Starting phenix.real_space_refine on Tue May 5 16:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic4_35354/05_2026/8ic4_35354_neut.cif" } resolution = 3.2 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= 0.005 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 22 5.49 5 S 242 5.16 5 C 20701 2.51 5 N 5080 2.21 5 O 5592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31638 Number of models: 1 Model: "" Number of chains: 35 Chain: "D" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain: "J" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1178 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain breaks: 2 Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 721 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, '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: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2588 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 16, 'TRANS': 301} 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: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 439 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 835 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} 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: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 765 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 11, 'TRANS': 79} Chain breaks: 1 Chain: "j" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 574 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "k" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 18, 'TRANS': 136} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} 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: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1038 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "p" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1415 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 10, 'TRANS': 156} 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: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 207 Unusual residues: {' ZN': 1, '3PE': 3, 'CDL': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "M" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 168 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "d" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "h" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 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: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 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: 7.04, per 1000 atoms: 0.22 Number of scatterers: 31638 At special positions: 0 Unit cell: (187.58, 139.44, 148.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 242 16.00 P 22 15.00 O 5592 8.00 N 5080 7.00 C 20701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS Y 20 " - pdb=" SG CYS Y 77 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 97 " - pdb=" SG CYS Y 117 " distance=2.36 Simple disulfide: pdb=" SG CYS e 33 " - pdb=" SG CYS e 66 " distance=2.02 Simple disulfide: pdb=" SG CYS e 43 " - pdb=" SG CYS e 56 " distance=2.05 Simple disulfide: pdb=" SG CYS o 59 " - pdb=" SG CYS o 90 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 704 " pdb="ZN ZN L 704 " - pdb=" NE2 HIS L 348 " 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7222 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 5 sheets defined 68.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.747A pdb=" N GLN D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.550A 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 22 Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.747A pdb=" N GLY J 52 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 removed outlier: 3.747A pdb=" N PHE J 67 " --> pdb=" O MET J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 109 removed outlier: 3.951A pdb=" N TYR J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 144 through 146 No H-bonds generated for 'chain 'J' and resid 144 through 146' Processing helix chain 'J' and resid 150 through 171 removed outlier: 4.041A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 25 through 51 removed outlier: 3.632A pdb=" N GLU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) 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: 3.584A pdb=" N LEU K 64 " --> pdb=" O PRO K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'L' and resid 2 through 24 removed outlier: 4.114A 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: 4.418A 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: 3.540A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 191 removed outlier: 3.607A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 202 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 237 removed outlier: 3.677A 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: 3.535A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 270 removed outlier: 4.062A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.529A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.683A 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: 5.302A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 488 Processing helix chain 'L' and resid 488 through 509 removed outlier: 4.122A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 525 removed outlier: 4.012A pdb=" N SER L 521 " --> pdb=" O ASN L 517 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE L 522 " --> pdb=" O PRO L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 534 removed outlier: 3.563A 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: 3.838A pdb=" N SER L 545 " --> pdb=" O SER L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 561 Processing helix chain 'L' and resid 562 through 579 removed outlier: 3.683A pdb=" N THR L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER L 567 " --> pdb=" O PRO L 563 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR L 571 " --> pdb=" O SER L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 605 removed outlier: 3.501A pdb=" N TYR L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 Processing helix chain 'M' and resid 10 through 18 Processing helix chain 'M' and resid 22 through 39 Processing helix chain 'M' and resid 40 through 43 Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.506A 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: 3.685A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 91 through 111 removed outlier: 3.575A 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: 3.919A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.742A pdb=" N GLU M 222 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 234 Processing helix chain 'M' and resid 234 through 247 removed outlier: 4.145A 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: 3.509A pdb=" N ALA M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.504A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 Processing helix chain 'M' and resid 305 through 338 Processing helix chain 'M' and resid 347 through 351 Processing helix chain 'M' and resid 352 through 367 removed outlier: 3.518A pdb=" N ALA M 356 " --> pdb=" O PHE M 352 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 389 Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.145A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.553A pdb=" N THR N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 removed outlier: 3.530A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.577A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.532A 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: 3.800A 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: 3.834A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.753A 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: 4.196A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 273 removed outlier: 4.131A 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: 3.518A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 317 removed outlier: 4.072A pdb=" N LYS N 312 " --> pdb=" O ASN N 308 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET N 313 " --> pdb=" O ASN N 309 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET N 314 " --> pdb=" O ASN N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 335 removed outlier: 4.322A 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: 3.717A 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: 3.963A 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: 3.793A 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 244 Processing helix chain 'O' and resid 244 through 253 removed outlier: 3.509A pdb=" N GLU O 251 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.560A pdb=" N LEU O 294 " --> pdb=" O THR O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 300 through 305 Processing helix chain 'O' and resid 306 through 310 removed outlier: 3.651A pdb=" N ILE O 310 " --> pdb=" O TYR O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 332 Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.660A 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: 3.633A 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: 3.610A 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: 3.675A pdb=" N ARG d 78 " --> pdb=" O PHE d 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 11 Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 36 through 42 Processing helix chain 'e' and resid 48 through 52 Processing helix chain 'e' and resid 54 through 56 No H-bonds generated for 'chain 'e' and resid 54 through 56' Processing helix chain 'e' and resid 57 through 67 removed outlier: 3.672A pdb=" N GLU e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 89 removed outlier: 3.521A pdb=" N MET e 73 " --> pdb=" O ARG e 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 34 removed outlier: 3.768A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'f' and resid 41 through 45 Processing helix chain 'g' and resid 77 through 84 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: 3.823A 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: 3.582A 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: 3.950A 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 116 through 126 removed outlier: 3.670A pdb=" N ILE h 121 " --> pdb=" O ILE h 117 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 164 removed outlier: 4.071A pdb=" N ASN h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG h 161 " --> pdb=" O ARG h 157 " (cutoff:3.500A) Processing helix chain '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 74 Processing helix chain 'i' and resid 75 through 89 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: 3.604A 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: 3.520A pdb=" N LEU j 97 " --> pdb=" O THR j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 33 through 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: 4.337A pdb=" N TYR k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY k 61 " --> pdb=" O TRP k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 3.514A pdb=" N VAL k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 88 Processing helix chain 'l' and resid 33 through 37 Processing helix chain 'l' and resid 44 through 55 removed outlier: 3.838A 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 48 removed outlier: 3.881A pdb=" N VAL m 34 " --> pdb=" O ARG m 30 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU m 37 " --> pdb=" O GLN m 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER m 38 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE m 39 " --> pdb=" O GLU m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 74 removed outlier: 3.597A pdb=" N ILE m 66 " --> pdb=" O ASP m 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP m 68 " --> pdb=" O ALA m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 Processing helix chain 'm' and resid 95 through 101 Processing helix chain 'm' and resid 101 through 119 removed outlier: 3.808A 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: 3.605A pdb=" N ARG n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.862A pdb=" N CYS n 42 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET n 44 " --> pdb=" O PHE n 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA n 46 " --> pdb=" O CYS n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 74 removed outlier: 3.515A pdb=" N ARG n 65 " --> pdb=" O THR n 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.836A 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 4 through 11 Processing helix chain 'o' and resid 18 through 22 removed outlier: 3.908A 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: 4.034A pdb=" N LYS o 97 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 41 removed outlier: 3.741A pdb=" N TYR p 32 " --> pdb=" O ASN p 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU p 33 " --> pdb=" O PRO p 29 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU p 39 " --> pdb=" O LYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 59 removed outlier: 4.254A pdb=" N ASN p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 113 removed outlier: 3.524A 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: 3.882A 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: 3.734A pdb=" N GLU p 130 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 3.665A 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 169 removed outlier: 3.756A 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: 3.959A pdb=" N GLU p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 81 removed outlier: 6.267A pdb=" N MET L 78 " --> pdb=" O HIS L 67 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS L 67 " --> pdb=" O MET L 78 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N PHE L 80 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 7.359A 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: 6.344A 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: 5.842A pdb=" N GLU h 97 " --> pdb=" O TYR p 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 1690 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: 5.84 Time building geometry restraints manager: 4.24 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: 4823 1.29 - 1.42: 8482 1.42 - 1.56: 18633 1.56 - 1.69: 91 1.69 - 1.82: 437 Bond restraints: 32466 Sorted by residual: bond pdb=" O6 EHZ n 201 " pdb=" P1 EHZ n 201 " ideal model delta sigma weight residual 2.378 1.646 0.732 2.00e-02 2.50e+03 1.34e+03 bond pdb=" N PRO L 265 " pdb=" CD PRO L 265 " ideal model delta sigma weight residual 1.473 1.666 -0.193 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 1.285 0.188 1.40e-02 5.10e+03 1.81e+02 bond pdb=" C LYS e 91 " pdb=" N TYR e 92 " ideal model delta sigma weight residual 1.331 1.508 -0.177 1.37e-02 5.33e+03 1.67e+02 ... (remaining 32461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.54: 43351 6.54 - 13.08: 529 13.08 - 19.62: 22 19.62 - 26.16: 0 26.16 - 32.71: 2 Bond angle restraints: 43904 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 110.70 128.46 -17.76 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 110.70 128.28 -17.58 1.22e+00 6.72e-01 2.08e+02 angle pdb=" N TYR O 118 " pdb=" CA TYR O 118 " pdb=" C TYR O 118 " ideal model delta sigma weight residual 111.07 125.94 -14.87 1.07e+00 8.73e-01 1.93e+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 ILE M 104 " pdb=" CA ILE M 104 " pdb=" C ILE M 104 " ideal model delta sigma weight residual 110.30 99.08 11.22 9.70e-01 1.06e+00 1.34e+02 ... (remaining 43899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.72: 18794 26.72 - 53.45: 760 53.45 - 80.17: 129 80.17 - 106.89: 3 106.89 - 133.61: 3 Dihedral angle restraints: 19689 sinusoidal: 8517 harmonic: 11172 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 93.00 160.87 -67.87 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" O1B ADP O 401 " pdb=" O3A ADP O 401 " pdb=" PB ADP O 401 " pdb=" PA ADP O 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.38 133.61 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 19686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3732 0.106 - 0.211: 825 0.211 - 0.317: 182 0.317 - 0.423: 34 0.423 - 0.528: 10 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CA ASP L 554 " pdb=" N ASP L 554 " pdb=" C ASP L 554 " pdb=" CB ASP L 554 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" CA 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 6.16e+00 chirality pdb=" CA PHE M 151 " pdb=" N PHE M 151 " pdb=" C PHE M 151 " pdb=" CB PHE M 151 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.12e+00 ... (remaining 4780 not shown) Planarity restraints: 5390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER l 125 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER l 125 " -0.071 2.00e-02 2.50e+03 pdb=" O SER l 125 " 0.027 2.00e-02 2.50e+03 pdb=" N TRP l 126 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE i 105 " -0.067 5.00e-02 4.00e+02 9.83e-02 1.55e+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 3.73e-02 1.39e+01 pdb=" C LEU L 546 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU L 546 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS L 547 " -0.021 2.00e-02 2.50e+03 ... (remaining 5387 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 772 2.61 - 3.18: 32430 3.18 - 3.75: 50880 3.75 - 4.33: 74198 4.33 - 4.90: 115536 Nonbonded interactions: 273816 Sorted by model distance: 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 2.059 3.120 nonbonded pdb=" O ASN L 579 " pdb=" OD1 ASN L 579 " model vdw 2.062 3.040 nonbonded pdb=" OG SER J 9 " pdb=" ND2 ASN K 7 " model vdw 2.080 3.120 nonbonded pdb=" NZ LYS L 455 " pdb=" OE1 GLN j 57 " model vdw 2.098 3.120 ... (remaining 273811 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: 9.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.732 32475 Z= 0.968 Angle : 1.863 42.481 43920 Z= 1.327 Chirality : 0.098 0.528 4783 Planarity : 0.007 0.098 5390 Dihedral : 14.143 133.615 12443 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 42.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 0.21 % Allowed : 5.47 % Favored : 94.33 % Cbeta Deviations : 1.05 % 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: -2.53 (0.12), residues: 3750 helix: -1.24 (0.10), residues: 2383 sheet: -1.75 (1.06), residues: 18 loop : -2.30 (0.15), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG p 162 TYR 0.036 0.002 TYR l 153 PHE 0.029 0.002 PHE h 171 TRP 0.030 0.002 TRP L 407 HIS 0.008 0.001 HIS l 106 Details of bonding type rmsd covalent geometry : bond 0.01355 (32466) covalent geometry : angle 1.85122 (43904) SS BOND : bond 0.16506 ( 8) SS BOND : angle 11.03471 ( 16) hydrogen bonds : bond 0.22813 ( 1690) hydrogen bonds : angle 8.68913 ( 4905) metal coordination : bond 0.29782 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1533 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1526 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 56 PHE cc_start: 0.8672 (t80) cc_final: 0.8240 (t80) REVERT: J 64 LEU cc_start: 0.8515 (mm) cc_final: 0.8272 (mm) REVERT: J 98 MET cc_start: 0.7586 (tpt) cc_final: 0.7284 (mmt) REVERT: J 125 MET cc_start: 0.7803 (mmm) cc_final: 0.7453 (mtm) REVERT: J 134 MET cc_start: 0.7636 (tpp) cc_final: 0.6968 (mtt) REVERT: J 158 SER cc_start: 0.8937 (t) cc_final: 0.8680 (p) REVERT: L 74 MET cc_start: 0.7979 (ttm) cc_final: 0.7710 (ttm) REVERT: L 480 LEU cc_start: 0.7298 (tt) cc_final: 0.7025 (tt) REVERT: M 126 LEU cc_start: 0.7517 (mp) cc_final: 0.7314 (mp) REVERT: M 272 THR cc_start: 0.8274 (p) cc_final: 0.7954 (p) REVERT: M 279 GLN cc_start: 0.7200 (tp-100) cc_final: 0.6973 (tp-100) REVERT: M 344 MET cc_start: 0.6864 (mtp) cc_final: 0.6625 (mtm) REVERT: M 399 ASN cc_start: 0.8325 (t0) cc_final: 0.7970 (t0) REVERT: M 403 THR cc_start: 0.9036 (m) cc_final: 0.8607 (m) REVERT: M 420 THR cc_start: 0.8349 (m) cc_final: 0.7895 (p) REVERT: N 117 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7160 (mm-30) REVERT: N 243 MET cc_start: 0.6439 (mmm) cc_final: 0.6146 (mmp) REVERT: O 63 ASP cc_start: 0.4569 (m-30) cc_final: 0.4268 (m-30) REVERT: O 68 SER cc_start: 0.7281 (p) cc_final: 0.7029 (m) REVERT: U 120 MET cc_start: 0.7455 (mtm) cc_final: 0.7158 (mtp) REVERT: Y 127 PHE cc_start: 0.8443 (t80) cc_final: 0.8217 (t80) REVERT: f 39 ASN cc_start: 0.7878 (t0) cc_final: 0.6790 (t0) REVERT: l 47 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6997 (mt-10) REVERT: l 82 SER cc_start: 0.8124 (p) cc_final: 0.7746 (p) REVERT: l 153 TYR cc_start: 0.7290 (p90) cc_final: 0.6946 (p90) REVERT: n 138 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7550 (ttmt) REVERT: o 57 ASP cc_start: 0.6191 (p0) cc_final: 0.5514 (p0) REVERT: p 73 ASP cc_start: 0.7163 (p0) cc_final: 0.6771 (p0) outliers start: 7 outliers final: 1 residues processed: 1528 average time/residue: 0.2152 time to fit residues: 519.2526 Evaluate side-chains 908 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 907 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 60 HIS L 2 ASN L 58 ASN L 165 ASN L 207 ASN L 209 ASN L 264 HIS L 269 ASN L 309 GLN L 321 GLN ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN L 452 ASN L 572 ASN L 579 ASN M 51 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 169 ASN M 175 ASN M 193 ASN M 213 HIS ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS M 304 GLN M 331 ASN M 338 HIS M 390 ASN N 63 GLN N 87 GLN N 120 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN N 235 ASN N 274 ASN N 310 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 132 GLN O 142 GLN O 175 ASN ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 306 ASN U 115 GLN d 8 HIS d 61 GLN d 88 HIS e 29 ASN e 45 HIS g 130 ASN ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 HIS i 83 HIS i 89 HIS j 54 GLN l 106 HIS n 12 HIS n 14 GLN n 74 ASN ** o 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN o 55 GLN o 110 GLN p 23 GLN p 124 ASN p 131 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103875 restraints weight = 64293.593| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.39 r_work: 0.3395 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32475 Z= 0.199 Angle : 0.785 12.768 43920 Z= 0.407 Chirality : 0.047 0.399 4783 Planarity : 0.006 0.064 5390 Dihedral : 13.294 162.813 4868 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 3.28 % Allowed : 14.74 % Favored : 81.98 % 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: -0.45 (0.13), residues: 3750 helix: 0.18 (0.10), residues: 2437 sheet: -0.69 (1.23), residues: 18 loop : -1.06 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 60 TYR 0.038 0.002 TYR L 422 PHE 0.042 0.003 PHE c 29 TRP 0.022 0.002 TRP L 484 HIS 0.015 0.002 HIS L 332 Details of bonding type rmsd covalent geometry : bond 0.00439 (32466) covalent geometry : angle 0.78464 (43904) SS BOND : bond 0.03118 ( 8) SS BOND : angle 1.97598 ( 16) hydrogen bonds : bond 0.06202 ( 1690) hydrogen bonds : angle 5.30070 ( 4905) metal coordination : bond 0.01183 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1009 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 PHE cc_start: 0.8687 (m-10) cc_final: 0.8426 (m-80) REVERT: J 125 MET cc_start: 0.7727 (mmm) cc_final: 0.7038 (mtm) REVERT: J 134 MET cc_start: 0.7537 (tpp) cc_final: 0.6772 (mtt) REVERT: K 34 GLU cc_start: 0.8567 (tp30) cc_final: 0.8241 (tp30) REVERT: L 74 MET cc_start: 0.8806 (ttm) cc_final: 0.8326 (ttm) REVERT: L 116 ARG cc_start: 0.9158 (ttm110) cc_final: 0.8940 (ttp80) REVERT: L 202 MET cc_start: 0.7946 (mtt) cc_final: 0.7603 (mmp) REVERT: L 258 PHE cc_start: 0.8381 (t80) cc_final: 0.7863 (t80) REVERT: L 480 LEU cc_start: 0.7646 (tt) cc_final: 0.7437 (tt) REVERT: L 504 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8638 (mp) REVERT: L 596 ILE cc_start: 0.8949 (mm) cc_final: 0.8603 (mt) REVERT: M 399 ASN cc_start: 0.8337 (t0) cc_final: 0.7941 (t160) REVERT: M 403 THR cc_start: 0.9213 (m) cc_final: 0.8857 (m) REVERT: M 420 THR cc_start: 0.8625 (m) cc_final: 0.8019 (p) REVERT: N 83 THR cc_start: 0.8979 (t) cc_final: 0.8775 (p) REVERT: N 293 TYR cc_start: 0.8671 (m-80) cc_final: 0.8389 (m-80) REVERT: O 80 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8165 (mt0) REVERT: O 316 GLU cc_start: 0.8261 (mp0) cc_final: 0.8015 (mm-30) REVERT: Y 83 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7655 (mtp-110) REVERT: Y 85 LYS cc_start: 0.7489 (mttp) cc_final: 0.7223 (mttp) REVERT: Y 91 ASN cc_start: 0.7330 (m110) cc_final: 0.6748 (m-40) REVERT: Y 120 MET cc_start: 0.8756 (tpp) cc_final: 0.8377 (tpp) REVERT: Y 127 PHE cc_start: 0.8787 (t80) cc_final: 0.8445 (t80) REVERT: c 67 LEU cc_start: 0.8914 (mt) cc_final: 0.8619 (tp) REVERT: d 27 ASN cc_start: 0.8320 (p0) cc_final: 0.8070 (p0) REVERT: d 37 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8653 (mp) REVERT: d 50 MET cc_start: 0.8232 (ttt) cc_final: 0.7312 (ttp) REVERT: e 14 LEU cc_start: 0.8580 (pp) cc_final: 0.8340 (pp) REVERT: e 18 PHE cc_start: 0.7283 (p90) cc_final: 0.6649 (p90) REVERT: g 74 TYR cc_start: 0.8855 (m-80) cc_final: 0.8568 (m-80) REVERT: g 84 ASN cc_start: 0.8804 (t0) cc_final: 0.8498 (t0) REVERT: g 125 LYS cc_start: 0.8425 (tptm) cc_final: 0.8058 (tptm) REVERT: h 105 TYR cc_start: 0.7249 (t80) cc_final: 0.6754 (t80) REVERT: j 68 TRP cc_start: 0.7677 (t60) cc_final: 0.6352 (t60) REVERT: j 97 LEU cc_start: 0.8880 (mt) cc_final: 0.8624 (mp) REVERT: k 39 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8203 (tt0) REVERT: k 75 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8093 (tttp) REVERT: l 77 MET cc_start: 0.8735 (ttm) cc_final: 0.8449 (mtp) REVERT: l 82 SER cc_start: 0.7863 (p) cc_final: 0.7629 (p) REVERT: l 153 TYR cc_start: 0.7625 (p90) cc_final: 0.7029 (p90) REVERT: l 177 GLU cc_start: 0.8069 (mp0) cc_final: 0.7812 (mp0) REVERT: m 31 ARG cc_start: 0.8477 (ttm110) cc_final: 0.7916 (ptp90) REVERT: m 62 ASP cc_start: 0.8354 (t0) cc_final: 0.8109 (t0) REVERT: n 44 MET cc_start: 0.7782 (tpp) cc_final: 0.7301 (tpp) REVERT: o 25 PHE cc_start: 0.7063 (m-10) cc_final: 0.6789 (m-10) REVERT: o 31 PHE cc_start: 0.7525 (m-80) cc_final: 0.7259 (m-80) REVERT: o 35 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8491 (mmtp) REVERT: o 76 ASN cc_start: 0.8743 (t0) cc_final: 0.8403 (t0) REVERT: o 121 ARG cc_start: 0.7963 (ttt180) cc_final: 0.7659 (tpp-160) REVERT: p 103 MET cc_start: 0.8322 (tpp) cc_final: 0.8073 (tpp) REVERT: p 165 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7678 (mp0) outliers start: 111 outliers final: 49 residues processed: 1076 average time/residue: 0.2031 time to fit residues: 352.0685 Evaluate side-chains 892 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 840 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 494 SER Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 279 ASN Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 8 HIS Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 55 THR Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 182 SER Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 LYS Chi-restraints excluded: chain l residue 74 ASP Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain o residue 12 ASP Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 85 ILE Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 330 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 chunk 295 optimal weight: 7.9990 chunk 360 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 333 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 200 GLN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 ASN M 193 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN N 316 HIS N 317 GLN N 342 GLN ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 279 ASN O 292 HIS d 8 HIS e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 54 GLN l 80 ASN n 12 HIS o 61 HIS p 91 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101659 restraints weight = 64279.035| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.40 r_work: 0.3368 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32475 Z= 0.158 Angle : 0.694 14.347 43920 Z= 0.352 Chirality : 0.045 0.387 4783 Planarity : 0.006 0.075 5390 Dihedral : 12.650 179.113 4866 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 3.13 % Allowed : 17.25 % Favored : 79.62 % 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: 0.20 (0.14), residues: 3750 helix: 0.61 (0.10), residues: 2443 sheet: 0.20 (1.28), residues: 23 loop : -0.64 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG l 116 TYR 0.032 0.002 TYR L 422 PHE 0.022 0.002 PHE K 41 TRP 0.022 0.001 TRP L 484 HIS 0.009 0.001 HIS c 62 Details of bonding type rmsd covalent geometry : bond 0.00360 (32466) covalent geometry : angle 0.69301 (43904) SS BOND : bond 0.00473 ( 8) SS BOND : angle 2.02691 ( 16) hydrogen bonds : bond 0.04972 ( 1690) hydrogen bonds : angle 4.82591 ( 4905) metal coordination : bond 0.00220 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 932 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 98 MET cc_start: 0.6905 (ptt) cc_final: 0.6329 (mmt) REVERT: J 125 MET cc_start: 0.7634 (mmm) cc_final: 0.6992 (mtm) REVERT: L 116 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8963 (ttp80) REVERT: L 202 MET cc_start: 0.7944 (mtt) cc_final: 0.7680 (mmp) REVERT: L 389 PHE cc_start: 0.8523 (t80) cc_final: 0.8090 (t80) REVERT: L 596 ILE cc_start: 0.8901 (mm) cc_final: 0.8664 (mt) REVERT: M 139 GLN cc_start: 0.8399 (mp10) cc_final: 0.8192 (mp10) REVERT: M 301 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8822 (mm) REVERT: M 403 THR cc_start: 0.9143 (m) cc_final: 0.8809 (t) REVERT: M 420 THR cc_start: 0.8613 (m) cc_final: 0.8092 (p) REVERT: N 78 TYR cc_start: 0.8643 (t80) cc_final: 0.8292 (t80) REVERT: N 271 MET cc_start: 0.8931 (mmm) cc_final: 0.8715 (mmm) REVERT: O 143 TYR cc_start: 0.8062 (t80) cc_final: 0.7348 (t80) REVERT: O 226 GLU cc_start: 0.5561 (tt0) cc_final: 0.5192 (tp30) REVERT: O 275 TYR cc_start: 0.7434 (m-80) cc_final: 0.7232 (m-80) REVERT: O 278 TYR cc_start: 0.7668 (m-80) cc_final: 0.7405 (m-80) REVERT: O 316 GLU cc_start: 0.8217 (mp0) cc_final: 0.7965 (mm-30) REVERT: U 124 ASP cc_start: 0.8348 (m-30) cc_final: 0.8144 (m-30) REVERT: Y 46 ASN cc_start: 0.8323 (t0) cc_final: 0.8018 (t0) REVERT: Y 83 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7737 (mtp-110) REVERT: Y 85 LYS cc_start: 0.7598 (mttp) cc_final: 0.7176 (mtmt) REVERT: Y 127 PHE cc_start: 0.8894 (t80) cc_final: 0.8686 (t80) REVERT: c 67 LEU cc_start: 0.8998 (mt) cc_final: 0.8749 (tp) REVERT: d 27 ASN cc_start: 0.8285 (p0) cc_final: 0.7951 (p0) REVERT: d 37 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8775 (mp) REVERT: d 49 ARG cc_start: 0.8372 (mmt90) cc_final: 0.7888 (mmt90) REVERT: d 50 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7647 (ttt) REVERT: d 81 TYR cc_start: 0.9039 (t80) cc_final: 0.8827 (t80) REVERT: e 18 PHE cc_start: 0.7406 (p90) cc_final: 0.6824 (p90) REVERT: e 37 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7417 (tm-30) REVERT: e 73 MET cc_start: 0.9225 (ttm) cc_final: 0.8926 (ttp) REVERT: g 84 ASN cc_start: 0.8851 (t0) cc_final: 0.8490 (t0) REVERT: g 125 LYS cc_start: 0.8467 (tptm) cc_final: 0.8224 (tppp) REVERT: g 135 MET cc_start: 0.8875 (ttm) cc_final: 0.8603 (tpp) REVERT: g 139 TYR cc_start: 0.4783 (t80) cc_final: 0.4461 (t80) REVERT: h 69 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7810 (ttp-170) REVERT: h 105 TYR cc_start: 0.7353 (t80) cc_final: 0.7134 (t80) REVERT: j 97 LEU cc_start: 0.9029 (mt) cc_final: 0.8704 (mt) REVERT: k 31 GLU cc_start: 0.8706 (pm20) cc_final: 0.8419 (pm20) REVERT: k 39 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8305 (tt0) REVERT: l 77 MET cc_start: 0.8747 (ttm) cc_final: 0.8382 (mtp) REVERT: l 177 GLU cc_start: 0.8159 (mp0) cc_final: 0.7882 (mp0) REVERT: m 31 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8275 (ttm110) REVERT: m 51 TYR cc_start: 0.9177 (t80) cc_final: 0.8894 (t80) REVERT: m 62 ASP cc_start: 0.8475 (t0) cc_final: 0.8229 (t0) REVERT: m 125 PHE cc_start: 0.9094 (m-10) cc_final: 0.8770 (m-80) REVERT: m 129 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6965 (p90) REVERT: n 44 MET cc_start: 0.7836 (tpp) cc_final: 0.7357 (tpp) REVERT: o 16 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6441 (mm-30) REVERT: o 31 PHE cc_start: 0.7697 (m-80) cc_final: 0.7428 (m-80) REVERT: o 44 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7076 (tm-30) REVERT: o 48 ASP cc_start: 0.8130 (m-30) cc_final: 0.7918 (m-30) REVERT: o 76 ASN cc_start: 0.8825 (t0) cc_final: 0.8468 (t0) outliers start: 106 outliers final: 53 residues processed: 991 average time/residue: 0.1876 time to fit residues: 304.6650 Evaluate side-chains 879 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 821 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 279 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain d residue 8 HIS Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 55 THR Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 129 TYR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 12 ASP Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 28 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 364 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 chunk 353 optimal weight: 0.3980 chunk 332 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 192 ASN L 194 ASN L 200 GLN L 230 HIS ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 ASN M 48 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 HIS U 115 GLN d 8 HIS d 79 GLN e 45 HIS h 170 GLN l 80 ASN l 84 HIS l 165 ASN ** m 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 51 HIS n 73 GLN ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095276 restraints weight = 63978.338| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.35 r_work: 0.3257 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 32475 Z= 0.239 Angle : 0.721 12.566 43920 Z= 0.366 Chirality : 0.047 0.394 4783 Planarity : 0.005 0.067 5390 Dihedral : 12.323 170.305 4866 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 4.14 % Allowed : 18.02 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3750 helix: 0.66 (0.10), residues: 2442 sheet: 0.12 (1.34), residues: 23 loop : -0.52 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 71 TYR 0.026 0.002 TYR L 422 PHE 0.027 0.002 PHE e 63 TRP 0.023 0.002 TRP L 484 HIS 0.017 0.002 HIS d 8 Details of bonding type rmsd covalent geometry : bond 0.00560 (32466) covalent geometry : angle 0.72095 (43904) SS BOND : bond 0.00361 ( 8) SS BOND : angle 1.00034 ( 16) hydrogen bonds : bond 0.04944 ( 1690) hydrogen bonds : angle 4.77137 ( 4905) metal coordination : bond 0.00184 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 868 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8058 (mm-30) REVERT: J 44 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8910 (mm) REVERT: J 98 MET cc_start: 0.6884 (ptt) cc_final: 0.6259 (mmt) REVERT: J 125 MET cc_start: 0.7741 (mmm) cc_final: 0.7075 (mtm) REVERT: L 74 MET cc_start: 0.8832 (ttp) cc_final: 0.8617 (ttm) REVERT: L 116 ARG cc_start: 0.9292 (ttm110) cc_final: 0.8990 (ttp80) REVERT: L 202 MET cc_start: 0.8129 (mtt) cc_final: 0.7817 (mmp) REVERT: L 366 MET cc_start: 0.8846 (mtp) cc_final: 0.8599 (mtt) REVERT: L 389 PHE cc_start: 0.8620 (t80) cc_final: 0.8096 (t80) REVERT: M 98 MET cc_start: 0.8540 (mmm) cc_final: 0.8180 (mmm) REVERT: M 123 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: M 179 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8824 (mp) REVERT: M 257 MET cc_start: 0.9242 (ttm) cc_final: 0.8917 (ttm) REVERT: M 298 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9257 (mt) REVERT: M 301 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8882 (mm) REVERT: M 403 THR cc_start: 0.9340 (m) cc_final: 0.9006 (p) REVERT: N 215 MET cc_start: 0.7876 (tpp) cc_final: 0.7555 (tpp) REVERT: N 271 MET cc_start: 0.9002 (mmm) cc_final: 0.8785 (mmm) REVERT: O 56 TYR cc_start: 0.6809 (p90) cc_final: 0.5996 (p90) REVERT: O 76 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7561 (tp30) REVERT: O 79 GLN cc_start: 0.8566 (tp40) cc_final: 0.8251 (mt0) REVERT: O 106 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7357 (mp) REVERT: O 143 TYR cc_start: 0.8134 (t80) cc_final: 0.7400 (t80) REVERT: O 226 GLU cc_start: 0.5799 (tt0) cc_final: 0.5272 (tp30) REVERT: O 275 TYR cc_start: 0.7467 (m-80) cc_final: 0.7254 (m-80) REVERT: O 316 GLU cc_start: 0.8259 (mp0) cc_final: 0.8049 (mm-30) REVERT: Y 46 ASN cc_start: 0.8559 (t0) cc_final: 0.8258 (t0) REVERT: Y 83 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7720 (mtp-110) REVERT: Y 127 PHE cc_start: 0.8903 (t80) cc_final: 0.8691 (t80) REVERT: d 27 ASN cc_start: 0.8289 (p0) cc_final: 0.8001 (p0) REVERT: d 37 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8826 (mp) REVERT: d 49 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7997 (mmt90) REVERT: d 50 MET cc_start: 0.7895 (ttt) cc_final: 0.7692 (ttt) REVERT: e 5 ASP cc_start: 0.7443 (t0) cc_final: 0.7197 (t0) REVERT: e 37 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7578 (tm-30) REVERT: g 139 TYR cc_start: 0.5705 (t80) cc_final: 0.5283 (t80) REVERT: h 69 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7809 (ttp-110) REVERT: h 105 TYR cc_start: 0.7696 (t80) cc_final: 0.7110 (t80) REVERT: h 182 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7689 (p) REVERT: j 95 GLU cc_start: 0.8659 (mp0) cc_final: 0.7947 (tm-30) REVERT: k 31 GLU cc_start: 0.8759 (pm20) cc_final: 0.8408 (pm20) REVERT: k 78 LYS cc_start: 0.8393 (mmtm) cc_final: 0.8120 (ttmm) REVERT: l 177 GLU cc_start: 0.8232 (mp0) cc_final: 0.7932 (mp0) REVERT: m 61 GLU cc_start: 0.7984 (pm20) cc_final: 0.7664 (mp0) REVERT: m 113 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8103 (tm-30) REVERT: m 125 PHE cc_start: 0.9152 (m-10) cc_final: 0.8938 (m-80) REVERT: n 44 MET cc_start: 0.7955 (tpp) cc_final: 0.7471 (tpp) REVERT: n 143 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7497 (mt-10) REVERT: o 31 PHE cc_start: 0.7802 (m-80) cc_final: 0.7539 (m-80) REVERT: o 44 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7001 (tm-30) REVERT: o 48 ASP cc_start: 0.8393 (m-30) cc_final: 0.7930 (m-30) REVERT: o 76 ASN cc_start: 0.9028 (t0) cc_final: 0.8638 (t0) REVERT: p 93 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8146 (mtp85) REVERT: p 104 ASN cc_start: 0.8525 (m-40) cc_final: 0.8150 (m-40) REVERT: p 165 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7885 (mp0) outliers start: 140 outliers final: 91 residues processed: 948 average time/residue: 0.1883 time to fit residues: 294.1357 Evaluate side-chains 909 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 809 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 319 ILE Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 8 HIS Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain f residue 55 THR Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 182 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 165 ASN Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 129 TYR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 12 ASP Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 32 optimal weight: 1.9990 chunk 306 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN K 25 HIS L 321 GLN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 279 ASN U 115 GLN d 8 HIS e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 80 ASN l 148 HIS ** m 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098083 restraints weight = 64052.065| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.40 r_work: 0.3292 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32475 Z= 0.141 Angle : 0.644 11.478 43920 Z= 0.324 Chirality : 0.043 0.401 4783 Planarity : 0.005 0.065 5390 Dihedral : 11.945 169.059 4866 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.49 % Allowed : 19.62 % Favored : 76.90 % 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: 3750 helix: 0.86 (0.11), residues: 2435 sheet: -0.16 (1.19), residues: 25 loop : -0.46 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 340 TYR 0.026 0.002 TYR L 422 PHE 0.022 0.002 PHE M 151 TRP 0.026 0.001 TRP L 484 HIS 0.009 0.001 HIS n 51 Details of bonding type rmsd covalent geometry : bond 0.00319 (32466) covalent geometry : angle 0.64347 (43904) SS BOND : bond 0.00672 ( 8) SS BOND : angle 1.71928 ( 16) hydrogen bonds : bond 0.04441 ( 1690) hydrogen bonds : angle 4.56006 ( 4905) metal coordination : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 860 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7868 (mm-30) REVERT: J 73 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.6051 (mtt) REVERT: J 98 MET cc_start: 0.6811 (ptt) cc_final: 0.6269 (mmt) REVERT: J 125 MET cc_start: 0.7719 (mmm) cc_final: 0.7061 (mtm) REVERT: J 171 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7594 (ptm-80) REVERT: K 34 GLU cc_start: 0.8541 (tp30) cc_final: 0.8331 (tp30) REVERT: L 74 MET cc_start: 0.8878 (ttp) cc_final: 0.8638 (ttm) REVERT: L 116 ARG cc_start: 0.9291 (ttm110) cc_final: 0.9010 (ttp80) REVERT: L 202 MET cc_start: 0.8074 (mtt) cc_final: 0.7738 (mmp) REVERT: L 389 PHE cc_start: 0.8541 (t80) cc_final: 0.8319 (t80) REVERT: L 509 MET cc_start: 0.6223 (ttm) cc_final: 0.5911 (ttt) REVERT: M 47 GLU cc_start: 0.7696 (tt0) cc_final: 0.7432 (tt0) REVERT: M 123 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: M 139 GLN cc_start: 0.8276 (mp10) cc_final: 0.8070 (mm-40) REVERT: M 179 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8792 (mp) REVERT: M 301 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8999 (mm) REVERT: M 378 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8135 (mt-10) REVERT: M 403 THR cc_start: 0.9257 (m) cc_final: 0.8968 (p) REVERT: N 34 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: N 271 MET cc_start: 0.8941 (mmm) cc_final: 0.8714 (mmm) REVERT: O 56 TYR cc_start: 0.6670 (p90) cc_final: 0.6081 (p90) REVERT: O 106 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7314 (mp) REVERT: O 143 TYR cc_start: 0.8073 (t80) cc_final: 0.7352 (t80) REVERT: O 226 GLU cc_start: 0.5916 (tt0) cc_final: 0.5216 (tp30) REVERT: O 283 TRP cc_start: 0.8123 (m100) cc_final: 0.7612 (m100) REVERT: O 316 GLU cc_start: 0.8218 (mp0) cc_final: 0.7988 (mm-30) REVERT: Y 41 TYR cc_start: 0.7495 (m-80) cc_final: 0.7069 (m-80) REVERT: Y 46 ASN cc_start: 0.8623 (t0) cc_final: 0.8284 (t0) REVERT: Y 127 PHE cc_start: 0.8893 (t80) cc_final: 0.8685 (t80) REVERT: d 27 ASN cc_start: 0.8218 (p0) cc_final: 0.7876 (p0) REVERT: d 37 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8838 (mp) REVERT: d 49 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7988 (mmm-85) REVERT: e 18 PHE cc_start: 0.7697 (p90) cc_final: 0.7235 (p90) REVERT: e 37 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7490 (tm-30) REVERT: g 135 MET cc_start: 0.9079 (ttm) cc_final: 0.8732 (ttt) REVERT: g 139 TYR cc_start: 0.5870 (t80) cc_final: 0.5365 (t80) REVERT: h 69 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7798 (ttp-110) REVERT: h 93 ILE cc_start: 0.9046 (mm) cc_final: 0.8810 (mm) REVERT: h 182 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7707 (p) REVERT: i 24 LYS cc_start: 0.8338 (tppt) cc_final: 0.7888 (tptp) REVERT: j 97 LEU cc_start: 0.8962 (mt) cc_final: 0.8655 (mt) REVERT: k 31 GLU cc_start: 0.8801 (pm20) cc_final: 0.8421 (pm20) REVERT: l 77 MET cc_start: 0.8693 (ttm) cc_final: 0.8432 (mtp) REVERT: l 177 GLU cc_start: 0.8306 (mp0) cc_final: 0.8005 (mp0) REVERT: m 31 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8061 (ptp90) REVERT: m 61 GLU cc_start: 0.8057 (pm20) cc_final: 0.7693 (mp0) REVERT: m 108 ASP cc_start: 0.8707 (t70) cc_final: 0.8460 (t0) REVERT: m 113 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8029 (tm-30) REVERT: n 44 MET cc_start: 0.7909 (tpp) cc_final: 0.7522 (tpp) REVERT: n 143 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7252 (mt-10) REVERT: o 31 PHE cc_start: 0.7877 (m-80) cc_final: 0.7654 (m-80) REVERT: o 44 GLN cc_start: 0.7720 (tm-30) cc_final: 0.6982 (tm-30) REVERT: o 48 ASP cc_start: 0.8299 (m-30) cc_final: 0.7850 (m-30) REVERT: o 76 ASN cc_start: 0.8979 (t0) cc_final: 0.8540 (t0) REVERT: p 93 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7724 (mtp85) REVERT: p 165 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7930 (mp0) outliers start: 118 outliers final: 77 residues processed: 929 average time/residue: 0.1902 time to fit residues: 290.3513 Evaluate side-chains 891 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 805 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 301 ILE Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 205 ILE Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain h residue 182 SER Chi-restraints excluded: chain i residue 7 ASP Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 12 ASP Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN K 7 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 594 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 HIS ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 GLN l 80 ASN p 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096080 restraints weight = 64135.863| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.36 r_work: 0.3261 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32475 Z= 0.176 Angle : 0.663 11.191 43920 Z= 0.334 Chirality : 0.044 0.399 4783 Planarity : 0.005 0.064 5390 Dihedral : 11.707 169.896 4866 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 4.37 % Allowed : 19.88 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3750 helix: 0.89 (0.11), residues: 2438 sheet: -0.30 (1.17), residues: 25 loop : -0.46 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 340 TYR 0.024 0.002 TYR n 80 PHE 0.020 0.002 PHE M 151 TRP 0.030 0.001 TRP L 484 HIS 0.009 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00413 (32466) covalent geometry : angle 0.66213 (43904) SS BOND : bond 0.00772 ( 8) SS BOND : angle 2.23152 ( 16) hydrogen bonds : bond 0.04496 ( 1690) hydrogen bonds : angle 4.57914 ( 4905) metal coordination : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 830 time to evaluate : 1.228 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: D 45 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7799 (mm-30) REVERT: D 53 TYR cc_start: 0.6430 (m-80) cc_final: 0.6192 (m-80) REVERT: J 46 PHE cc_start: 0.8871 (m-80) cc_final: 0.8407 (m-80) REVERT: J 73 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6044 (mtt) REVERT: J 98 MET cc_start: 0.6783 (ptt) cc_final: 0.6207 (mmt) REVERT: J 125 MET cc_start: 0.7850 (mmm) cc_final: 0.7210 (mtm) REVERT: K 53 SER cc_start: 0.9043 (t) cc_final: 0.8609 (t) REVERT: L 116 ARG cc_start: 0.9320 (ttm110) cc_final: 0.8995 (ttp80) REVERT: L 202 MET cc_start: 0.8129 (mtt) cc_final: 0.7766 (mmp) REVERT: L 509 MET cc_start: 0.6338 (ttm) cc_final: 0.6069 (ttt) REVERT: M 98 MET cc_start: 0.8537 (mmm) cc_final: 0.8223 (mmm) REVERT: M 123 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: M 139 GLN cc_start: 0.8339 (mp10) cc_final: 0.7775 (mm-40) REVERT: M 179 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8810 (mp) REVERT: M 340 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7667 (mtm180) REVERT: M 378 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8129 (mt-10) REVERT: N 20 THR cc_start: 0.9459 (m) cc_final: 0.9069 (p) REVERT: N 215 MET cc_start: 0.7825 (tpp) cc_final: 0.7478 (tpp) REVERT: N 271 MET cc_start: 0.8971 (mmm) cc_final: 0.8727 (mmm) REVERT: O 56 TYR cc_start: 0.6699 (p90) cc_final: 0.6216 (p90) REVERT: O 106 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7297 (mp) REVERT: O 143 TYR cc_start: 0.8085 (t80) cc_final: 0.7360 (t80) REVERT: O 226 GLU cc_start: 0.5920 (tt0) cc_final: 0.5295 (tp30) REVERT: O 249 MET cc_start: 0.7929 (mmt) cc_final: 0.7530 (mmm) REVERT: O 283 TRP cc_start: 0.8104 (m100) cc_final: 0.7551 (m100) REVERT: Y 46 ASN cc_start: 0.8586 (t0) cc_final: 0.8292 (t0) REVERT: Y 127 PHE cc_start: 0.8911 (t80) cc_final: 0.8696 (t80) REVERT: c 29 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.5607 (p90) REVERT: d 9 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8030 (mt-10) REVERT: d 37 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8823 (mp) REVERT: d 49 ARG cc_start: 0.8338 (mmt90) cc_final: 0.8072 (mmm-85) REVERT: e 37 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7602 (tm-30) REVERT: f 52 GLU cc_start: 0.7490 (tt0) cc_final: 0.7277 (tt0) REVERT: h 69 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7796 (ttp-110) REVERT: h 93 ILE cc_start: 0.9063 (mm) cc_final: 0.8830 (mm) REVERT: h 182 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7814 (p) REVERT: i 26 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8599 (tp40) REVERT: j 95 GLU cc_start: 0.8533 (mp0) cc_final: 0.7910 (tm-30) REVERT: k 31 GLU cc_start: 0.8839 (pm20) cc_final: 0.8441 (pm20) REVERT: k 78 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8172 (ttmm) REVERT: l 77 MET cc_start: 0.8734 (ttm) cc_final: 0.8462 (mtp) REVERT: l 177 GLU cc_start: 0.8332 (mp0) cc_final: 0.8018 (mp0) REVERT: m 24 ASP cc_start: 0.7126 (t0) cc_final: 0.6793 (t0) REVERT: m 31 ARG cc_start: 0.8617 (ttm110) cc_final: 0.7908 (ptp90) REVERT: m 61 GLU cc_start: 0.8096 (pm20) cc_final: 0.7753 (mp0) REVERT: m 108 ASP cc_start: 0.8726 (t70) cc_final: 0.8481 (t0) REVERT: m 113 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8094 (tm-30) REVERT: n 44 MET cc_start: 0.7992 (tpp) cc_final: 0.7585 (tpp) REVERT: n 118 TYR cc_start: 0.8272 (t80) cc_final: 0.8032 (t80) REVERT: n 143 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7466 (mt-10) REVERT: o 16 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: o 20 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7760 (mp0) REVERT: o 31 PHE cc_start: 0.7887 (m-80) cc_final: 0.7664 (m-80) REVERT: o 44 GLN cc_start: 0.7680 (tm-30) cc_final: 0.6926 (tm-30) REVERT: o 48 ASP cc_start: 0.8424 (m-30) cc_final: 0.7861 (m-30) REVERT: o 76 ASN cc_start: 0.9069 (t0) cc_final: 0.8604 (t0) REVERT: p 165 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7973 (mp0) outliers start: 148 outliers final: 98 residues processed: 922 average time/residue: 0.1882 time to fit residues: 286.4474 Evaluate side-chains 896 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 787 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain h residue 182 SER Chi-restraints excluded: chain i residue 26 GLN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 83 HIS Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 153 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 0.9990 chunk 221 optimal weight: 0.1980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN L 361 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 HIS ** O 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 GLN n 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098055 restraints weight = 64015.501| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.36 r_work: 0.3293 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32475 Z= 0.134 Angle : 0.646 10.785 43920 Z= 0.322 Chirality : 0.043 0.398 4783 Planarity : 0.005 0.065 5390 Dihedral : 11.486 169.225 4866 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 3.84 % Allowed : 20.53 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3750 helix: 1.02 (0.11), residues: 2438 sheet: -0.16 (1.12), residues: 25 loop : -0.40 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 340 TYR 0.024 0.001 TYR L 422 PHE 0.024 0.002 PHE L 263 TRP 0.032 0.001 TRP L 484 HIS 0.008 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00302 (32466) covalent geometry : angle 0.64442 (43904) SS BOND : bond 0.00799 ( 8) SS BOND : angle 2.52293 ( 16) hydrogen bonds : bond 0.04243 ( 1690) hydrogen bonds : angle 4.49606 ( 4905) metal coordination : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 850 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7796 (mm-30) REVERT: D 61 TRP cc_start: 0.4914 (m-10) cc_final: 0.4666 (m-10) REVERT: D 68 ASP cc_start: 0.7673 (t70) cc_final: 0.7349 (t0) REVERT: J 8 LEU cc_start: 0.9346 (mt) cc_final: 0.9093 (mp) REVERT: J 32 LEU cc_start: 0.8508 (tp) cc_final: 0.8187 (tt) REVERT: J 46 PHE cc_start: 0.8868 (m-80) cc_final: 0.8482 (m-80) REVERT: J 73 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.6004 (mtt) REVERT: J 98 MET cc_start: 0.6802 (ptt) cc_final: 0.6325 (mmt) REVERT: J 125 MET cc_start: 0.7852 (mmm) cc_final: 0.7207 (mtm) REVERT: L 116 ARG cc_start: 0.9301 (ttm110) cc_final: 0.8950 (ttp80) REVERT: L 145 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: L 202 MET cc_start: 0.8060 (mtt) cc_final: 0.7760 (mmp) REVERT: L 509 MET cc_start: 0.6351 (ttm) cc_final: 0.6101 (ttt) REVERT: M 98 MET cc_start: 0.8480 (mmm) cc_final: 0.8126 (mmm) REVERT: M 123 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: M 139 GLN cc_start: 0.8278 (mp10) cc_final: 0.7758 (mm-40) REVERT: M 179 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8766 (mp) REVERT: M 201 MET cc_start: 0.8498 (tpp) cc_final: 0.8245 (mmm) REVERT: M 340 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7681 (mtm180) REVERT: M 378 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8061 (mt-10) REVERT: N 215 MET cc_start: 0.7755 (tpp) cc_final: 0.7388 (tpp) REVERT: N 237 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8844 (p) REVERT: N 240 MET cc_start: 0.8895 (ttm) cc_final: 0.8629 (tpp) REVERT: N 271 MET cc_start: 0.8938 (mmm) cc_final: 0.8726 (mmm) REVERT: O 106 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7317 (mp) REVERT: O 143 TYR cc_start: 0.8078 (t80) cc_final: 0.7335 (t80) REVERT: O 226 GLU cc_start: 0.5959 (tt0) cc_final: 0.5280 (tp30) REVERT: O 283 TRP cc_start: 0.8096 (m100) cc_final: 0.7515 (m100) REVERT: U 76 LEU cc_start: 0.9372 (mt) cc_final: 0.8819 (mt) REVERT: U 139 MET cc_start: 0.7251 (mmm) cc_final: 0.6946 (mmt) REVERT: Y 46 ASN cc_start: 0.8630 (t0) cc_final: 0.8374 (t0) REVERT: Y 127 PHE cc_start: 0.8861 (t80) cc_final: 0.8658 (t80) REVERT: c 29 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5588 (p90) REVERT: c 46 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8967 (mt) REVERT: d 37 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8825 (mp) REVERT: d 49 ARG cc_start: 0.8302 (mmt90) cc_final: 0.8026 (mmm-85) REVERT: e 37 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7593 (tm-30) REVERT: g 135 MET cc_start: 0.9153 (ttm) cc_final: 0.8803 (ttt) REVERT: g 139 TYR cc_start: 0.6269 (t80) cc_final: 0.5845 (t80) REVERT: h 69 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7793 (ttp-110) REVERT: h 93 ILE cc_start: 0.9032 (mm) cc_final: 0.8800 (mm) REVERT: i 24 LYS cc_start: 0.8186 (tppt) cc_final: 0.7719 (tptp) REVERT: j 95 GLU cc_start: 0.8532 (mp0) cc_final: 0.7982 (tm-30) REVERT: k 31 GLU cc_start: 0.8862 (pm20) cc_final: 0.8454 (pm20) REVERT: k 60 MET cc_start: 0.8704 (tpp) cc_final: 0.8334 (tpp) REVERT: k 78 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8130 (ttmm) REVERT: l 77 MET cc_start: 0.8710 (ttm) cc_final: 0.8467 (mtp) REVERT: l 177 GLU cc_start: 0.8298 (mp0) cc_final: 0.8000 (mp0) REVERT: m 24 ASP cc_start: 0.7137 (t0) cc_final: 0.6853 (t0) REVERT: m 31 ARG cc_start: 0.8635 (ttm110) cc_final: 0.8044 (ptp90) REVERT: m 61 GLU cc_start: 0.8105 (pm20) cc_final: 0.7749 (mp0) REVERT: m 108 ASP cc_start: 0.8700 (t70) cc_final: 0.8440 (t0) REVERT: m 113 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8033 (tm-30) REVERT: n 44 MET cc_start: 0.7919 (tpp) cc_final: 0.7553 (tpp) REVERT: n 143 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7240 (mt-10) REVERT: o 16 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: o 31 PHE cc_start: 0.7856 (m-80) cc_final: 0.7641 (m-80) REVERT: o 44 GLN cc_start: 0.7747 (tm-30) cc_final: 0.6706 (tm-30) REVERT: o 48 ASP cc_start: 0.8427 (m-30) cc_final: 0.7696 (m-30) REVERT: o 76 ASN cc_start: 0.9016 (t0) cc_final: 0.8539 (t0) REVERT: o 84 GLN cc_start: 0.9034 (tp40) cc_final: 0.8709 (tp40) REVERT: p 35 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8148 (pttt) REVERT: p 93 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7902 (mtp85) REVERT: p 165 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8088 (mp0) outliers start: 130 outliers final: 87 residues processed: 928 average time/residue: 0.1816 time to fit residues: 277.4783 Evaluate side-chains 901 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 802 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 200 MET Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 83 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 125 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 275 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 221 optimal weight: 0.0170 chunk 336 optimal weight: 0.0270 chunk 356 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN K 7 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 HIS U 115 GLN e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 51 HIS p 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098063 restraints weight = 63713.850| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.36 r_work: 0.3304 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32475 Z= 0.133 Angle : 0.661 11.639 43920 Z= 0.329 Chirality : 0.043 0.385 4783 Planarity : 0.005 0.065 5390 Dihedral : 11.238 169.464 4866 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 3.34 % Allowed : 21.27 % Favored : 75.39 % 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: 0.80 (0.14), residues: 3750 helix: 1.06 (0.11), residues: 2437 sheet: 0.22 (1.11), residues: 25 loop : -0.35 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 176 TYR 0.025 0.001 TYR n 118 PHE 0.038 0.002 PHE L 389 TRP 0.037 0.001 TRP L 484 HIS 0.009 0.001 HIS n 51 Details of bonding type rmsd covalent geometry : bond 0.00301 (32466) covalent geometry : angle 0.65780 (43904) SS BOND : bond 0.00835 ( 8) SS BOND : angle 3.47989 ( 16) hydrogen bonds : bond 0.04189 ( 1690) hydrogen bonds : angle 4.48150 ( 4905) metal coordination : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 833 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7765 (mm-30) REVERT: D 52 MET cc_start: 0.8272 (tpt) cc_final: 0.7809 (tpt) REVERT: D 61 TRP cc_start: 0.4884 (m-10) cc_final: 0.4644 (m-10) REVERT: D 68 ASP cc_start: 0.7649 (t70) cc_final: 0.7351 (t0) REVERT: J 32 LEU cc_start: 0.8500 (tp) cc_final: 0.8179 (tt) REVERT: J 46 PHE cc_start: 0.8896 (m-80) cc_final: 0.8579 (m-80) REVERT: J 98 MET cc_start: 0.6926 (ptt) cc_final: 0.6289 (mmt) REVERT: J 125 MET cc_start: 0.7840 (mmm) cc_final: 0.7181 (mtm) REVERT: L 116 ARG cc_start: 0.9300 (ttm110) cc_final: 0.8938 (ttp80) REVERT: L 202 MET cc_start: 0.8097 (mtt) cc_final: 0.7789 (mmp) REVERT: L 509 MET cc_start: 0.6465 (ttm) cc_final: 0.6233 (ttt) REVERT: M 98 MET cc_start: 0.8479 (mmm) cc_final: 0.8080 (mmm) REVERT: M 123 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: M 139 GLN cc_start: 0.8230 (mp10) cc_final: 0.7730 (mm-40) REVERT: M 179 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8744 (mp) REVERT: M 201 MET cc_start: 0.8541 (tpp) cc_final: 0.8315 (mmm) REVERT: M 248 ILE cc_start: 0.9027 (tp) cc_final: 0.8804 (mt) REVERT: M 340 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7660 (mtm180) REVERT: M 378 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8133 (mt-10) REVERT: N 20 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9033 (p) REVERT: N 237 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (p) REVERT: N 271 MET cc_start: 0.8862 (mmm) cc_final: 0.8566 (mmm) REVERT: O 106 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7314 (mp) REVERT: O 143 TYR cc_start: 0.8054 (t80) cc_final: 0.7305 (t80) REVERT: O 226 GLU cc_start: 0.5974 (tt0) cc_final: 0.5284 (tp30) REVERT: O 283 TRP cc_start: 0.8088 (m100) cc_final: 0.7488 (m100) REVERT: U 155 TYR cc_start: 0.9028 (p90) cc_final: 0.8690 (p90) REVERT: Y 46 ASN cc_start: 0.8658 (t0) cc_final: 0.8426 (t0) REVERT: Y 127 PHE cc_start: 0.8869 (t80) cc_final: 0.8666 (t80) REVERT: c 29 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5667 (p90) REVERT: c 46 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8972 (mt) REVERT: d 37 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8815 (mp) REVERT: d 49 ARG cc_start: 0.8340 (mmt90) cc_final: 0.8068 (mmm-85) REVERT: e 37 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7657 (tm-30) REVERT: e 87 MET cc_start: 0.7094 (ppp) cc_final: 0.6015 (ptm) REVERT: f 35 THR cc_start: 0.8645 (t) cc_final: 0.8348 (m) REVERT: f 52 GLU cc_start: 0.7446 (tt0) cc_final: 0.7094 (tt0) REVERT: g 135 MET cc_start: 0.9116 (ttm) cc_final: 0.8768 (ttt) REVERT: g 139 TYR cc_start: 0.6351 (t80) cc_final: 0.5908 (t80) REVERT: h 69 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7851 (ttp-110) REVERT: h 93 ILE cc_start: 0.9019 (mm) cc_final: 0.8783 (mm) REVERT: i 24 LYS cc_start: 0.8209 (tppt) cc_final: 0.7938 (tptp) REVERT: j 95 GLU cc_start: 0.8533 (mp0) cc_final: 0.8013 (tm-30) REVERT: k 31 GLU cc_start: 0.8871 (pm20) cc_final: 0.8444 (pm20) REVERT: k 60 MET cc_start: 0.8693 (tpp) cc_final: 0.8441 (mmp) REVERT: k 78 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8124 (ttmm) REVERT: l 77 MET cc_start: 0.8719 (ttm) cc_final: 0.8508 (mtp) REVERT: l 177 GLU cc_start: 0.8291 (mp0) cc_final: 0.7985 (mp0) REVERT: m 24 ASP cc_start: 0.7237 (t0) cc_final: 0.6986 (t0) REVERT: m 31 ARG cc_start: 0.8621 (ttm110) cc_final: 0.8027 (ptp90) REVERT: m 61 GLU cc_start: 0.8084 (pm20) cc_final: 0.7744 (mp0) REVERT: m 108 ASP cc_start: 0.8666 (t70) cc_final: 0.8436 (t0) REVERT: m 113 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8079 (tm-30) REVERT: n 44 MET cc_start: 0.7931 (tpp) cc_final: 0.7553 (tpp) REVERT: n 143 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7122 (mt-10) REVERT: o 16 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6496 (mm-30) REVERT: o 20 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7839 (mp0) REVERT: o 31 PHE cc_start: 0.7797 (m-80) cc_final: 0.7596 (m-80) REVERT: o 44 GLN cc_start: 0.7734 (tm-30) cc_final: 0.6692 (tm-30) REVERT: o 48 ASP cc_start: 0.8431 (m-30) cc_final: 0.7677 (m-30) REVERT: o 76 ASN cc_start: 0.9018 (t0) cc_final: 0.8527 (t0) REVERT: o 84 GLN cc_start: 0.9019 (tp40) cc_final: 0.8719 (tp40) REVERT: p 35 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8190 (pttt) REVERT: p 93 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7947 (mtp85) outliers start: 113 outliers final: 81 residues processed: 898 average time/residue: 0.1846 time to fit residues: 273.2192 Evaluate side-chains 887 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 796 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 83 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 81 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 24 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 231 optimal weight: 0.4980 chunk 214 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN K 7 ASN L 165 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 HIS ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 HIS U 115 GLN e 45 HIS ** h 170 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.116974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097988 restraints weight = 63726.300| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.37 r_work: 0.3303 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32475 Z= 0.139 Angle : 0.671 11.233 43920 Z= 0.331 Chirality : 0.044 0.371 4783 Planarity : 0.005 0.064 5390 Dihedral : 11.068 170.040 4866 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 3.25 % Allowed : 21.45 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3750 helix: 1.08 (0.11), residues: 2443 sheet: 0.52 (1.11), residues: 25 loop : -0.37 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 176 TYR 0.023 0.001 TYR L 422 PHE 0.050 0.002 PHE L 389 TRP 0.039 0.001 TRP L 484 HIS 0.009 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00321 (32466) covalent geometry : angle 0.66897 (43904) SS BOND : bond 0.00802 ( 8) SS BOND : angle 2.87999 ( 16) hydrogen bonds : bond 0.04191 ( 1690) hydrogen bonds : angle 4.47973 ( 4905) metal coordination : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 826 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7830 (mm-30) REVERT: D 52 MET cc_start: 0.8323 (tpt) cc_final: 0.7921 (tpt) REVERT: D 61 TRP cc_start: 0.4851 (m-10) cc_final: 0.4623 (m-10) REVERT: D 68 ASP cc_start: 0.7696 (t70) cc_final: 0.7378 (t0) REVERT: J 32 LEU cc_start: 0.8495 (tp) cc_final: 0.8173 (tt) REVERT: J 46 PHE cc_start: 0.8877 (m-80) cc_final: 0.8566 (m-80) REVERT: J 98 MET cc_start: 0.6861 (ptt) cc_final: 0.6239 (mmt) REVERT: J 125 MET cc_start: 0.7911 (mmm) cc_final: 0.7328 (mtm) REVERT: K 89 TYR cc_start: 0.7216 (m-10) cc_final: 0.6783 (m-10) REVERT: K 92 ASN cc_start: 0.8571 (m110) cc_final: 0.8370 (p0) REVERT: L 75 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8360 (mm-30) REVERT: L 116 ARG cc_start: 0.9281 (ttm110) cc_final: 0.8949 (ttp80) REVERT: L 145 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: L 202 MET cc_start: 0.8089 (mtt) cc_final: 0.7820 (mmp) REVERT: L 389 PHE cc_start: 0.8068 (t80) cc_final: 0.7833 (t80) REVERT: M 98 MET cc_start: 0.8485 (mmm) cc_final: 0.8121 (mmm) REVERT: M 123 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: M 139 GLN cc_start: 0.8253 (mp10) cc_final: 0.7775 (mm-40) REVERT: M 179 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8729 (mp) REVERT: M 201 MET cc_start: 0.8532 (tpp) cc_final: 0.8324 (mmm) REVERT: M 248 ILE cc_start: 0.9030 (tp) cc_final: 0.8824 (mt) REVERT: M 340 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7731 (mtm180) REVERT: M 378 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8141 (mt-10) REVERT: N 20 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9088 (p) REVERT: N 187 MET cc_start: 0.8024 (mmm) cc_final: 0.7801 (mmm) REVERT: N 215 MET cc_start: 0.7720 (tpp) cc_final: 0.7391 (tpt) REVERT: N 237 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (p) REVERT: N 271 MET cc_start: 0.8880 (mmm) cc_final: 0.8613 (mmm) REVERT: O 106 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7310 (mp) REVERT: O 143 TYR cc_start: 0.8056 (t80) cc_final: 0.7306 (t80) REVERT: O 226 GLU cc_start: 0.6102 (tt0) cc_final: 0.5349 (tp30) REVERT: O 283 TRP cc_start: 0.8069 (m100) cc_final: 0.7484 (m100) REVERT: U 155 TYR cc_start: 0.9024 (p90) cc_final: 0.8635 (p90) REVERT: Y 46 ASN cc_start: 0.8665 (t0) cc_final: 0.8440 (t0) REVERT: Y 127 PHE cc_start: 0.8864 (t80) cc_final: 0.8652 (t80) REVERT: c 29 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.5709 (p90) REVERT: c 46 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8972 (mt) REVERT: d 37 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (mp) REVERT: d 49 ARG cc_start: 0.8321 (mmt90) cc_final: 0.8056 (mmm-85) REVERT: e 37 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7733 (tm-30) REVERT: e 87 MET cc_start: 0.7219 (ppp) cc_final: 0.6219 (ptm) REVERT: f 35 THR cc_start: 0.8645 (t) cc_final: 0.8343 (m) REVERT: f 52 GLU cc_start: 0.7434 (tt0) cc_final: 0.7030 (tt0) REVERT: h 69 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7879 (ttp-110) REVERT: h 93 ILE cc_start: 0.9021 (mm) cc_final: 0.8789 (mm) REVERT: i 24 LYS cc_start: 0.8236 (tppt) cc_final: 0.7959 (tptp) REVERT: i 93 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8419 (mptt) REVERT: i 115 GLU cc_start: 0.8293 (tt0) cc_final: 0.7969 (tm-30) REVERT: i 116 VAL cc_start: 0.9096 (m) cc_final: 0.8594 (p) REVERT: j 95 GLU cc_start: 0.8543 (mp0) cc_final: 0.8058 (tm-30) REVERT: k 60 MET cc_start: 0.8723 (tpp) cc_final: 0.8509 (mmp) REVERT: k 78 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8135 (ttmm) REVERT: l 77 MET cc_start: 0.8721 (ttm) cc_final: 0.8423 (mtp) REVERT: l 177 GLU cc_start: 0.8272 (mp0) cc_final: 0.7980 (mp0) REVERT: m 24 ASP cc_start: 0.7428 (t0) cc_final: 0.7195 (t0) REVERT: m 31 ARG cc_start: 0.8585 (ttm110) cc_final: 0.7971 (ptp90) REVERT: m 61 GLU cc_start: 0.8061 (pm20) cc_final: 0.7718 (mp0) REVERT: m 108 ASP cc_start: 0.8673 (t70) cc_final: 0.8449 (t0) REVERT: m 113 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8077 (tm-30) REVERT: n 44 MET cc_start: 0.7927 (tpp) cc_final: 0.7543 (tpp) REVERT: o 16 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6418 (mm-30) REVERT: o 44 GLN cc_start: 0.7722 (tm-30) cc_final: 0.6688 (tm-30) REVERT: o 48 ASP cc_start: 0.8431 (m-30) cc_final: 0.7688 (m-30) REVERT: o 76 ASN cc_start: 0.9036 (t0) cc_final: 0.8540 (t0) REVERT: o 84 GLN cc_start: 0.9035 (tp40) cc_final: 0.8734 (tp40) REVERT: p 35 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8187 (pttt) REVERT: p 93 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7947 (mtp85) outliers start: 110 outliers final: 85 residues processed: 890 average time/residue: 0.1870 time to fit residues: 273.9551 Evaluate side-chains 890 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 794 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 453 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 83 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 ASN Chi-restraints excluded: chain p residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 199 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 24 optimal weight: 0.0570 chunk 245 optimal weight: 0.0170 chunk 182 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 330 optimal weight: 0.0060 chunk 5 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 HIS d 61 GLN e 29 ASN e 45 HIS ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099537 restraints weight = 63867.679| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.39 r_work: 0.3326 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32475 Z= 0.131 Angle : 0.681 13.317 43920 Z= 0.334 Chirality : 0.044 0.375 4783 Planarity : 0.005 0.064 5390 Dihedral : 10.851 170.291 4866 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.54 % Allowed : 22.33 % Favored : 75.13 % 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: 0.90 (0.14), residues: 3750 helix: 1.13 (0.11), residues: 2430 sheet: 0.45 (1.05), residues: 25 loop : -0.29 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 176 TYR 0.025 0.001 TYR L 422 PHE 0.049 0.002 PHE L 389 TRP 0.039 0.001 TRP N 114 HIS 0.009 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00291 (32466) covalent geometry : angle 0.67908 (43904) SS BOND : bond 0.00791 ( 8) SS BOND : angle 2.85090 ( 16) hydrogen bonds : bond 0.04116 ( 1690) hydrogen bonds : angle 4.47395 ( 4905) metal coordination : bond 0.00058 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 857 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7856 (mm-30) REVERT: D 53 TYR cc_start: 0.6980 (m-80) cc_final: 0.6778 (m-80) REVERT: D 61 TRP cc_start: 0.4859 (m-10) cc_final: 0.4643 (m-10) REVERT: D 68 ASP cc_start: 0.7684 (t70) cc_final: 0.7369 (t0) REVERT: J 46 PHE cc_start: 0.8835 (m-80) cc_final: 0.8522 (m-80) REVERT: J 98 MET cc_start: 0.6865 (ptt) cc_final: 0.6235 (mmt) REVERT: J 125 MET cc_start: 0.7900 (mmm) cc_final: 0.7378 (mtm) REVERT: K 89 TYR cc_start: 0.7143 (m-10) cc_final: 0.6746 (m-10) REVERT: L 75 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8349 (mm-30) REVERT: L 116 ARG cc_start: 0.9274 (ttm110) cc_final: 0.8945 (ttp80) REVERT: L 145 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: L 202 MET cc_start: 0.8003 (mtt) cc_final: 0.7452 (mmp) REVERT: L 226 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8087 (mm-40) REVERT: L 509 MET cc_start: 0.6087 (ttm) cc_final: 0.5727 (ttt) REVERT: M 59 ASP cc_start: 0.8219 (p0) cc_final: 0.8002 (p0) REVERT: M 98 MET cc_start: 0.8450 (mmm) cc_final: 0.8065 (mmm) REVERT: M 123 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: M 179 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8708 (mp) REVERT: M 201 MET cc_start: 0.8517 (tpp) cc_final: 0.8314 (mmm) REVERT: M 245 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8698 (mmt180) REVERT: M 378 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8075 (mt-10) REVERT: N 20 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9106 (p) REVERT: N 59 TYR cc_start: 0.8586 (t80) cc_final: 0.8246 (t80) REVERT: N 215 MET cc_start: 0.7658 (tpp) cc_final: 0.7301 (tpp) REVERT: N 271 MET cc_start: 0.8808 (mmm) cc_final: 0.8546 (mmm) REVERT: O 106 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7298 (mp) REVERT: O 143 TYR cc_start: 0.8073 (t80) cc_final: 0.7332 (t80) REVERT: O 226 GLU cc_start: 0.6122 (tt0) cc_final: 0.5308 (tp30) REVERT: O 283 TRP cc_start: 0.7989 (m100) cc_final: 0.7476 (m100) REVERT: O 291 PHE cc_start: 0.8208 (m-80) cc_final: 0.7902 (m-80) REVERT: Y 46 ASN cc_start: 0.8686 (t0) cc_final: 0.8428 (t0) REVERT: Y 127 PHE cc_start: 0.8866 (t80) cc_final: 0.8663 (t80) REVERT: c 29 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.5781 (p90) REVERT: c 46 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8969 (mt) REVERT: e 37 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7733 (tm-30) REVERT: e 87 MET cc_start: 0.7218 (ppp) cc_final: 0.6249 (ptm) REVERT: f 35 THR cc_start: 0.8575 (t) cc_final: 0.8306 (m) REVERT: g 135 MET cc_start: 0.9062 (ttm) cc_final: 0.8756 (ttt) REVERT: g 139 TYR cc_start: 0.6419 (t80) cc_final: 0.5978 (t80) REVERT: h 69 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7902 (ttp-110) REVERT: h 93 ILE cc_start: 0.8986 (mm) cc_final: 0.8754 (mm) REVERT: i 24 LYS cc_start: 0.8116 (tppt) cc_final: 0.7788 (tptp) REVERT: i 93 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8417 (mptt) REVERT: i 115 GLU cc_start: 0.8367 (tt0) cc_final: 0.8010 (tm-30) REVERT: i 116 VAL cc_start: 0.9081 (m) cc_final: 0.8584 (p) REVERT: j 95 GLU cc_start: 0.8480 (mp0) cc_final: 0.8177 (tm-30) REVERT: k 78 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8111 (ttmm) REVERT: l 177 GLU cc_start: 0.8256 (mp0) cc_final: 0.7974 (mp0) REVERT: m 31 ARG cc_start: 0.8609 (ttm110) cc_final: 0.8026 (ptp90) REVERT: m 61 GLU cc_start: 0.8078 (pm20) cc_final: 0.7717 (mp0) REVERT: m 108 ASP cc_start: 0.8616 (t70) cc_final: 0.8390 (t0) REVERT: n 44 MET cc_start: 0.7884 (tpp) cc_final: 0.7504 (tpp) REVERT: o 16 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: o 20 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7792 (mp0) REVERT: o 44 GLN cc_start: 0.7757 (tm-30) cc_final: 0.6728 (tm-30) REVERT: o 48 ASP cc_start: 0.8408 (m-30) cc_final: 0.7689 (m-30) REVERT: o 76 ASN cc_start: 0.9013 (t0) cc_final: 0.8502 (t0) REVERT: o 84 GLN cc_start: 0.8972 (tp40) cc_final: 0.8679 (tp40) REVERT: p 35 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8201 (pttt) REVERT: p 93 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7931 (mtp85) outliers start: 86 outliers final: 63 residues processed: 905 average time/residue: 0.1900 time to fit residues: 281.4886 Evaluate side-chains 889 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 818 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain L residue 489 THR Chi-restraints excluded: chain L residue 531 SER Chi-restraints excluded: chain L residue 567 SER Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 600 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 35 PHE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain c residue 29 PHE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain h residue 165 ASP Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 83 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 172 THR Chi-restraints excluded: chain o residue 16 GLU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 241 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 308 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 317 optimal weight: 0.0370 chunk 307 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN N 316 HIS d 61 GLN e 45 HIS ** g 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099129 restraints weight = 64271.608| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.39 r_work: 0.3312 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 32475 Z= 0.138 Angle : 0.691 13.034 43920 Z= 0.338 Chirality : 0.045 0.571 4783 Planarity : 0.005 0.063 5390 Dihedral : 10.636 170.848 4866 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 2.69 % Allowed : 22.69 % Favored : 74.62 % 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: 0.93 (0.14), residues: 3750 helix: 1.15 (0.11), residues: 2433 sheet: 0.33 (0.93), residues: 32 loop : -0.28 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 340 TYR 0.025 0.001 TYR M 256 PHE 0.053 0.002 PHE L 389 TRP 0.036 0.001 TRP N 114 HIS 0.010 0.001 HIS L 248 Details of bonding type rmsd covalent geometry : bond 0.00319 (32466) covalent geometry : angle 0.68795 (43904) SS BOND : bond 0.00976 ( 8) SS BOND : angle 3.27495 ( 16) hydrogen bonds : bond 0.04110 ( 1690) hydrogen bonds : angle 4.48341 ( 4905) metal coordination : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8463.67 seconds wall clock time: 146 minutes 2.72 seconds (8762.72 seconds total)