 12698 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 44.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 0.29 % Allowed : 5.58 % Favored : 94.13 % Cbeta Deviations : 1.22 % 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: -2.61 (0.12), residues: 3761 helix: -1.27 (0.10), residues: 2394 sheet: -1.92 (1.15), residues: 18 loop : -2.40 (0.15), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG p 162 TYR 0.035 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 j 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01401 / 0.97 (32706) covalent geometry : angle 1.91157 / 1.35 (44186) SS BOND : bond 0.16495 / 10.23 ( 8) SS BOND : angle 11.02814 / 6.49 ( 16) hydrogen bonds : bond 0.22965 / 14.69 ( 1691) hydrogen bonds : angle 8.81205 / 6.26 ( 4905) Misc. bond : bond 0.75191 / 39.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1410 time to evaluate : 1.173 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: J 1 MET cc_start: 0.5410 (tmm) cc_final: 0.5090 (mtt) REVERT: J 134 MET cc_start: 0.6998 (mmm) cc_final: 0.6757 (mtt) REVERT: K 95 LEU cc_start: 0.7995 (mt) cc_final: 0.7761 (mp) REVERT: L 88 LEU cc_start: 0.9289 (tp) cc_final: 0.8973 (tp) REVERT: L 199 GLN cc_start: 0.8345 (mp10) cc_final: 0.7140 (mp10) REVERT: L 446 ASN cc_start: 0.8261 (m-40) cc_final: 0.8057 (m110) REVERT: M 111 SER cc_start: 0.7937 (p) cc_final: 0.7434 (p) REVERT: M 437 MET cc_start: 0.8339 (mmt) cc_final: 0.8111 (mpp) REVERT: O 40 LEU cc_start: 0.7301 (mp) cc_final: 0.7063 (tp) REVERT: U 122 MET cc_start: 0.8321 (mmp) cc_final: 0.7876 (mmm) REVERT: U 130 ILE cc_start: 0.8643 (mm) cc_final: 0.8255 (mm) REVERT: d 54 MET cc_start: 0.7290 (mtp) cc_final: 0.6924 (ttp) REVERT: d 55 ARG cc_start: 0.7437 (mtt-85) cc_final: 0.7062 (mmt-90) REVERT: e 27 TYR cc_start: 0.8273 (m-80) cc_final: 0.7771 (m-80) REVERT: g 63 ASN cc_start: 0.8000 (t0) cc_final: 0.7655 (t0) REVERT: h 86 ILE cc_start: 0.8673 (mm) cc_final: 0.8070 (mm) REVERT: h 90 ASN cc_start: 0.8529 (m-40) cc_final: 0.8203 (m-40) REVERT: i 100 SER cc_start: 0.8862 (t) cc_final: 0.8521 (p) REVERT: i 104 ILE cc_start: 0.8504 (pt) cc_final: 0.7622 (mt) REVERT: j 49 GLN cc_start: 0.7453 (tp-100) cc_final: 0.7234 (pt0) REVERT: j 90 SER cc_start: 0.9036 (t) cc_final: 0.8251 (t) REVERT: j 91 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7024 (mm-40) REVERT: l 36 MET cc_start: 0.7430 (ttm) cc_final: 0.6946 (ttm) REVERT: l 63 GLU cc_start: 0.8078 (tt0) cc_final: 0.7760 (tt0) REVERT: l 108 ASP cc_start: 0.8425 (m-30) cc_final: 0.8169 (m-30) REVERT: l 159 LYS cc_start: 0.8647 (tttp) cc_final: 0.8234 (tttt) REVERT: l 164 ASN cc_start: 0.8260 (m-40) cc_final: 0.7999 (m-40) REVERT: m 29 THR cc_start: 0.8639 (m) cc_final: 0.8325 (m) REVERT: m 62 ASP cc_start: 0.8313 (t0) cc_final: 0.8109 (t0) REVERT: m 86 ASN cc_start: 0.7866 (t0) cc_final: 0.7602 (t0) REVERT: n 94 TYR cc_start: 0.8521 (m-80) cc_final: 0.8165 (m-80) REVERT: n 120 SER cc_start: 0.8476 (t) cc_final: 0.8121 (p) REVERT: n 134 ASP cc_start: 0.7800 (m-30) cc_final: 0.7581 (p0) REVERT: o 52 THR cc_start: 0.8769 (m) cc_final: 0.8405 (p) REVERT: p 73 ASP cc_start: 0.7275 (p0) cc_final: 0.7063 (p0) REVERT: p 149 TYR cc_start: 0.8627 (m-10) cc_final: 0.8333 (m-80) outliers start: 10 outliers final: 2 residues processed: 1413 average time/residue: 0.2212 time to fit residues: 491.1665 Evaluate side-chains 922 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 920 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain i residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN D 60 HIS K 7 ASN L 2 ASN L 57 ASN L 194 ASN L 230 HIS ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 321 GLN ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN L 572 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 192 ASN M 213 HIS M 331 ASN M 349 GLN M 390 ASN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 134 GLN N 186 HIS N 222 ASN N 228 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 310 ASN O 80 GLN ** O 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 HIS ** O 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 299 GLN O 323 GLN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 ASN d 8 HIS e 45 HIS f 45 GLN g 68 ASN ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 GLN ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 ASN l 84 HIS l 91 GLN l 106 HIS n 12 HIS n 33 HIS n 53 ASN ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 67 GLN p 91 GLN p 100 GLN p 104 ASN p 131 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107934 restraints weight = 48897.742| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.11 r_work: 0.3190 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32715 Z= 0.205 Angle : 0.810 12.517 44202 Z= 0.416 Chirality : 0.047 0.481 4796 Planarity : 0.007 0.065 5411 Dihedral : 13.200 146.647 5112 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 3.30 % Allowed : 13.81 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 3761 helix: 0.17 (0.10), residues: 2425 sheet: -1.36 (1.21), residues: 18 loop : -1.29 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG n 135 TYR 0.040 0.002 TYR L 422 PHE 0.028 0.002 PHE X 169 TRP 0.019 0.002 TRP j 66 HIS 0.014 0.002 HIS L 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (32706) covalent geometry : angle 0.80400 / 0.41 (44186) SS BOND : bond 0.00691 / 0.48 ( 8) SS BOND : angle 5.13427 / 3.26 ( 16) hydrogen bonds : bond 0.06003 / 3.86 ( 1691) hydrogen bonds : angle 5.27003 / 3.75 ( 4905) Misc. bond : bond 0.00488 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 980 time to evaluate : 1.140 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 1 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.4720 (mtt) REVERT: J 64 LEU cc_start: 0.8950 (mp) cc_final: 0.8725 (mp) REVERT: J 67 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7224 (t80) REVERT: J 127 GLU cc_start: 0.5225 (mp0) cc_final: 0.4368 (tt0) REVERT: J 134 MET cc_start: 0.7887 (mmm) cc_final: 0.7263 (mtt) REVERT: K 21 MET cc_start: 0.8308 (mtp) cc_final: 0.7971 (mtm) REVERT: K 27 MET cc_start: 0.8857 (tpp) cc_final: 0.8156 (tpp) REVERT: K 31 LEU cc_start: 0.9178 (tp) cc_final: 0.8831 (mt) REVERT: L 71 MET cc_start: 0.8594 (tpp) cc_final: 0.8358 (mmt) REVERT: L 132 THR cc_start: 0.9407 (m) cc_final: 0.9136 (p) REVERT: L 175 ASN cc_start: 0.8350 (m-40) cc_final: 0.8113 (m110) REVERT: L 493 ILE cc_start: 0.8731 (tp) cc_final: 0.8346 (tp) REVERT: L 546 LEU cc_start: 0.8708 (tp) cc_final: 0.8504 (tp) REVERT: L 589 MET cc_start: 0.8404 (ttp) cc_final: 0.7999 (tpp) REVERT: L 593 ILE cc_start: 0.8976 (mm) cc_final: 0.8674 (mp) REVERT: M 38 SER cc_start: 0.9535 (t) cc_final: 0.9099 (p) REVERT: M 46 ASP cc_start: 0.8587 (t0) cc_final: 0.8281 (t0) REVERT: M 135 ARG cc_start: 0.9064 (tpt90) cc_final: 0.8770 (tpt90) REVERT: M 246 ILE cc_start: 0.9567 (tp) cc_final: 0.9293 (tp) REVERT: M 271 MET cc_start: 0.8483 (mmm) cc_final: 0.7865 (mtp) REVERT: M 275 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8763 (pt) REVERT: M 301 ILE cc_start: 0.9328 (mm) cc_final: 0.9089 (mt) REVERT: M 336 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7803 (mtt90) REVERT: M 423 MET cc_start: 0.7238 (mmp) cc_final: 0.6704 (mmt) REVERT: N 170 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8702 (mt) REVERT: N 243 MET cc_start: 0.8090 (mmm) cc_final: 0.7736 (mmp) REVERT: N 247 MET cc_start: 0.8743 (mtm) cc_final: 0.8542 (mtp) REVERT: O 56 TYR cc_start: 0.7549 (p90) cc_final: 0.7198 (p90) REVERT: O 76 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7002 (tp30) REVERT: O 105 ASP cc_start: 0.7236 (t0) cc_final: 0.7029 (t0) REVERT: O 108 PHE cc_start: 0.7293 (m-80) cc_final: 0.7008 (m-80) REVERT: O 296 MET cc_start: 0.7003 (mtp) cc_final: 0.6472 (mtp) REVERT: O 300 ASP cc_start: 0.7267 (t0) cc_final: 0.6562 (m-30) REVERT: U 96 GLU cc_start: 0.8450 (tp30) cc_final: 0.8173 (tp30) REVERT: U 125 GLU cc_start: 0.8316 (tp30) cc_final: 0.8006 (tp30) REVERT: U 143 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7966 (mp0) REVERT: c 41 TRP cc_start: 0.8011 (m100) cc_final: 0.7741 (m100) REVERT: d 16 ASP cc_start: 0.8314 (p0) cc_final: 0.7554 (t0) REVERT: d 67 SER cc_start: 0.9269 (t) cc_final: 0.8540 (p) REVERT: d 97 HIS cc_start: 0.8322 (m90) cc_final: 0.7758 (m90) REVERT: e 4 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (mt) REVERT: e 18 PHE cc_start: 0.8142 (p90) cc_final: 0.7824 (p90) REVERT: e 27 TYR cc_start: 0.8687 (m-80) cc_final: 0.7682 (m-80) REVERT: e 82 GLN cc_start: 0.7484 (tp40) cc_final: 0.7280 (tp40) REVERT: e 92 TYR cc_start: 0.7426 (t80) cc_final: 0.6702 (m-80) REVERT: f 48 LEU cc_start: 0.8278 (mp) cc_final: 0.7953 (mp) REVERT: f 51 ASN cc_start: 0.7608 (t0) cc_final: 0.7391 (t0) REVERT: g 94 SER cc_start: 0.9443 (t) cc_final: 0.9183 (m) REVERT: g 144 LYS cc_start: 0.8815 (mttm) cc_final: 0.8600 (mttm) REVERT: h 86 ILE cc_start: 0.9062 (mm) cc_final: 0.8756 (mm) REVERT: h 155 GLU cc_start: 0.8115 (tp30) cc_final: 0.7795 (tp30) REVERT: h 180 ASP cc_start: 0.8371 (t0) cc_final: 0.8098 (t0) REVERT: i 88 TYR cc_start: 0.9126 (m-80) cc_final: 0.8571 (m-80) REVERT: j 49 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7259 (pt0) REVERT: j 73 PHE cc_start: 0.8321 (t80) cc_final: 0.8080 (t80) REVERT: j 86 TYR cc_start: 0.9386 (t80) cc_final: 0.9090 (t80) REVERT: j 88 ASP cc_start: 0.9031 (t0) cc_final: 0.7936 (t0) REVERT: j 90 SER cc_start: 0.9272 (t) cc_final: 0.8380 (p) REVERT: j 91 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7585 (mp10) REVERT: k 60 MET cc_start: 0.8747 (tpp) cc_final: 0.8363 (tpp) REVERT: k 81 PHE cc_start: 0.8898 (t80) cc_final: 0.8578 (t80) REVERT: l 31 HIS cc_start: 0.5648 (p-80) cc_final: 0.5358 (p-80) REVERT: l 36 MET cc_start: 0.8630 (ttm) cc_final: 0.8222 (ttp) REVERT: l 63 GLU cc_start: 0.8901 (tt0) cc_final: 0.8641 (tt0) REVERT: l 129 MET cc_start: 0.9107 (ttm) cc_final: 0.8845 (mtt) REVERT: l 165 ASN cc_start: 0.8848 (t0) cc_final: 0.8483 (t0) REVERT: m 7 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8326 (ttmm) REVERT: m 31 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7645 (mtp-110) REVERT: m 51 TYR cc_start: 0.9072 (t80) cc_final: 0.8835 (t80) REVERT: m 62 ASP cc_start: 0.8629 (t0) cc_final: 0.8336 (t0) REVERT: o 29 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7892 (tp) REVERT: o 38 VAL cc_start: 0.8676 (t) cc_final: 0.8425 (p) REVERT: o 55 GLN cc_start: 0.9097 (mt0) cc_final: 0.8757 (mt0) REVERT: o 69 CYS cc_start: 0.7216 (OUTLIER) cc_final: 0.7014 (p) REVERT: o 76 ASN cc_start: 0.8281 (t0) cc_final: 0.8031 (t0) REVERT: o 91 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8474 (mm-30) REVERT: o 97 LYS cc_start: 0.8866 (mttm) cc_final: 0.8530 (mtpp) REVERT: o 103 GLU cc_start: 0.8260 (tp30) cc_final: 0.7926 (tp30) REVERT: p 100 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8091 (mm110) REVERT: p 103 MET cc_start: 0.8873 (tpp) cc_final: 0.8532 (mmm) REVERT: p 114 GLN cc_start: 0.8890 (tm-30) cc_final: 0.7784 (tm-30) REVERT: p 121 TYR cc_start: 0.9164 (p90) cc_final: 0.8418 (p90) REVERT: p 153 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8241 (mtm110) REVERT: p 172 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8594 (pp30) outliers start: 112 outliers final: 56 residues processed: 1036 average time/residue: 0.2114 time to fit residues: 350.5519 Evaluate side-chains 886 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 823 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 170 HIS Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 49 ASN Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 149 LEU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 146 VAL Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain p residue 15 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 276 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 264 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 366 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN L 230 HIS ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN M 349 GLN N 125 HIS N 273 ASN O 286 GLN O 292 HIS ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 HIS h 181 HIS i 26 GLN i 83 HIS l 56 ASN l 80 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 HIS o 4 HIS o 110 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104281 restraints weight = 49372.564| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.13 r_work: 0.3149 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32715 Z= 0.167 Angle : 0.688 13.226 44202 Z= 0.347 Chirality : 0.044 0.343 4796 Planarity : 0.005 0.068 5411 Dihedral : 12.790 144.562 5109 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 3.07 % Allowed : 15.49 % Favored : 81.45 % 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: 0.11 (0.14), residues: 3761 helix: 0.63 (0.11), residues: 2415 sheet: -0.16 (1.27), residues: 23 loop : -0.83 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 162 TYR 0.031 0.002 TYR L 422 PHE 0.027 0.002 PHE X 169 TRP 0.016 0.001 TRP n 102 HIS 0.014 0.001 HIS L 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (32706) covalent geometry : angle 0.68513 / 0.35 (44186) SS BOND : bond 0.01198 / 0.81 ( 8) SS BOND : angle 3.57152 / 2.10 ( 16) hydrogen bonds : bond 0.04995 / 3.23 ( 1691) hydrogen bonds : angle 4.72437 / 3.37 ( 4905) Misc. bond : bond 0.00203 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 871 time to evaluate : 1.272 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 1 MET cc_start: 0.5324 (OUTLIER) cc_final: 0.4780 (mtt) REVERT: J 64 LEU cc_start: 0.9002 (mp) cc_final: 0.8580 (mp) REVERT: J 65 VAL cc_start: 0.8598 (p) cc_final: 0.8352 (m) REVERT: J 67 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7052 (t80) REVERT: J 127 GLU cc_start: 0.4989 (mp0) cc_final: 0.4271 (tt0) REVERT: J 134 MET cc_start: 0.7876 (mmm) cc_final: 0.7420 (mtt) REVERT: K 27 MET cc_start: 0.8751 (tpp) cc_final: 0.8064 (tpp) REVERT: K 31 LEU cc_start: 0.9146 (tp) cc_final: 0.8849 (mm) REVERT: L 129 LEU cc_start: 0.8985 (mt) cc_final: 0.8676 (mt) REVERT: L 132 THR cc_start: 0.9384 (m) cc_final: 0.9114 (p) REVERT: L 521 SER cc_start: 0.9160 (m) cc_final: 0.8823 (t) REVERT: L 589 MET cc_start: 0.8284 (ttp) cc_final: 0.7905 (ttm) REVERT: L 593 ILE cc_start: 0.8972 (mm) cc_final: 0.8739 (mp) REVERT: M 38 SER cc_start: 0.9616 (t) cc_final: 0.9224 (p) REVERT: M 135 ARG cc_start: 0.9080 (tpt90) cc_final: 0.8823 (tpt90) REVERT: M 177 MET cc_start: 0.8582 (mmm) cc_final: 0.8352 (ttm) REVERT: M 271 MET cc_start: 0.8458 (mmm) cc_final: 0.8199 (mtp) REVERT: M 275 ILE cc_start: 0.9063 (pp) cc_final: 0.8740 (pt) REVERT: M 278 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8075 (mtp180) REVERT: M 376 MET cc_start: 0.8358 (mtp) cc_final: 0.8077 (mtp) REVERT: M 410 MET cc_start: 0.8810 (ttm) cc_final: 0.8594 (ttm) REVERT: N 43 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8658 (mmm) REVERT: N 170 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8787 (mt) REVERT: N 190 MET cc_start: 0.8724 (mtm) cc_final: 0.8431 (mtm) REVERT: N 227 ILE cc_start: 0.7699 (pt) cc_final: 0.7442 (mt) REVERT: N 243 MET cc_start: 0.8393 (mmm) cc_final: 0.8184 (mmp) REVERT: N 296 LEU cc_start: 0.8610 (tp) cc_final: 0.8409 (tp) REVERT: N 329 LEU cc_start: 0.8159 (mt) cc_final: 0.7955 (mt) REVERT: O 47 ASP cc_start: 0.7934 (t0) cc_final: 0.7456 (t0) REVERT: O 52 LYS cc_start: 0.7674 (mttt) cc_final: 0.7187 (mtmm) REVERT: O 56 TYR cc_start: 0.7594 (p90) cc_final: 0.7195 (p90) REVERT: O 105 ASP cc_start: 0.7530 (t0) cc_final: 0.7147 (t0) REVERT: O 107 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: O 108 PHE cc_start: 0.7340 (m-80) cc_final: 0.7052 (m-80) REVERT: O 113 SER cc_start: 0.8006 (m) cc_final: 0.7706 (p) REVERT: O 296 MET cc_start: 0.7016 (mtp) cc_final: 0.6606 (mtt) REVERT: O 300 ASP cc_start: 0.7249 (t0) cc_final: 0.6430 (m-30) REVERT: O 302 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7931 (t) REVERT: U 96 GLU cc_start: 0.8511 (tp30) cc_final: 0.8138 (tp30) REVERT: U 125 GLU cc_start: 0.8546 (tp30) cc_final: 0.8203 (tp30) REVERT: Y 13 GLU cc_start: 0.8115 (tp30) cc_final: 0.7882 (tm-30) REVERT: Y 46 ASN cc_start: 0.8614 (t0) cc_final: 0.8208 (t0) REVERT: Y 55 VAL cc_start: 0.8642 (t) cc_final: 0.8436 (m) REVERT: c 56 ILE cc_start: 0.9023 (mt) cc_final: 0.8778 (mp) REVERT: d 1 MET cc_start: 0.5996 (tpt) cc_final: 0.5701 (tpt) REVERT: d 16 ASP cc_start: 0.8455 (p0) cc_final: 0.7661 (t0) REVERT: d 49 ARG cc_start: 0.8470 (mmt90) cc_final: 0.8261 (mmt90) REVERT: d 67 SER cc_start: 0.9319 (t) cc_final: 0.8582 (p) REVERT: d 97 HIS cc_start: 0.8368 (m90) cc_final: 0.8164 (m90) REVERT: e 18 PHE cc_start: 0.8239 (p90) cc_final: 0.8024 (p90) REVERT: e 27 TYR cc_start: 0.8696 (m-80) cc_final: 0.7764 (m-80) REVERT: e 74 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7872 (tpp-160) REVERT: e 92 TYR cc_start: 0.7480 (t80) cc_final: 0.6681 (m-80) REVERT: g 51 MET cc_start: 0.5593 (mtt) cc_final: 0.5329 (mtt) REVERT: g 75 ASP cc_start: 0.8521 (t0) cc_final: 0.8248 (t70) REVERT: g 81 ASP cc_start: 0.8932 (t70) cc_final: 0.8451 (t70) REVERT: g 85 MET cc_start: 0.8532 (tmm) cc_final: 0.8151 (tmm) REVERT: g 94 SER cc_start: 0.9468 (t) cc_final: 0.9130 (p) REVERT: g 139 TYR cc_start: 0.6464 (t80) cc_final: 0.6198 (t80) REVERT: h 180 ASP cc_start: 0.8580 (t0) cc_final: 0.8162 (t0) REVERT: i 87 LYS cc_start: 0.9183 (tttt) cc_final: 0.8633 (tttm) REVERT: i 88 TYR cc_start: 0.9180 (m-80) cc_final: 0.8588 (m-80) REVERT: j 49 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7413 (pt0) REVERT: j 86 TYR cc_start: 0.9295 (t80) cc_final: 0.8971 (t80) REVERT: j 88 ASP cc_start: 0.9004 (t0) cc_final: 0.8656 (t0) REVERT: j 90 SER cc_start: 0.9300 (t) cc_final: 0.8481 (p) REVERT: j 91 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7648 (mm110) REVERT: k 81 PHE cc_start: 0.8827 (t80) cc_final: 0.8462 (t80) REVERT: l 36 MET cc_start: 0.8571 (ttm) cc_final: 0.8207 (ttp) REVERT: l 63 GLU cc_start: 0.8947 (tt0) cc_final: 0.8740 (tt0) REVERT: l 95 SER cc_start: 0.9398 (t) cc_final: 0.9166 (p) REVERT: l 165 ASN cc_start: 0.8961 (t0) cc_final: 0.8607 (t0) REVERT: m 7 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8501 (ttmm) REVERT: m 51 TYR cc_start: 0.9106 (t80) cc_final: 0.8840 (t80) REVERT: m 62 ASP cc_start: 0.8769 (t0) cc_final: 0.8472 (t0) REVERT: o 29 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8019 (tp) REVERT: o 55 GLN cc_start: 0.9006 (mt0) cc_final: 0.8798 (mt0) REVERT: o 76 ASN cc_start: 0.8380 (t0) cc_final: 0.8050 (t0) REVERT: o 91 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8708 (mm-30) REVERT: o 97 LYS cc_start: 0.8838 (mttm) cc_final: 0.8565 (mtpp) REVERT: o 103 GLU cc_start: 0.8314 (tp30) cc_final: 0.8078 (tp30) REVERT: o 117 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7980 (pp) REVERT: p 103 MET cc_start: 0.8964 (tpp) cc_final: 0.8681 (mmm) REVERT: p 114 GLN cc_start: 0.8962 (tm-30) cc_final: 0.7836 (tm-30) REVERT: p 146 LEU cc_start: 0.8563 (mt) cc_final: 0.8358 (mp) REVERT: p 165 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: p 172 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8626 (pp30) outliers start: 104 outliers final: 57 residues processed: 928 average time/residue: 0.2094 time to fit residues: 313.0868 Evaluate side-chains 854 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 788 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain f residue 24 CYS Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 149 LEU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 26 GLN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 103 ASP 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 m residue 17 THR Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 157 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 349 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN M 54 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN e 45 HIS ** g 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN l 148 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 = 0.3565 r_free = 0.3565 target = 0.125639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102780 restraints weight = 49099.783| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.09 r_work: 0.3135 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32715 Z= 0.153 Angle : 0.649 11.484 44202 Z= 0.324 Chirality : 0.043 0.327 4796 Planarity : 0.005 0.067 5411 Dihedral : 12.576 142.296 5109 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 3.24 % Allowed : 16.81 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3761 helix: 0.79 (0.11), residues: 2430 sheet: -0.27 (1.32), residues: 23 loop : -0.65 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 162 TYR 0.028 0.001 TYR L 422 PHE 0.019 0.002 PHE N 292 TRP 0.019 0.001 TRP X 170 HIS 0.006 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (32706) covalent geometry : angle 0.64535 / 0.32 (44186) SS BOND : bond 0.00199 / 0.11 ( 8) SS BOND : angle 3.50179 / 2.02 ( 16) hydrogen bonds : bond 0.04527 / 2.93 ( 1691) hydrogen bonds : angle 4.50975 / 3.21 ( 4905) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 827 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4891 (mtt) REVERT: J 64 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8589 (mp) REVERT: J 67 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7022 (t80) REVERT: J 127 GLU cc_start: 0.5101 (mp0) cc_final: 0.4252 (tt0) REVERT: J 134 MET cc_start: 0.7951 (mmm) cc_final: 0.7486 (mtt) REVERT: K 27 MET cc_start: 0.8756 (tpp) cc_final: 0.7977 (tpp) REVERT: K 31 LEU cc_start: 0.9065 (tp) cc_final: 0.8829 (mm) REVERT: K 91 GLN cc_start: 0.8452 (pm20) cc_final: 0.7849 (pm20) REVERT: L 71 MET cc_start: 0.8581 (tpp) cc_final: 0.8155 (mmt) REVERT: L 129 LEU cc_start: 0.8990 (mt) cc_final: 0.8693 (mt) REVERT: L 132 THR cc_start: 0.9374 (m) cc_final: 0.9138 (p) REVERT: L 521 SER cc_start: 0.9149 (m) cc_final: 0.8828 (t) REVERT: M 38 SER cc_start: 0.9629 (t) cc_final: 0.9291 (p) REVERT: M 46 ASP cc_start: 0.8656 (t0) cc_final: 0.8262 (t70) REVERT: M 135 ARG cc_start: 0.9103 (tpt90) cc_final: 0.8864 (tpt90) REVERT: M 271 MET cc_start: 0.8363 (mmm) cc_final: 0.7904 (mtp) REVERT: M 275 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8794 (pt) REVERT: M 278 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7933 (mtp180) REVERT: M 376 MET cc_start: 0.8376 (mtp) cc_final: 0.8021 (mtp) REVERT: M 410 MET cc_start: 0.8858 (ttm) cc_final: 0.8634 (ttm) REVERT: M 423 MET cc_start: 0.7444 (mmp) cc_final: 0.6592 (mmt) REVERT: M 459 MET cc_start: 0.8599 (ptp) cc_final: 0.8232 (ptp) REVERT: N 10 TYR cc_start: 0.9007 (m-80) cc_final: 0.8760 (m-80) REVERT: N 43 MET cc_start: 0.9001 (mmm) cc_final: 0.8695 (mmm) REVERT: N 190 MET cc_start: 0.8699 (mtm) cc_final: 0.8339 (mtm) REVERT: N 215 MET cc_start: 0.9140 (mmm) cc_final: 0.8935 (tpt) REVERT: O 47 ASP cc_start: 0.8006 (t0) cc_final: 0.7505 (t0) REVERT: O 52 LYS cc_start: 0.7677 (mttt) cc_final: 0.7235 (mtmm) REVERT: O 56 TYR cc_start: 0.7631 (p90) cc_final: 0.7157 (p90) REVERT: O 102 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8326 (mtt90) REVERT: O 105 ASP cc_start: 0.7650 (t0) cc_final: 0.7230 (t0) REVERT: O 107 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: O 108 PHE cc_start: 0.7424 (m-80) cc_final: 0.7094 (m-80) REVERT: O 113 SER cc_start: 0.8149 (m) cc_final: 0.7931 (p) REVERT: O 189 GLU cc_start: 0.8159 (tp30) cc_final: 0.7622 (tp30) REVERT: O 202 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7545 (m170) REVERT: U 96 GLU cc_start: 0.8568 (tp30) cc_final: 0.8151 (tp30) REVERT: U 125 GLU cc_start: 0.8716 (tp30) cc_final: 0.8351 (tp30) REVERT: Y 46 ASN cc_start: 0.8872 (t0) cc_final: 0.8549 (t0) REVERT: Y 55 VAL cc_start: 0.8653 (t) cc_final: 0.8440 (m) REVERT: Y 133 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8494 (mm-30) REVERT: d 16 ASP cc_start: 0.8532 (p0) cc_final: 0.7732 (t0) REVERT: d 49 ARG cc_start: 0.8506 (mmt90) cc_final: 0.8164 (mmt90) REVERT: d 67 SER cc_start: 0.9310 (t) cc_final: 0.8600 (p) REVERT: d 97 HIS cc_start: 0.8466 (m90) cc_final: 0.8182 (m90) REVERT: e 18 PHE cc_start: 0.8443 (p90) cc_final: 0.8166 (p90) REVERT: e 27 TYR cc_start: 0.8782 (m-80) cc_final: 0.7860 (m-80) REVERT: e 92 TYR cc_start: 0.7476 (t80) cc_final: 0.6668 (m-80) REVERT: g 51 MET cc_start: 0.5262 (mtt) cc_final: 0.4891 (mtt) REVERT: g 75 ASP cc_start: 0.8615 (t0) cc_final: 0.8341 (t70) REVERT: g 81 ASP cc_start: 0.8999 (t70) cc_final: 0.8595 (t70) REVERT: g 85 MET cc_start: 0.8580 (tmm) cc_final: 0.8183 (tmm) REVERT: h 180 ASP cc_start: 0.8485 (t0) cc_final: 0.8096 (t0) REVERT: i 87 LYS cc_start: 0.9150 (tttt) cc_final: 0.8718 (tttm) REVERT: i 88 TYR cc_start: 0.9166 (m-80) cc_final: 0.8633 (m-80) REVERT: j 49 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7497 (pt0) REVERT: j 86 TYR cc_start: 0.9309 (t80) cc_final: 0.8918 (t80) REVERT: j 88 ASP cc_start: 0.8989 (t0) cc_final: 0.8727 (t0) REVERT: j 90 SER cc_start: 0.9329 (t) cc_final: 0.8520 (p) REVERT: j 91 GLN cc_start: 0.8591 (mm-40) cc_final: 0.7655 (mm110) REVERT: k 31 GLU cc_start: 0.8552 (pm20) cc_final: 0.8342 (pm20) REVERT: k 81 PHE cc_start: 0.8833 (t80) cc_final: 0.8511 (t80) REVERT: l 36 MET cc_start: 0.8595 (ttm) cc_final: 0.8214 (ttp) REVERT: l 63 GLU cc_start: 0.8948 (tt0) cc_final: 0.8746 (tt0) REVERT: l 95 SER cc_start: 0.9444 (t) cc_final: 0.9224 (p) REVERT: l 165 ASN cc_start: 0.9065 (t0) cc_final: 0.8734 (t0) REVERT: l 185 ASP cc_start: 0.8415 (t0) cc_final: 0.8162 (t0) REVERT: m 51 TYR cc_start: 0.9123 (t80) cc_final: 0.8914 (t80) REVERT: m 62 ASP cc_start: 0.8765 (t0) cc_final: 0.8482 (t0) REVERT: m 120 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8354 (mtmm) REVERT: o 55 GLN cc_start: 0.8990 (mt0) cc_final: 0.8753 (mt0) REVERT: o 76 ASN cc_start: 0.8416 (t0) cc_final: 0.7997 (t0) REVERT: o 80 CYS cc_start: 0.4758 (OUTLIER) cc_final: 0.3630 (p) REVERT: o 91 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8758 (mm-30) REVERT: o 97 LYS cc_start: 0.8823 (mttm) cc_final: 0.8559 (mtpp) REVERT: o 103 GLU cc_start: 0.8316 (tp30) cc_final: 0.8069 (tp30) REVERT: o 117 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7917 (pp) REVERT: p 90 MET cc_start: 0.9193 (mmp) cc_final: 0.8957 (mmm) REVERT: p 103 MET cc_start: 0.9001 (tpp) cc_final: 0.8707 (mmm) REVERT: p 114 GLN cc_start: 0.8799 (tm-30) cc_final: 0.7753 (tm-30) REVERT: p 153 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8637 (mtp85) REVERT: p 165 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: p 172 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8610 (pp30) outliers start: 110 outliers final: 72 residues processed: 892 average time/residue: 0.2066 time to fit residues: 298.8719 Evaluate side-chains 862 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 781 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 202 HIS Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain f residue 24 CYS Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 112 MET Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 149 LEU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 103 ASP 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 m residue 17 THR Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 80 CYS Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 15 SER Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 177 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 324 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 289 ASN O 306 ASN c 36 ASN d 97 HIS ** g 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN l 83 GLN l 100 ASN l 148 HIS ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 110 GLN ** p 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102885 restraints weight = 49100.069| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.14 r_work: 0.3128 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32715 Z= 0.141 Angle : 0.628 11.879 44202 Z= 0.311 Chirality : 0.042 0.316 4796 Planarity : 0.005 0.065 5411 Dihedral : 12.251 141.713 5109 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 3.66 % Allowed : 17.14 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3761 helix: 0.91 (0.11), residues: 2432 sheet: -0.06 (1.37), residues: 23 loop : -0.56 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 162 TYR 0.026 0.001 TYR L 422 PHE 0.032 0.002 PHE X 169 TRP 0.020 0.001 TRP X 170 HIS 0.037 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (32706) covalent geometry : angle 0.62632 / 0.31 (44186) SS BOND : bond 0.00408 / 0.23 ( 8) SS BOND : angle 2.42328 / 1.49 ( 16) hydrogen bonds : bond 0.04292 / 2.79 ( 1691) hydrogen bonds : angle 4.39343 / 3.13 ( 4905) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 840 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4920 (mtt) REVERT: J 64 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8512 (mp) REVERT: J 65 VAL cc_start: 0.8679 (p) cc_final: 0.8424 (m) REVERT: J 67 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7333 (t80) REVERT: J 134 MET cc_start: 0.7948 (mmm) cc_final: 0.7508 (mtt) REVERT: K 27 MET cc_start: 0.8715 (tpp) cc_final: 0.7955 (tpp) REVERT: L 116 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8775 (ttm-80) REVERT: L 132 THR cc_start: 0.9347 (m) cc_final: 0.9138 (p) REVERT: L 521 SER cc_start: 0.9146 (m) cc_final: 0.8830 (t) REVERT: M 38 SER cc_start: 0.9633 (t) cc_final: 0.9355 (p) REVERT: M 135 ARG cc_start: 0.9137 (tpt90) cc_final: 0.8881 (tpt90) REVERT: M 275 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8766 (pt) REVERT: M 278 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7974 (mtp180) REVERT: M 410 MET cc_start: 0.8869 (ttm) cc_final: 0.8509 (ttm) REVERT: N 10 TYR cc_start: 0.8999 (m-80) cc_final: 0.8756 (m-80) REVERT: N 27 MET cc_start: 0.8522 (mmm) cc_final: 0.8290 (mmm) REVERT: N 43 MET cc_start: 0.9089 (mmm) cc_final: 0.8784 (mmm) REVERT: N 79 LYS cc_start: 0.7725 (tttt) cc_final: 0.7486 (tppt) REVERT: N 104 MET cc_start: 0.9010 (ttm) cc_final: 0.8748 (ttm) REVERT: N 126 MET cc_start: 0.6622 (mmp) cc_final: 0.6369 (mmp) REVERT: N 248 LEU cc_start: 0.8819 (mt) cc_final: 0.8567 (mp) REVERT: N 313 MET cc_start: 0.7814 (ttm) cc_final: 0.7399 (ttp) REVERT: O 47 ASP cc_start: 0.8060 (t0) cc_final: 0.7593 (t0) REVERT: O 52 LYS cc_start: 0.7711 (mttt) cc_final: 0.7313 (mtmm) REVERT: O 56 TYR cc_start: 0.7618 (p90) cc_final: 0.7232 (p90) REVERT: O 102 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8324 (mtt90) REVERT: O 105 ASP cc_start: 0.7696 (t0) cc_final: 0.7217 (t0) REVERT: O 107 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: O 108 PHE cc_start: 0.7410 (m-80) cc_final: 0.7071 (m-80) REVERT: O 113 SER cc_start: 0.8395 (m) cc_final: 0.8071 (p) REVERT: O 189 GLU cc_start: 0.8011 (tp30) cc_final: 0.7441 (tp30) REVERT: O 296 MET cc_start: 0.6795 (mtt) cc_final: 0.6547 (mtm) REVERT: U 125 GLU cc_start: 0.8797 (tp30) cc_final: 0.8453 (tp30) REVERT: U 139 MET cc_start: 0.7890 (mmt) cc_final: 0.7516 (mmm) REVERT: U 152 LYS cc_start: 0.9032 (mttp) cc_final: 0.8773 (mttp) REVERT: Y 46 ASN cc_start: 0.8959 (t0) cc_final: 0.8746 (t0) REVERT: Y 55 VAL cc_start: 0.8641 (t) cc_final: 0.8433 (m) REVERT: Y 133 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8483 (mm-30) REVERT: Y 137 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (tt) REVERT: c 75 LEU cc_start: 0.8574 (tp) cc_final: 0.8317 (tt) REVERT: d 16 ASP cc_start: 0.8534 (p0) cc_final: 0.7793 (t0) REVERT: d 47 MET cc_start: 0.9242 (ttm) cc_final: 0.8956 (ttp) REVERT: d 49 ARG cc_start: 0.8539 (mmt90) cc_final: 0.8248 (mmt90) REVERT: d 67 SER cc_start: 0.9280 (t) cc_final: 0.8536 (p) REVERT: d 97 HIS cc_start: 0.8410 (m-70) cc_final: 0.8055 (m-70) REVERT: d 106 LYS cc_start: 0.8462 (mmmm) cc_final: 0.7836 (mtmt) REVERT: d 111 GLU cc_start: 0.8960 (mp0) cc_final: 0.8756 (mt-10) REVERT: e 4 LEU cc_start: 0.8442 (mp) cc_final: 0.8110 (mt) REVERT: e 27 TYR cc_start: 0.8820 (m-80) cc_final: 0.7796 (m-80) REVERT: e 74 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7902 (tpp-160) REVERT: e 92 TYR cc_start: 0.7527 (t80) cc_final: 0.6703 (m-80) REVERT: f 33 LYS cc_start: 0.9026 (tttm) cc_final: 0.8661 (ttpt) REVERT: g 51 MET cc_start: 0.5228 (mtt) cc_final: 0.4932 (mtt) REVERT: g 75 ASP cc_start: 0.8644 (t0) cc_final: 0.8345 (t70) REVERT: g 81 ASP cc_start: 0.9030 (t70) cc_final: 0.8619 (t70) REVERT: g 85 MET cc_start: 0.8633 (tmm) cc_final: 0.8275 (tmm) REVERT: g 86 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7887 (mtt-85) REVERT: g 144 LYS cc_start: 0.8900 (mttm) cc_final: 0.8563 (mtpp) REVERT: h 86 ILE cc_start: 0.9184 (mm) cc_final: 0.8890 (mm) REVERT: h 157 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8097 (mtt-85) REVERT: h 180 ASP cc_start: 0.8581 (t0) cc_final: 0.8147 (t0) REVERT: i 26 GLN cc_start: 0.8560 (tp40) cc_final: 0.8256 (tp40) REVERT: i 87 LYS cc_start: 0.9167 (tttt) cc_final: 0.8748 (tttm) REVERT: i 88 TYR cc_start: 0.9148 (m-80) cc_final: 0.8551 (m-80) REVERT: j 49 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7537 (pt0) REVERT: j 73 PHE cc_start: 0.8380 (t80) cc_final: 0.8149 (t80) REVERT: j 86 TYR cc_start: 0.9292 (t80) cc_final: 0.8823 (t80) REVERT: j 88 ASP cc_start: 0.8981 (t0) cc_final: 0.8729 (t0) REVERT: j 90 SER cc_start: 0.9353 (t) cc_final: 0.8547 (p) REVERT: j 91 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7479 (mm110) REVERT: k 45 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.8292 (ttm170) REVERT: k 81 PHE cc_start: 0.8811 (t80) cc_final: 0.8531 (t80) REVERT: l 36 MET cc_start: 0.8572 (ttm) cc_final: 0.8264 (ttp) REVERT: l 95 SER cc_start: 0.9470 (t) cc_final: 0.9261 (p) REVERT: l 165 ASN cc_start: 0.9126 (t0) cc_final: 0.8739 (t0) REVERT: m 62 ASP cc_start: 0.8776 (t0) cc_final: 0.8492 (t0) REVERT: m 120 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8758 (ttmm) REVERT: n 95 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7672 (mm-30) REVERT: o 55 GLN cc_start: 0.8996 (mt0) cc_final: 0.8700 (mt0) REVERT: o 76 ASN cc_start: 0.8426 (t0) cc_final: 0.7901 (t0) REVERT: o 97 LYS cc_start: 0.8792 (mttm) cc_final: 0.8551 (mtpp) REVERT: o 103 GLU cc_start: 0.8337 (tp30) cc_final: 0.8128 (tp30) REVERT: o 117 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7974 (pp) REVERT: p 90 MET cc_start: 0.9198 (mmp) cc_final: 0.8689 (mmp) REVERT: p 103 MET cc_start: 0.9016 (tpp) cc_final: 0.8673 (mmm) REVERT: p 114 GLN cc_start: 0.8874 (tm-30) cc_final: 0.7897 (tm-30) REVERT: p 165 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: p 172 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8580 (pp30) outliers start: 124 outliers final: 76 residues processed: 916 average time/residue: 0.2056 time to fit residues: 306.2038 Evaluate side-chains 866 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 782 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 415 GLN Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 137 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain l residue 44 THR 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 m residue 17 THR Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain p residue 87 GLU Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 5 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 361 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 ASN ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN M 51 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN N 228 ASN N 289 ASN c 36 ASN h 181 HIS l 80 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 110 GLN ** p 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099504 restraints weight = 49262.142| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.13 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32715 Z= 0.189 Angle : 0.658 11.504 44202 Z= 0.326 Chirality : 0.044 0.304 4796 Planarity : 0.005 0.064 5411 Dihedral : 12.194 146.572 5109 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 17.02 % Favored : 79.00 % 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: 0.60 (0.14), residues: 3761 helix: 0.97 (0.11), residues: 2441 sheet: -0.46 (1.43), residues: 18 loop : -0.57 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 416 TYR 0.022 0.002 TYR M 406 PHE 0.026 0.002 PHE X 169 TRP 0.014 0.001 TRP M 359 HIS 0.024 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (32706) covalent geometry : angle 0.65646 / 0.33 (44186) SS BOND : bond 0.00813 / 0.42 ( 8) SS BOND : angle 2.54945 / 1.80 ( 16) hydrogen bonds : bond 0.04367 / 2.85 ( 1691) hydrogen bonds : angle 4.38063 / 3.12 ( 4905) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 825 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4923 (mtt) REVERT: J 64 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8517 (mp) REVERT: J 67 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7842 (t80) REVERT: J 134 MET cc_start: 0.8148 (mmm) cc_final: 0.7529 (mtt) REVERT: J 171 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7320 (ttp80) REVERT: K 24 SER cc_start: 0.8662 (m) cc_final: 0.8396 (p) REVERT: K 27 MET cc_start: 0.8843 (tpp) cc_final: 0.8110 (tpp) REVERT: K 91 GLN cc_start: 0.8469 (pm20) cc_final: 0.7935 (pm20) REVERT: L 116 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8770 (ttm-80) REVERT: L 132 THR cc_start: 0.9363 (m) cc_final: 0.9147 (p) REVERT: L 193 MET cc_start: 0.7343 (tpp) cc_final: 0.7103 (mmt) REVERT: L 521 SER cc_start: 0.9152 (m) cc_final: 0.8805 (t) REVERT: M 38 SER cc_start: 0.9626 (t) cc_final: 0.9346 (p) REVERT: M 46 ASP cc_start: 0.8769 (t0) cc_final: 0.8357 (t70) REVERT: M 135 ARG cc_start: 0.9195 (tpt90) cc_final: 0.8896 (tpt90) REVERT: M 245 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8604 (mmm-85) REVERT: M 275 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8831 (pt) REVERT: N 27 MET cc_start: 0.8652 (mmm) cc_final: 0.8414 (mmm) REVERT: N 43 MET cc_start: 0.9161 (mmm) cc_final: 0.8896 (mmm) REVERT: N 104 MET cc_start: 0.9134 (ttm) cc_final: 0.8880 (ttm) REVERT: N 237 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8862 (p) REVERT: O 47 ASP cc_start: 0.8126 (t0) cc_final: 0.7728 (t0) REVERT: O 52 LYS cc_start: 0.7741 (mttt) cc_final: 0.7377 (mtmm) REVERT: O 56 TYR cc_start: 0.7554 (p90) cc_final: 0.7087 (p90) REVERT: O 105 ASP cc_start: 0.7649 (t0) cc_final: 0.7152 (t0) REVERT: O 107 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: O 108 PHE cc_start: 0.7524 (m-80) cc_final: 0.7137 (m-80) REVERT: O 113 SER cc_start: 0.8439 (m) cc_final: 0.8113 (p) REVERT: O 141 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7971 (mm) REVERT: O 189 GLU cc_start: 0.7976 (tp30) cc_final: 0.7431 (tp30) REVERT: O 280 LYS cc_start: 0.7558 (pttm) cc_final: 0.7246 (pttm) REVERT: O 296 MET cc_start: 0.6829 (mtt) cc_final: 0.6135 (mtm) REVERT: O 300 ASP cc_start: 0.7554 (t0) cc_final: 0.6873 (m-30) REVERT: U 96 GLU cc_start: 0.8306 (mp0) cc_final: 0.8031 (mp0) REVERT: U 125 GLU cc_start: 0.8869 (tp30) cc_final: 0.8154 (tp30) REVERT: U 129 GLU cc_start: 0.8863 (tt0) cc_final: 0.8431 (tt0) REVERT: U 152 LYS cc_start: 0.9055 (mttp) cc_final: 0.8797 (mttp) REVERT: Y 55 VAL cc_start: 0.8671 (t) cc_final: 0.8447 (m) REVERT: d 16 ASP cc_start: 0.8629 (p0) cc_final: 0.7835 (t0) REVERT: d 47 MET cc_start: 0.9261 (ttm) cc_final: 0.8978 (ttp) REVERT: d 49 ARG cc_start: 0.8544 (mmt90) cc_final: 0.8305 (mmt90) REVERT: d 67 SER cc_start: 0.9290 (t) cc_final: 0.8588 (p) REVERT: d 106 LYS cc_start: 0.8526 (mmmm) cc_final: 0.7967 (mtmt) REVERT: d 111 GLU cc_start: 0.8999 (mp0) cc_final: 0.8799 (mt-10) REVERT: e 4 LEU cc_start: 0.8557 (mp) cc_final: 0.8208 (mt) REVERT: e 27 TYR cc_start: 0.8838 (m-80) cc_final: 0.7862 (m-80) REVERT: e 74 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8003 (tpp-160) REVERT: e 92 TYR cc_start: 0.7485 (t80) cc_final: 0.6635 (m-80) REVERT: g 51 MET cc_start: 0.5224 (mtt) cc_final: 0.5008 (mtt) REVERT: g 75 ASP cc_start: 0.8717 (t0) cc_final: 0.8153 (t70) REVERT: g 81 ASP cc_start: 0.9110 (t70) cc_final: 0.8640 (t70) REVERT: g 85 MET cc_start: 0.8780 (tmm) cc_final: 0.8339 (tmm) REVERT: h 86 ILE cc_start: 0.9188 (mm) cc_final: 0.8888 (mm) REVERT: h 157 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8098 (mmt90) REVERT: h 180 ASP cc_start: 0.8547 (t0) cc_final: 0.8104 (t0) REVERT: i 26 GLN cc_start: 0.8566 (tp40) cc_final: 0.8135 (mm110) REVERT: i 87 LYS cc_start: 0.9189 (tttt) cc_final: 0.8321 (tttt) REVERT: i 88 TYR cc_start: 0.9188 (m-80) cc_final: 0.7977 (m-80) REVERT: j 49 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7616 (pt0) REVERT: j 73 PHE cc_start: 0.8417 (t80) cc_final: 0.8166 (t80) REVERT: j 88 ASP cc_start: 0.8977 (t0) cc_final: 0.8641 (t0) REVERT: j 90 SER cc_start: 0.9403 (t) cc_final: 0.8549 (p) REVERT: j 91 GLN cc_start: 0.8613 (mm-40) cc_final: 0.7610 (mm110) REVERT: k 45 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8381 (ttm110) REVERT: k 81 PHE cc_start: 0.8814 (t80) cc_final: 0.8542 (t80) REVERT: l 36 MET cc_start: 0.8669 (ttm) cc_final: 0.8251 (ttp) REVERT: l 148 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7716 (t-90) REVERT: l 165 ASN cc_start: 0.9186 (t0) cc_final: 0.8827 (t0) REVERT: m 62 ASP cc_start: 0.8846 (t0) cc_final: 0.8586 (t0) REVERT: m 120 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8787 (ttmm) REVERT: n 95 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7875 (mm-30) REVERT: o 55 GLN cc_start: 0.8998 (mt0) cc_final: 0.8678 (mt0) REVERT: o 76 ASN cc_start: 0.8566 (t0) cc_final: 0.8012 (t0) REVERT: o 97 LYS cc_start: 0.8796 (mttm) cc_final: 0.8526 (mtpp) REVERT: o 103 GLU cc_start: 0.8394 (tp30) cc_final: 0.8174 (tp30) REVERT: o 117 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (pp) REVERT: p 59 ASN cc_start: 0.8470 (p0) cc_final: 0.8181 (p0) REVERT: p 103 MET cc_start: 0.9081 (tpp) cc_final: 0.8699 (mmm) REVERT: p 114 GLN cc_start: 0.8823 (tm-30) cc_final: 0.7864 (tm-30) REVERT: p 172 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8564 (pp30) outliers start: 135 outliers final: 86 residues processed: 910 average time/residue: 0.2068 time to fit residues: 305.7443 Evaluate side-chains 880 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 785 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 48 ASN 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 155 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 24 CYS Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 148 GLU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 100 ASN 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 m residue 17 THR Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 29 SER Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 87 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 276 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 293 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 335 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 354 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 ASN ** L 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 304 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN l 148 HIS p 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101886 restraints weight = 48947.866| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.10 r_work: 0.3107 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32715 Z= 0.139 Angle : 0.652 20.608 44202 Z= 0.319 Chirality : 0.042 0.310 4796 Planarity : 0.005 0.064 5411 Dihedral : 12.056 149.244 5109 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 3.22 % Allowed : 18.05 % Favored : 78.73 % 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: 0.71 (0.14), residues: 3761 helix: 1.06 (0.11), residues: 2452 sheet: -0.86 (1.36), residues: 18 loop : -0.52 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 176 TYR 0.025 0.001 TYR L 422 PHE 0.029 0.001 PHE M 380 TRP 0.015 0.001 TRP X 170 HIS 0.004 0.001 HIS L 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (32706) covalent geometry : angle 0.64688 / 0.32 (44186) SS BOND : bond 0.00618 / 0.45 ( 8) SS BOND : angle 4.38707 / 3.28 ( 16) hydrogen bonds : bond 0.04163 / 2.71 ( 1691) hydrogen bonds : angle 4.30094 / 3.06 ( 4905) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 822 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4881 (mtt) REVERT: J 64 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8444 (mp) REVERT: J 67 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7546 (t80) REVERT: J 134 MET cc_start: 0.8139 (mmm) cc_final: 0.7530 (mtt) REVERT: J 171 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7339 (ttp80) REVERT: K 24 SER cc_start: 0.8699 (m) cc_final: 0.8427 (p) REVERT: K 27 MET cc_start: 0.8778 (tpp) cc_final: 0.8195 (tpp) REVERT: K 34 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8195 (mm-30) REVERT: K 91 GLN cc_start: 0.8363 (pm20) cc_final: 0.7826 (pm20) REVERT: L 23 MET cc_start: 0.9013 (mtp) cc_final: 0.8778 (mtp) REVERT: L 132 THR cc_start: 0.9339 (m) cc_final: 0.9127 (p) REVERT: L 347 ILE cc_start: 0.9198 (mt) cc_final: 0.8988 (mp) REVERT: L 521 SER cc_start: 0.9156 (m) cc_final: 0.8827 (t) REVERT: M 38 SER cc_start: 0.9580 (t) cc_final: 0.9333 (p) REVERT: M 47 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7314 (tm-30) REVERT: M 48 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7696 (p0) REVERT: M 135 ARG cc_start: 0.9192 (tpt90) cc_final: 0.8906 (tpt90) REVERT: M 302 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8338 (mtp) REVERT: M 304 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: N 10 TYR cc_start: 0.9006 (m-80) cc_final: 0.8743 (m-80) REVERT: N 43 MET cc_start: 0.9174 (mmm) cc_final: 0.8718 (mmm) REVERT: N 102 LEU cc_start: 0.8927 (mt) cc_final: 0.8692 (mt) REVERT: N 104 MET cc_start: 0.9139 (ttm) cc_final: 0.8908 (ttm) REVERT: N 175 MET cc_start: 0.8991 (mmm) cc_final: 0.8768 (mmt) REVERT: N 237 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8930 (p) REVERT: N 313 MET cc_start: 0.7809 (ttm) cc_final: 0.7550 (ttp) REVERT: O 47 ASP cc_start: 0.8090 (t0) cc_final: 0.7795 (t0) REVERT: O 52 LYS cc_start: 0.7732 (mttt) cc_final: 0.7389 (mtmm) REVERT: O 56 TYR cc_start: 0.7556 (p90) cc_final: 0.7118 (p90) REVERT: O 102 ARG cc_start: 0.8657 (mtp-110) cc_final: 0.8394 (mtt90) REVERT: O 105 ASP cc_start: 0.7661 (t70) cc_final: 0.7143 (t0) REVERT: O 107 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: O 108 PHE cc_start: 0.7577 (m-80) cc_final: 0.7196 (m-80) REVERT: O 113 SER cc_start: 0.8462 (m) cc_final: 0.8139 (p) REVERT: O 141 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8032 (mm) REVERT: O 189 GLU cc_start: 0.7971 (tp30) cc_final: 0.7410 (tp30) REVERT: O 277 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6778 (tptp) REVERT: O 296 MET cc_start: 0.6762 (mtt) cc_final: 0.6478 (mtm) REVERT: U 96 GLU cc_start: 0.8405 (mp0) cc_final: 0.8090 (mp0) REVERT: U 125 GLU cc_start: 0.8896 (tp30) cc_final: 0.8204 (tp30) REVERT: U 129 GLU cc_start: 0.8786 (tt0) cc_final: 0.8469 (tt0) REVERT: U 152 LYS cc_start: 0.9043 (mttp) cc_final: 0.8804 (mttp) REVERT: Y 19 GLN cc_start: 0.8667 (mt0) cc_final: 0.8043 (tp-100) REVERT: Y 55 VAL cc_start: 0.8668 (t) cc_final: 0.8446 (m) REVERT: d 16 ASP cc_start: 0.8611 (p0) cc_final: 0.7914 (t0) REVERT: d 47 MET cc_start: 0.9223 (ttm) cc_final: 0.8932 (ttp) REVERT: d 49 ARG cc_start: 0.8508 (mmt90) cc_final: 0.8283 (mmt90) REVERT: d 61 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8567 (mt0) REVERT: d 67 SER cc_start: 0.9286 (t) cc_final: 0.8566 (p) REVERT: d 106 LYS cc_start: 0.8539 (mmmm) cc_final: 0.7982 (mtmt) REVERT: e 4 LEU cc_start: 0.8601 (mp) cc_final: 0.8258 (mt) REVERT: e 27 TYR cc_start: 0.8873 (m-80) cc_final: 0.7841 (m-80) REVERT: e 74 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7901 (tpp-160) REVERT: e 92 TYR cc_start: 0.7474 (t80) cc_final: 0.6672 (m-80) REVERT: f 33 LYS cc_start: 0.9046 (tttm) cc_final: 0.8683 (ttpt) REVERT: g 51 MET cc_start: 0.5098 (mtt) cc_final: 0.4754 (mtt) REVERT: g 75 ASP cc_start: 0.8728 (t0) cc_final: 0.8125 (t70) REVERT: g 81 ASP cc_start: 0.9088 (t70) cc_final: 0.8658 (t70) REVERT: g 85 MET cc_start: 0.8838 (tmm) cc_final: 0.8414 (tmm) REVERT: g 144 LYS cc_start: 0.8895 (mttm) cc_final: 0.8482 (mtpp) REVERT: h 86 ILE cc_start: 0.9168 (mm) cc_final: 0.8907 (mm) REVERT: h 105 TYR cc_start: 0.8047 (t80) cc_final: 0.7794 (t80) REVERT: h 157 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8063 (mmt90) REVERT: h 180 ASP cc_start: 0.8454 (t0) cc_final: 0.7761 (t0) REVERT: h 182 SER cc_start: 0.9150 (m) cc_final: 0.8840 (p) REVERT: i 26 GLN cc_start: 0.8514 (tp40) cc_final: 0.8099 (mm110) REVERT: i 87 LYS cc_start: 0.9205 (tttt) cc_final: 0.8446 (tttt) REVERT: i 88 TYR cc_start: 0.9173 (m-80) cc_final: 0.7940 (m-80) REVERT: j 49 GLN cc_start: 0.8249 (tp-100) cc_final: 0.8029 (tp40) REVERT: j 73 PHE cc_start: 0.8399 (t80) cc_final: 0.8150 (t80) REVERT: j 88 ASP cc_start: 0.8953 (t0) cc_final: 0.8597 (t0) REVERT: j 90 SER cc_start: 0.9447 (t) cc_final: 0.8636 (p) REVERT: j 91 GLN cc_start: 0.8620 (mm-40) cc_final: 0.7576 (mm110) REVERT: k 45 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8327 (ttm110) REVERT: k 81 PHE cc_start: 0.8803 (t80) cc_final: 0.8553 (t80) REVERT: l 36 MET cc_start: 0.8636 (ttm) cc_final: 0.8249 (ttp) REVERT: l 118 ASP cc_start: 0.8450 (t0) cc_final: 0.7909 (t0) REVERT: l 165 ASN cc_start: 0.9191 (t0) cc_final: 0.8881 (t0) REVERT: m 50 GLN cc_start: 0.8536 (tt0) cc_final: 0.8240 (mt0) REVERT: m 51 TYR cc_start: 0.8978 (t80) cc_final: 0.8716 (t80) REVERT: m 62 ASP cc_start: 0.8844 (t0) cc_final: 0.8558 (t0) REVERT: m 89 LEU cc_start: 0.9195 (tt) cc_final: 0.8978 (tt) REVERT: m 120 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8805 (ttmm) REVERT: n 95 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7853 (mm-30) REVERT: o 18 ASP cc_start: 0.8206 (t70) cc_final: 0.7795 (t0) REVERT: o 55 GLN cc_start: 0.8940 (mt0) cc_final: 0.8641 (mt0) REVERT: o 76 ASN cc_start: 0.8544 (t0) cc_final: 0.8019 (t0) REVERT: o 97 LYS cc_start: 0.8738 (mttm) cc_final: 0.8484 (mtpp) REVERT: o 103 GLU cc_start: 0.8395 (tp30) cc_final: 0.8181 (tp30) REVERT: o 117 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8047 (pp) REVERT: p 39 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9001 (mm) REVERT: p 90 MET cc_start: 0.9183 (mmp) cc_final: 0.8675 (mmp) REVERT: p 103 MET cc_start: 0.9085 (tpp) cc_final: 0.8730 (mmm) REVERT: p 114 GLN cc_start: 0.8798 (tm-30) cc_final: 0.7805 (tm-30) REVERT: p 172 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8588 (pp30) outliers start: 109 outliers final: 82 residues processed: 881 average time/residue: 0.2061 time to fit residues: 295.4396 Evaluate side-chains 870 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 776 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain l residue 44 THR 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 181 VAL Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 78 LEU Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 124 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 212 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 216 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 282 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 345 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN L 200 GLN L 332 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN l 100 ASN l 148 HIS o 110 GLN p 124 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099932 restraints weight = 49612.710| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.12 r_work: 0.3089 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32715 Z= 0.182 Angle : 0.675 18.680 44202 Z= 0.330 Chirality : 0.044 0.325 4796 Planarity : 0.005 0.063 5411 Dihedral : 12.008 149.223 5109 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 3.36 % Allowed : 18.73 % Favored : 77.91 % 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: 0.73 (0.14), residues: 3761 helix: 1.10 (0.11), residues: 2450 sheet: -1.08 (1.33), residues: 17 loop : -0.57 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 176 TYR 0.023 0.002 TYR M 406 PHE 0.028 0.002 PHE Y 138 TRP 0.015 0.001 TRP X 170 HIS 0.012 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (32706) covalent geometry : angle 0.67125 / 0.33 (44186) SS BOND : bond 0.00417 / 0.29 ( 8) SS BOND : angle 3.92689 / 2.93 ( 16) hydrogen bonds : bond 0.04243 / 2.76 ( 1691) hydrogen bonds : angle 4.33097 / 3.08 ( 4905) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 794 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.4906 (mtt) REVERT: J 64 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8419 (mp) REVERT: J 67 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7548 (t80) REVERT: J 134 MET cc_start: 0.8151 (mmm) cc_final: 0.7541 (mtt) REVERT: K 24 SER cc_start: 0.8752 (m) cc_final: 0.8489 (p) REVERT: K 27 MET cc_start: 0.8768 (tpp) cc_final: 0.8082 (tpp) REVERT: K 34 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8243 (mm-30) REVERT: K 91 GLN cc_start: 0.8376 (pm20) cc_final: 0.7840 (pm20) REVERT: L 23 MET cc_start: 0.9120 (mtp) cc_final: 0.8836 (mtp) REVERT: L 313 MET cc_start: 0.8799 (ptp) cc_final: 0.8437 (mtm) REVERT: L 521 SER cc_start: 0.9196 (m) cc_final: 0.8854 (t) REVERT: M 38 SER cc_start: 0.9630 (t) cc_final: 0.9388 (p) REVERT: M 39 LEU cc_start: 0.9185 (tp) cc_final: 0.8965 (tp) REVERT: M 114 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7586 (mm-30) REVERT: M 135 ARG cc_start: 0.9217 (tpt90) cc_final: 0.8930 (tpt90) REVERT: M 139 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7485 (mm-40) REVERT: M 302 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8199 (mtp) REVERT: M 310 MET cc_start: 0.8552 (tmm) cc_final: 0.8076 (tmm) REVERT: M 316 MET cc_start: 0.8569 (mtp) cc_final: 0.8335 (mtm) REVERT: N 10 TYR cc_start: 0.9021 (m-80) cc_final: 0.8756 (m-80) REVERT: N 43 MET cc_start: 0.9202 (mmm) cc_final: 0.8862 (mmm) REVERT: N 150 ASN cc_start: 0.8534 (t0) cc_final: 0.8187 (t0) REVERT: N 175 MET cc_start: 0.9062 (mmm) cc_final: 0.8851 (mmt) REVERT: N 203 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8316 (tt) REVERT: N 237 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8943 (p) REVERT: N 247 MET cc_start: 0.8637 (mtm) cc_final: 0.8399 (mtp) REVERT: N 284 MET cc_start: 0.8670 (mmt) cc_final: 0.8341 (mmm) REVERT: N 313 MET cc_start: 0.7768 (ttm) cc_final: 0.7352 (ttp) REVERT: O 52 LYS cc_start: 0.7738 (mttt) cc_final: 0.7417 (mtmm) REVERT: O 56 TYR cc_start: 0.7529 (p90) cc_final: 0.7077 (p90) REVERT: O 102 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8431 (mtt90) REVERT: O 105 ASP cc_start: 0.7641 (t70) cc_final: 0.7120 (t0) REVERT: O 107 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: O 108 PHE cc_start: 0.7637 (m-80) cc_final: 0.7216 (m-80) REVERT: O 113 SER cc_start: 0.8521 (m) cc_final: 0.8197 (p) REVERT: O 141 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8039 (mm) REVERT: O 189 GLU cc_start: 0.8012 (tp30) cc_final: 0.7477 (tp30) REVERT: O 198 TYR cc_start: 0.8561 (m-80) cc_final: 0.8317 (m-80) REVERT: O 249 MET cc_start: 0.6223 (mmm) cc_final: 0.5526 (mmm) REVERT: O 277 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6762 (tptp) REVERT: O 296 MET cc_start: 0.6815 (mtt) cc_final: 0.6097 (mtm) REVERT: O 300 ASP cc_start: 0.7661 (t0) cc_final: 0.6905 (m-30) REVERT: U 96 GLU cc_start: 0.8435 (mp0) cc_final: 0.8172 (mp0) REVERT: U 125 GLU cc_start: 0.8880 (tp30) cc_final: 0.8152 (tp30) REVERT: U 129 GLU cc_start: 0.8791 (tt0) cc_final: 0.8490 (tt0) REVERT: U 152 LYS cc_start: 0.9048 (mttp) cc_final: 0.8806 (mttp) REVERT: Y 19 GLN cc_start: 0.8643 (mt0) cc_final: 0.8039 (tp-100) REVERT: Y 22 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7794 (ttt90) REVERT: Y 55 VAL cc_start: 0.8727 (t) cc_final: 0.8502 (m) REVERT: d 16 ASP cc_start: 0.8667 (p0) cc_final: 0.7998 (t0) REVERT: d 47 MET cc_start: 0.9201 (ttm) cc_final: 0.8910 (ttp) REVERT: d 49 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8329 (mmt90) REVERT: d 67 SER cc_start: 0.9312 (t) cc_final: 0.8618 (p) REVERT: d 100 ASP cc_start: 0.9218 (m-30) cc_final: 0.8792 (m-30) REVERT: d 106 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8076 (mtmt) REVERT: e 4 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8296 (mt) REVERT: e 27 TYR cc_start: 0.8917 (m-80) cc_final: 0.7928 (m-80) REVERT: e 74 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7948 (tpp-160) REVERT: e 92 TYR cc_start: 0.7507 (t80) cc_final: 0.6636 (m-80) REVERT: f 33 LYS cc_start: 0.9100 (tttm) cc_final: 0.8752 (ttpt) REVERT: g 51 MET cc_start: 0.5151 (mtt) cc_final: 0.4906 (mtt) REVERT: g 75 ASP cc_start: 0.8824 (t0) cc_final: 0.8229 (t70) REVERT: g 81 ASP cc_start: 0.9135 (t70) cc_final: 0.8697 (t70) REVERT: g 85 MET cc_start: 0.8877 (tmm) cc_final: 0.8404 (tmm) REVERT: g 144 LYS cc_start: 0.8975 (mttm) cc_final: 0.8556 (mtpp) REVERT: h 72 LYS cc_start: 0.8642 (ttpt) cc_final: 0.7560 (tttp) REVERT: h 86 ILE cc_start: 0.9179 (mm) cc_final: 0.8931 (mm) REVERT: h 157 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8138 (mmt90) REVERT: h 180 ASP cc_start: 0.8453 (t0) cc_final: 0.7813 (t0) REVERT: h 182 SER cc_start: 0.9179 (m) cc_final: 0.8860 (p) REVERT: i 26 GLN cc_start: 0.8439 (tp40) cc_final: 0.8034 (mm110) REVERT: i 88 TYR cc_start: 0.9232 (m-80) cc_final: 0.8792 (m-80) REVERT: j 49 GLN cc_start: 0.8248 (tp-100) cc_final: 0.8028 (tp40) REVERT: j 73 PHE cc_start: 0.8452 (t80) cc_final: 0.8191 (t80) REVERT: j 88 ASP cc_start: 0.8973 (t0) cc_final: 0.8664 (t0) REVERT: j 90 SER cc_start: 0.9467 (t) cc_final: 0.8716 (p) REVERT: j 91 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7586 (mm110) REVERT: k 81 PHE cc_start: 0.8916 (t80) cc_final: 0.8677 (t80) REVERT: l 36 MET cc_start: 0.8754 (ttm) cc_final: 0.8295 (ttp) REVERT: l 118 ASP cc_start: 0.8409 (t0) cc_final: 0.7887 (t0) REVERT: l 165 ASN cc_start: 0.9235 (t0) cc_final: 0.8938 (t0) REVERT: m 19 ASP cc_start: 0.8436 (t0) cc_final: 0.8217 (t0) REVERT: m 50 GLN cc_start: 0.8507 (tt0) cc_final: 0.8255 (mt0) REVERT: m 51 TYR cc_start: 0.9066 (t80) cc_final: 0.8832 (t80) REVERT: m 62 ASP cc_start: 0.8843 (t0) cc_final: 0.8583 (t0) REVERT: m 89 LEU cc_start: 0.9205 (tt) cc_final: 0.9000 (tt) REVERT: m 120 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8839 (ttmm) REVERT: o 18 ASP cc_start: 0.8212 (t70) cc_final: 0.7803 (t0) REVERT: o 55 GLN cc_start: 0.9031 (mt0) cc_final: 0.8754 (mt0) REVERT: o 76 ASN cc_start: 0.8641 (t0) cc_final: 0.8037 (t0) REVERT: o 97 LYS cc_start: 0.8799 (mttm) cc_final: 0.8544 (mtpp) REVERT: o 117 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8054 (pp) REVERT: p 39 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9029 (mm) REVERT: p 73 ASP cc_start: 0.8386 (p0) cc_final: 0.7964 (p0) REVERT: p 90 MET cc_start: 0.9209 (mmp) cc_final: 0.8675 (mmp) REVERT: p 103 MET cc_start: 0.9065 (tpp) cc_final: 0.8648 (mmm) REVERT: p 114 GLN cc_start: 0.8929 (tm-30) cc_final: 0.7988 (tm-30) REVERT: p 172 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8611 (pp30) outliers start: 114 outliers final: 90 residues processed: 857 average time/residue: 0.2041 time to fit residues: 284.7547 Evaluate side-chains 870 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 768 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain M residue 23 THR 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 270 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 250 SER Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 24 CYS Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 148 GLU Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 78 LEU Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 87 GLU Chi-restraints excluded: chain p residue 124 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 165 optimal weight: 0.0030 chunk 353 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 HIS L 332 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 61 GLN ** e 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 80 ASN l 148 HIS p 124 ASN p 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101827 restraints weight = 49268.368| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.13 r_work: 0.3116 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32715 Z= 0.139 Angle : 0.660 15.687 44202 Z= 0.321 Chirality : 0.043 0.345 4796 Planarity : 0.005 0.063 5411 Dihedral : 11.887 149.475 5109 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 2.83 % Allowed : 19.59 % Favored : 77.58 % 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: 0.81 (0.14), residues: 3761 helix: 1.15 (0.11), residues: 2456 sheet: -0.78 (1.33), residues: 17 loop : -0.55 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 171 TYR 0.024 0.001 TYR L 422 PHE 0.022 0.001 PHE L 89 TRP 0.020 0.001 TRP M 307 HIS 0.007 0.001 HIS L 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (32706) covalent geometry : angle 0.65672 / 0.32 (44186) SS BOND : bond 0.00389 / 0.27 ( 8) SS BOND : angle 3.57679 / 2.60 ( 16) hydrogen bonds : bond 0.04098 / 2.65 ( 1691) hydrogen bonds : angle 4.28162 / 3.05 ( 4905) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 799 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4884 (mtt) REVERT: J 67 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7677 (t80) REVERT: J 71 THR cc_start: 0.9060 (m) cc_final: 0.8763 (p) REVERT: J 134 MET cc_start: 0.8197 (mmm) cc_final: 0.7544 (mtt) REVERT: J 171 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7174 (ttp80) REVERT: K 22 PHE cc_start: 0.8365 (m-10) cc_final: 0.7965 (m-80) REVERT: K 24 SER cc_start: 0.8740 (m) cc_final: 0.8478 (p) REVERT: K 27 MET cc_start: 0.8711 (tpp) cc_final: 0.8064 (tpp) REVERT: K 31 LEU cc_start: 0.9179 (mm) cc_final: 0.8872 (mm) REVERT: K 91 GLN cc_start: 0.8444 (pm20) cc_final: 0.7888 (pm20) REVERT: L 23 MET cc_start: 0.9125 (mtp) cc_final: 0.8838 (mtp) REVERT: L 313 MET cc_start: 0.8736 (ptp) cc_final: 0.8382 (mtm) REVERT: L 521 SER cc_start: 0.9192 (m) cc_final: 0.8863 (t) REVERT: M 38 SER cc_start: 0.9615 (t) cc_final: 0.9399 (p) REVERT: M 39 LEU cc_start: 0.9211 (tp) cc_final: 0.9008 (tp) REVERT: M 114 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7603 (mm-30) REVERT: M 135 ARG cc_start: 0.9180 (tpt90) cc_final: 0.8887 (tpt90) REVERT: M 139 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7492 (mm-40) REVERT: M 302 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: M 307 TRP cc_start: 0.8891 (m-10) cc_final: 0.8553 (m-10) REVERT: M 310 MET cc_start: 0.8604 (tmm) cc_final: 0.7969 (tmm) REVERT: N 10 TYR cc_start: 0.8985 (m-80) cc_final: 0.8733 (m-80) REVERT: N 43 MET cc_start: 0.9175 (mmm) cc_final: 0.8790 (mmm) REVERT: N 102 LEU cc_start: 0.8955 (mt) cc_final: 0.8741 (mt) REVERT: N 150 ASN cc_start: 0.8542 (t0) cc_final: 0.8204 (t0) REVERT: N 237 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8980 (p) REVERT: N 284 MET cc_start: 0.8640 (mmt) cc_final: 0.8314 (mmm) REVERT: O 52 LYS cc_start: 0.7796 (mttt) cc_final: 0.7561 (mtmm) REVERT: O 56 TYR cc_start: 0.7466 (p90) cc_final: 0.7117 (p90) REVERT: O 102 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8414 (mtt90) REVERT: O 105 ASP cc_start: 0.7596 (t70) cc_final: 0.6995 (t0) REVERT: O 107 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: O 108 PHE cc_start: 0.7644 (m-80) cc_final: 0.7223 (m-80) REVERT: O 113 SER cc_start: 0.8538 (m) cc_final: 0.8048 (p) REVERT: O 141 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7967 (mm) REVERT: O 189 GLU cc_start: 0.7977 (tp30) cc_final: 0.7415 (tp30) REVERT: O 198 TYR cc_start: 0.8542 (m-80) cc_final: 0.8289 (m-80) REVERT: O 249 MET cc_start: 0.6154 (mmm) cc_final: 0.5515 (mmm) REVERT: O 250 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8213 (p) REVERT: O 277 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6597 (tptp) REVERT: O 296 MET cc_start: 0.6824 (mtt) cc_final: 0.6109 (mtm) REVERT: O 300 ASP cc_start: 0.7559 (t0) cc_final: 0.6830 (m-30) REVERT: U 96 GLU cc_start: 0.8412 (mp0) cc_final: 0.8174 (mp0) REVERT: U 125 GLU cc_start: 0.8858 (tp30) cc_final: 0.8129 (tp30) REVERT: U 129 GLU cc_start: 0.8797 (tt0) cc_final: 0.8459 (tt0) REVERT: U 152 LYS cc_start: 0.9052 (mttp) cc_final: 0.8823 (mttp) REVERT: Y 19 GLN cc_start: 0.8629 (mt0) cc_final: 0.8043 (tp-100) REVERT: Y 22 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7475 (ttt90) REVERT: Y 55 VAL cc_start: 0.8702 (t) cc_final: 0.8473 (m) REVERT: d 2 MET cc_start: 0.8230 (mmm) cc_final: 0.7941 (mmp) REVERT: d 16 ASP cc_start: 0.8663 (p0) cc_final: 0.8041 (t0) REVERT: d 47 MET cc_start: 0.9176 (ttm) cc_final: 0.8937 (ttp) REVERT: d 61 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: d 67 SER cc_start: 0.9328 (t) cc_final: 0.8617 (p) REVERT: d 100 ASP cc_start: 0.9234 (m-30) cc_final: 0.9025 (m-30) REVERT: d 106 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8077 (mtmt) REVERT: e 4 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8275 (mt) REVERT: e 27 TYR cc_start: 0.8916 (m-80) cc_final: 0.7948 (m-80) REVERT: e 74 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7959 (tpp-160) REVERT: e 92 TYR cc_start: 0.7487 (t80) cc_final: 0.6641 (m-80) REVERT: f 33 LYS cc_start: 0.9077 (tttm) cc_final: 0.8730 (ttpt) REVERT: g 51 MET cc_start: 0.5109 (mtt) cc_final: 0.4856 (mtt) REVERT: g 75 ASP cc_start: 0.8780 (t0) cc_final: 0.8205 (t70) REVERT: g 81 ASP cc_start: 0.9111 (t70) cc_final: 0.8706 (t70) REVERT: g 85 MET cc_start: 0.8886 (tmm) cc_final: 0.8453 (tmm) REVERT: g 112 MET cc_start: 0.8530 (ttm) cc_final: 0.8312 (ttp) REVERT: g 144 LYS cc_start: 0.8940 (mttm) cc_final: 0.8553 (mtpp) REVERT: h 105 TYR cc_start: 0.8052 (t80) cc_final: 0.7826 (t80) REVERT: h 157 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8106 (mmt90) REVERT: h 180 ASP cc_start: 0.8406 (t0) cc_final: 0.7799 (t0) REVERT: h 182 SER cc_start: 0.9130 (m) cc_final: 0.8898 (p) REVERT: i 26 GLN cc_start: 0.8364 (tp40) cc_final: 0.7994 (mm110) REVERT: i 88 TYR cc_start: 0.9215 (m-80) cc_final: 0.8699 (m-80) REVERT: j 49 GLN cc_start: 0.8245 (tp-100) cc_final: 0.8035 (tp40) REVERT: j 73 PHE cc_start: 0.8444 (t80) cc_final: 0.8194 (t80) REVERT: j 88 ASP cc_start: 0.8907 (t0) cc_final: 0.8564 (t70) REVERT: j 90 SER cc_start: 0.9476 (t) cc_final: 0.8765 (p) REVERT: j 91 GLN cc_start: 0.8721 (mm-40) cc_final: 0.7637 (mm-40) REVERT: k 81 PHE cc_start: 0.8913 (t80) cc_final: 0.8684 (t80) REVERT: l 36 MET cc_start: 0.8690 (ttm) cc_final: 0.8268 (ttp) REVERT: l 165 ASN cc_start: 0.9242 (t0) cc_final: 0.8965 (t0) REVERT: m 51 TYR cc_start: 0.8994 (t80) cc_final: 0.8744 (t80) REVERT: m 62 ASP cc_start: 0.8738 (t0) cc_final: 0.8442 (t0) REVERT: m 89 LEU cc_start: 0.9190 (tt) cc_final: 0.8985 (tt) REVERT: m 120 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8834 (ttmm) REVERT: n 58 MET cc_start: 0.8450 (mmm) cc_final: 0.8217 (mtp) REVERT: n 106 TYR cc_start: 0.8952 (m-80) cc_final: 0.8749 (m-80) REVERT: o 18 ASP cc_start: 0.8232 (t70) cc_final: 0.7875 (t0) REVERT: o 55 GLN cc_start: 0.9000 (mt0) cc_final: 0.8699 (mt0) REVERT: o 76 ASN cc_start: 0.8593 (t0) cc_final: 0.8063 (t0) REVERT: o 97 LYS cc_start: 0.8771 (mttm) cc_final: 0.8533 (mtpp) REVERT: o 117 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8062 (pp) REVERT: p 39 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9021 (mm) REVERT: p 73 ASP cc_start: 0.8302 (p0) cc_final: 0.7899 (p0) REVERT: p 90 MET cc_start: 0.9166 (mmp) cc_final: 0.8556 (mmp) REVERT: p 103 MET cc_start: 0.9052 (tpp) cc_final: 0.8693 (mmm) REVERT: p 114 GLN cc_start: 0.8906 (tm-30) cc_final: 0.7996 (tm-30) REVERT: p 172 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8613 (pp30) outliers start: 96 outliers final: 78 residues processed: 851 average time/residue: 0.1990 time to fit residues: 276.3255 Evaluate side-chains 856 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 766 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 250 SER Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 117 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain l residue 44 THR 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 181 VAL Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 78 LEU Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 124 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 52 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 300 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 333 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 316 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN d 61 GLN ** e 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS l 148 HIS n 78 GLN p 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101899 restraints weight = 49555.725| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.12 r_work: 0.3120 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32715 Z= 0.143 Angle : 0.669 14.764 44202 Z= 0.325 Chirality : 0.043 0.341 4796 Planarity : 0.005 0.064 5411 Dihedral : 11.836 149.576 5109 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 2.92 % Allowed : 19.82 % Favored : 77.26 % 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: 0.85 (0.14), residues: 3761 helix: 1.18 (0.11), residues: 2451 sheet: -0.74 (1.35), residues: 17 loop : -0.51 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 171 TYR 0.023 0.001 TYR L 422 PHE 0.029 0.001 PHE Y 138 TRP 0.019 0.001 TRP X 170 HIS 0.015 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (32706) covalent geometry : angle 0.66601 / 0.32 (44186) SS BOND : bond 0.00217 / 0.14 ( 8) SS BOND : angle 3.33167 / 2.36 ( 16) hydrogen bonds : bond 0.04083 / 2.63 ( 1691) hydrogen bonds : angle 4.26747 / 3.04 ( 4905) Misc. bond : bond 0.00039 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 785 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4907 (mtt) REVERT: J 54 MET cc_start: 0.8432 (tpp) cc_final: 0.8118 (tpp) REVERT: J 64 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8360 (mp) REVERT: J 65 VAL cc_start: 0.8801 (p) cc_final: 0.8576 (m) REVERT: J 67 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7648 (t80) REVERT: J 71 THR cc_start: 0.9071 (m) cc_final: 0.8780 (p) REVERT: J 134 MET cc_start: 0.8189 (mmm) cc_final: 0.7522 (mtt) REVERT: J 171 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7170 (ttp80) REVERT: K 22 PHE cc_start: 0.8390 (m-10) cc_final: 0.8021 (m-80) REVERT: K 24 SER cc_start: 0.8618 (m) cc_final: 0.8402 (p) REVERT: K 27 MET cc_start: 0.8712 (tpp) cc_final: 0.8033 (tpp) REVERT: K 31 LEU cc_start: 0.9174 (mm) cc_final: 0.8861 (mm) REVERT: K 54 MET cc_start: 0.8621 (mtt) cc_final: 0.8359 (mtt) REVERT: K 91 GLN cc_start: 0.8457 (pm20) cc_final: 0.7913 (pm20) REVERT: L 23 MET cc_start: 0.9132 (mtp) cc_final: 0.8863 (mtp) REVERT: L 313 MET cc_start: 0.8703 (ptp) cc_final: 0.8354 (mtm) REVERT: L 521 SER cc_start: 0.9185 (m) cc_final: 0.8862 (t) REVERT: M 38 SER cc_start: 0.9605 (t) cc_final: 0.9392 (p) REVERT: M 135 ARG cc_start: 0.9174 (tpt90) cc_final: 0.8883 (tpt90) REVERT: M 139 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7378 (mm-40) REVERT: M 302 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: M 307 TRP cc_start: 0.8889 (m-10) cc_final: 0.8614 (m-10) REVERT: M 310 MET cc_start: 0.8369 (tmm) cc_final: 0.8078 (tmm) REVERT: M 376 MET cc_start: 0.8584 (mtp) cc_final: 0.8207 (mtp) REVERT: M 423 MET cc_start: 0.7241 (mmt) cc_final: 0.6417 (mmt) REVERT: N 10 TYR cc_start: 0.8994 (m-80) cc_final: 0.8746 (m-80) REVERT: N 43 MET cc_start: 0.9166 (mmm) cc_final: 0.8785 (mmm) REVERT: N 102 LEU cc_start: 0.8947 (mt) cc_final: 0.8723 (mt) REVERT: N 150 ASN cc_start: 0.8573 (t0) cc_final: 0.8230 (t0) REVERT: N 237 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8975 (p) REVERT: N 284 MET cc_start: 0.8641 (mmt) cc_final: 0.8316 (mmm) REVERT: N 313 MET cc_start: 0.7725 (ttm) cc_final: 0.7384 (ttp) REVERT: O 52 LYS cc_start: 0.7800 (mttt) cc_final: 0.7562 (mtmm) REVERT: O 56 TYR cc_start: 0.7489 (p90) cc_final: 0.7136 (p90) REVERT: O 102 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8382 (mtt90) REVERT: O 105 ASP cc_start: 0.7614 (t70) cc_final: 0.6795 (t0) REVERT: O 107 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: O 108 PHE cc_start: 0.7650 (m-80) cc_final: 0.7368 (m-10) REVERT: O 113 SER cc_start: 0.8373 (m) cc_final: 0.8087 (p) REVERT: O 189 GLU cc_start: 0.7986 (tp30) cc_final: 0.7428 (tp30) REVERT: O 198 TYR cc_start: 0.8543 (m-80) cc_final: 0.8291 (m-80) REVERT: O 249 MET cc_start: 0.6136 (mmm) cc_final: 0.5482 (mmm) REVERT: O 277 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6664 (tptp) REVERT: O 296 MET cc_start: 0.6781 (mtt) cc_final: 0.6009 (mtm) REVERT: O 300 ASP cc_start: 0.7567 (t0) cc_final: 0.6859 (m-30) REVERT: U 96 GLU cc_start: 0.8449 (mp0) cc_final: 0.8199 (mp0) REVERT: U 125 GLU cc_start: 0.8877 (tp30) cc_final: 0.8139 (tp30) REVERT: U 129 GLU cc_start: 0.8817 (tt0) cc_final: 0.8487 (tt0) REVERT: U 152 LYS cc_start: 0.9048 (mttp) cc_final: 0.8819 (mttp) REVERT: Y 19 GLN cc_start: 0.8658 (mt0) cc_final: 0.8081 (tp-100) REVERT: Y 22 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7435 (ttt90) REVERT: Y 55 VAL cc_start: 0.8695 (t) cc_final: 0.8474 (m) REVERT: d 2 MET cc_start: 0.8302 (mmm) cc_final: 0.8060 (mmp) REVERT: d 16 ASP cc_start: 0.8606 (p0) cc_final: 0.7968 (t0) REVERT: d 47 MET cc_start: 0.9184 (ttm) cc_final: 0.8918 (ttp) REVERT: d 67 SER cc_start: 0.9306 (t) cc_final: 0.8610 (p) REVERT: d 106 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8087 (mtmt) REVERT: e 4 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8320 (mt) REVERT: e 27 TYR cc_start: 0.8928 (m-80) cc_final: 0.7946 (m-80) REVERT: e 74 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7921 (tpp-160) REVERT: e 92 TYR cc_start: 0.7460 (t80) cc_final: 0.6604 (m-80) REVERT: g 51 MET cc_start: 0.5103 (mtt) cc_final: 0.4851 (mtt) REVERT: g 75 ASP cc_start: 0.8779 (t0) cc_final: 0.8494 (t70) REVERT: g 81 ASP cc_start: 0.9112 (t70) cc_final: 0.8686 (t70) REVERT: g 85 MET cc_start: 0.8879 (tmm) cc_final: 0.8415 (tmm) REVERT: g 144 LYS cc_start: 0.9004 (mttm) cc_final: 0.8609 (mtpp) REVERT: h 105 TYR cc_start: 0.8124 (t80) cc_final: 0.7905 (t80) REVERT: h 157 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8009 (mmt90) REVERT: h 180 ASP cc_start: 0.8389 (t0) cc_final: 0.7754 (t0) REVERT: h 182 SER cc_start: 0.9133 (m) cc_final: 0.8904 (p) REVERT: i 26 GLN cc_start: 0.8356 (tp40) cc_final: 0.7991 (mm110) REVERT: i 88 TYR cc_start: 0.9223 (m-80) cc_final: 0.8707 (m-80) REVERT: j 52 ARG cc_start: 0.8680 (tpp80) cc_final: 0.7974 (tmt170) REVERT: j 73 PHE cc_start: 0.8445 (t80) cc_final: 0.8182 (t80) REVERT: j 88 ASP cc_start: 0.8842 (t0) cc_final: 0.8515 (t70) REVERT: j 90 SER cc_start: 0.9473 (t) cc_final: 0.8768 (p) REVERT: j 91 GLN cc_start: 0.8733 (mm-40) cc_final: 0.7632 (mm-40) REVERT: k 81 PHE cc_start: 0.8911 (t80) cc_final: 0.8685 (t80) REVERT: l 36 MET cc_start: 0.8718 (ttm) cc_final: 0.8284 (ttp) REVERT: l 81 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8151 (mtt90) REVERT: l 153 TYR cc_start: 0.9174 (p90) cc_final: 0.8966 (p90) REVERT: l 165 ASN cc_start: 0.9242 (t0) cc_final: 0.8976 (t0) REVERT: m 51 TYR cc_start: 0.9008 (t80) cc_final: 0.8772 (t80) REVERT: m 62 ASP cc_start: 0.8728 (t0) cc_final: 0.8435 (t0) REVERT: m 89 LEU cc_start: 0.9194 (tt) cc_final: 0.8993 (tt) REVERT: m 120 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8769 (mtpt) REVERT: n 58 MET cc_start: 0.8421 (mmm) cc_final: 0.8194 (mtp) REVERT: o 18 ASP cc_start: 0.8224 (t70) cc_final: 0.7868 (t0) REVERT: o 55 GLN cc_start: 0.9003 (mt0) cc_final: 0.8686 (mt0) REVERT: o 76 ASN cc_start: 0.8610 (t0) cc_final: 0.8085 (t0) REVERT: o 97 LYS cc_start: 0.8758 (mttm) cc_final: 0.8520 (mtpp) REVERT: p 39 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (mm) REVERT: p 103 MET cc_start: 0.9087 (tpp) cc_final: 0.8709 (mmm) REVERT: p 114 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8045 (tm-30) outliers start: 99 outliers final: 84 residues processed: 835 average time/residue: 0.1967 time to fit residues: 267.3349 Evaluate side-chains 852 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 759 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 513 MET Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 596 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 302 MET Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain U residue 133 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 117 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 20 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 173 THR Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 103 ASP Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 11 THR Chi-restraints excluded: chain n residue 78 GLN Chi-restraints excluded: chain n residue 137 VAL Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 42 THR Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 78 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 87 GLU Chi-restraints excluded: chain p residue 124 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 138 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 245 optimal weight: 0.0870 chunk 330 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 302 optimal weight: 0.0670 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN ** e 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 HIS p 172 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101790 restraints weight = 49714.364| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.12 r_work: 0.3118 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 32715 Z= 0.216 Angle : 0.854 59.139 44202 Z= 0.468 Chirality : 0.043 0.469 4796 Planarity : 0.005 0.146 5411 Dihedral : 11.836 149.586 5109 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 3.01 % Allowed : 20.21 % Favored : 76.78 % Cbeta Deviations : 0.08 % 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: 0.86 (0.14), residues: 3761 helix: 1.18 (0.11), residues: 2451 sheet: -0.75 (1.36), residues: 17 loop : -0.51 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 49 TYR 0.084 0.002 TYR J 145 PHE 0.021 0.001 PHE N 292 TRP 0.018 0.001 TRP X 170 HIS 0.012 0.001 HIS l 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (32706) covalent geometry : angle 0.85176 / 0.47 (44186) SS BOND : bond 0.00427 / 0.20 ( 8) SS BOND : angle 3.51617 / 2.66 ( 16) hydrogen bonds : bond 0.04161 / 2.65 ( 1691) hydrogen bonds : angle 4.27158 / 3.04 ( 4905) Misc. bond : bond 0.00039 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10181.15 seconds wall clock time: 175 minutes 9.90 seconds (10509.90 seconds total)