Starting phenix.real_space_refine on Wed Mar 4 12:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ly9_30015/03_2026/6ly9_30015.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 9016 2.51 5 N 2431 2.21 5 O 2418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13888 Number of models: 1 Model: "" Number of chains: 16 Chain: "N" Number of atoms: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5083 Classifications: {'peptide': 649} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 613} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 523 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 510 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 513 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 511 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 503 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 513 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 80 Classifications: {'peptide': 20} Incomplete info: {'backbone_only': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 3.22, per 1000 atoms: 0.23 Number of scatterers: 13888 At special positions: 0 Unit cell: (140.8, 128.7, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 2418 8.00 N 2431 7.00 C 9016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " 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: 1.17 Conformation dependent library (CDL) restraints added in 356.1 milliseconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 81.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 32 removed outlier: 3.891A pdb=" N VAL N 30 " --> pdb=" O GLN N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 71 removed outlier: 4.230A pdb=" N ALA N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 129 Proline residue: N 93 - end of helix removed outlier: 4.454A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 148 through 161 removed outlier: 4.049A pdb=" N LEU N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 198 removed outlier: 3.583A pdb=" N ALA N 192 " --> pdb=" O ASP N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 244 Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 245 through 270 removed outlier: 3.556A pdb=" N LEU N 249 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 297 removed outlier: 3.890A pdb=" N HIS N 297 " --> pdb=" O ALA N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 330 No H-bonds generated for 'chain 'N' and resid 328 through 330' Processing helix chain 'N' and resid 331 through 336 removed outlier: 4.167A pdb=" N PHE N 336 " --> pdb=" O LEU N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 363 removed outlier: 4.175A pdb=" N VAL N 353 " --> pdb=" O PRO N 349 " (cutoff:3.500A) Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 364 through 385 removed outlier: 5.166A pdb=" N LEU N 370 " --> pdb=" O ILE N 366 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU N 371 " --> pdb=" O GLY N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 399 through 425 removed outlier: 4.277A pdb=" N LYS N 405 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL N 422 " --> pdb=" O VAL N 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE N 423 " --> pdb=" O VAL N 419 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 434 Processing helix chain 'N' and resid 459 through 489 Processing helix chain 'N' and resid 491 through 517 Processing helix chain 'N' and resid 524 through 543 Processing helix chain 'N' and resid 546 through 560 removed outlier: 4.313A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 589 removed outlier: 4.258A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 626 removed outlier: 5.389A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix Processing helix chain 'N' and resid 628 through 633 removed outlier: 4.043A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 46 removed outlier: 3.663A pdb=" N VAL O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing helix chain 'O' and resid 51 through 61 removed outlier: 3.537A pdb=" N ILE O 57 " --> pdb=" O GLY O 53 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 79 Processing helix chain 'P' and resid 8 through 46 removed outlier: 3.796A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 46 " --> pdb=" O VAL P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 80 Processing helix chain 'Q' and resid 8 through 47 removed outlier: 3.719A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 removed outlier: 3.775A pdb=" N ALA Q 55 " --> pdb=" O ASN Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 80 Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.683A pdb=" N ILE R 15 " --> pdb=" O ASP R 11 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 8 through 48 Processing helix chain 'S' and resid 51 through 60 Processing helix chain 'S' and resid 63 through 78 removed outlier: 3.703A pdb=" N GLY S 78 " --> pdb=" O PHE S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 48 removed outlier: 3.539A pdb=" N ALA T 33 " --> pdb=" O GLY T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 removed outlier: 4.050A pdb=" N PHE T 58 " --> pdb=" O THR T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 80 removed outlier: 4.243A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG T 79 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 48 removed outlier: 3.761A pdb=" N ALA U 16 " --> pdb=" O ARG U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 79 removed outlier: 4.405A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 46 removed outlier: 4.448A pdb=" N LEU V 14 " --> pdb=" O LEU V 10 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA V 46 " --> pdb=" O VAL V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 61 removed outlier: 3.571A pdb=" N GLY V 53 " --> pdb=" O ARG V 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 57 " --> pdb=" O GLY V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 79 removed outlier: 4.031A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG V 79 " --> pdb=" O ILE V 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 48 removed outlier: 3.889A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 60 removed outlier: 4.422A pdb=" N ILE W 57 " --> pdb=" O GLY W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 78 removed outlier: 4.167A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 48 removed outlier: 3.799A pdb=" N GLY X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.652A pdb=" N ILE X 57 " --> pdb=" O GLY X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 78 Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.833A pdb=" N ALA Y 16 " --> pdb=" O ARG Y 12 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL Y 17 " --> pdb=" O GLY Y 13 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 64 through 80 removed outlier: 3.824A pdb=" N ARG Y 79 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Y 80 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 48 removed outlier: 4.137A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU Z 47 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 removed outlier: 3.517A pdb=" N ALA Z 55 " --> pdb=" O ASN Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 79 removed outlier: 4.395A pdb=" N VAL Z 66 " --> pdb=" O PRO Z 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 18 removed outlier: 3.509A pdb=" N LEU M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 17 " --> pdb=" O ARG M 13 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 29 removed outlier: 4.268A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN M 26 " --> pdb=" O GLU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 43 removed outlier: 3.509A pdb=" N THR M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 Processing helix chain 'M' and resid 53 through 69 Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.691A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 106 removed outlier: 3.555A pdb=" N ALA M 83 " --> pdb=" O GLU M 79 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 130 removed outlier: 3.858A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 160 through 184 removed outlier: 3.815A pdb=" N GLU M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 208 removed outlier: 3.533A pdb=" N PHE M 205 " --> pdb=" O LEU M 201 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 278 No H-bonds generated for 'chain 'M' and resid 276 through 278' Processing helix chain 'M' and resid 283 through 309 removed outlier: 3.801A pdb=" N ARG M 306 " --> pdb=" O LEU M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 321 removed outlier: 4.257A pdb=" N VAL M 316 " --> pdb=" O PRO M 312 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU M 319 " --> pdb=" O GLN M 315 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL M 321 " --> pdb=" O GLU M 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 42 removed outlier: 3.590A pdb=" N LEU K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 21 removed outlier: 4.509A pdb=" N ALA L 14 " --> pdb=" O GLN L 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU L 15 " --> pdb=" O GLU L 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'N' and resid 139 through 140 Processing sheet with id=AA3, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'N' and resid 389 through 391 removed outlier: 3.534A pdb=" N LEU N 398 " --> pdb=" O LEU N 389 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE N 391 " --> pdb=" O LEU N 396 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU N 396 " --> pdb=" O ILE N 391 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3375 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: 2.62 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4642 1.34 - 1.46: 2968 1.46 - 1.58: 6451 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 14105 Sorted by residual: bond pdb=" CA ARG M 156 " pdb=" C ARG M 156 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.72e-02 3.38e+03 2.46e+00 bond pdb=" N LEU M 252 " pdb=" CA LEU M 252 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.19e-02 7.06e+03 2.04e+00 bond pdb=" C ASP N 346 " pdb=" N PRO N 347 " ideal model delta sigma weight residual 1.331 1.320 0.011 7.90e-03 1.60e+04 1.97e+00 bond pdb=" CB TRP N 358 " pdb=" CG TRP N 358 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.94e+00 bond pdb=" CG1 ILE Z 37 " pdb=" CD1 ILE Z 37 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18544 1.88 - 3.75: 439 3.75 - 5.63: 82 5.63 - 7.50: 16 7.50 - 9.38: 4 Bond angle restraints: 19085 Sorted by residual: angle pdb=" N LEU M 252 " pdb=" CA LEU M 252 " pdb=" C LEU M 252 " ideal model delta sigma weight residual 111.07 104.63 6.44 1.07e+00 8.73e-01 3.63e+01 angle pdb=" N ASN P 51 " pdb=" CA ASN P 51 " pdb=" C ASN P 51 " ideal model delta sigma weight residual 114.12 107.87 6.25 1.39e+00 5.18e-01 2.02e+01 angle pdb=" N VAL N 334 " pdb=" CA VAL N 334 " pdb=" C VAL N 334 " ideal model delta sigma weight residual 113.71 109.58 4.13 9.50e-01 1.11e+00 1.89e+01 angle pdb=" C GLY M 251 " pdb=" N LEU M 252 " pdb=" CA LEU M 252 " ideal model delta sigma weight residual 120.44 115.72 4.72 1.30e+00 5.92e-01 1.32e+01 angle pdb=" N GLY M 254 " pdb=" CA GLY M 254 " pdb=" C GLY M 254 " ideal model delta sigma weight residual 110.56 115.90 -5.34 1.66e+00 3.63e-01 1.03e+01 ... (remaining 19080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7333 17.95 - 35.89: 716 35.89 - 53.84: 130 53.84 - 71.78: 20 71.78 - 89.73: 9 Dihedral angle restraints: 8208 sinusoidal: 3099 harmonic: 5109 Sorted by residual: dihedral pdb=" CA GLU N 426 " pdb=" C GLU N 426 " pdb=" N PHE N 427 " pdb=" CA PHE N 427 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 137 " pdb=" C PHE N 137 " pdb=" N LEU N 138 " pdb=" CA LEU N 138 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS N 434 " pdb=" C HIS N 434 " pdb=" N LEU N 435 " pdb=" CA LEU N 435 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1637 0.046 - 0.091: 532 0.091 - 0.137: 78 0.137 - 0.183: 6 0.183 - 0.228: 1 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CG LEU N 435 " pdb=" CB LEU N 435 " pdb=" CD1 LEU N 435 " pdb=" CD2 LEU N 435 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TRP N 545 " pdb=" N TRP N 545 " pdb=" C TRP N 545 " pdb=" CB TRP N 545 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR N 339 " pdb=" CA THR N 339 " pdb=" OG1 THR N 339 " pdb=" CG2 THR N 339 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2251 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER P 50 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C SER P 50 " 0.040 2.00e-02 2.50e+03 pdb=" O SER P 50 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN P 51 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY N 12 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO N 13 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO N 13 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 13 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 427 " -0.007 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE N 427 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE N 427 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 427 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE N 427 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 427 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE N 427 " 0.004 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1559 2.74 - 3.28: 16317 3.28 - 3.82: 24357 3.82 - 4.36: 28536 4.36 - 4.90: 46679 Nonbonded interactions: 117448 Sorted by model distance: nonbonded pdb=" O GLU N 627 " pdb=" NZ LYS N 631 " model vdw 2.195 3.120 nonbonded pdb=" O SER N 251 " pdb=" OG1 THR N 254 " model vdw 2.200 3.040 nonbonded pdb=" O HIS N 65 " pdb=" OG SER N 68 " model vdw 2.212 3.040 nonbonded pdb=" NH1 ARG N 482 " pdb=" O LYS N 631 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN Q 34 " pdb=" O LEU Q 59 " model vdw 2.238 3.120 ... (remaining 117443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'O' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'P' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Q' and (resid 9 through 49 or (resid 50 and (name N or name CA or name C \ or name O )) or resid 51 through 80)) selection = (chain 'R' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'S' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 80)) selection = (chain 'T' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'U' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'V' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'W' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'X' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Y' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Z' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) } 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 group one per residue 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.006 0.054 14106 Z= 0.264 Angle : 0.746 9.380 19087 Z= 0.408 Chirality : 0.042 0.228 2254 Planarity : 0.004 0.052 2456 Dihedral : 14.600 89.729 4999 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.05 % Allowed : 10.01 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.16), residues: 1862 helix: -1.76 (0.11), residues: 1443 sheet: -4.05 (0.68), residues: 40 loop : -3.42 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 622 TYR 0.014 0.002 TYR N 373 PHE 0.028 0.002 PHE N 427 TRP 0.014 0.001 TRP N 545 HIS 0.007 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00584 (14105) covalent geometry : angle 0.74552 (19085) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.51947 ( 2) hydrogen bonds : bond 0.10166 ( 1133) hydrogen bonds : angle 5.43106 ( 3375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 457 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 155 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8155 (tm-30) REVERT: N 580 ASP cc_start: 0.8137 (t70) cc_final: 0.7686 (t0) REVERT: N 585 LEU cc_start: 0.8636 (tp) cc_final: 0.8435 (tp) REVERT: N 618 LEU cc_start: 0.9315 (tp) cc_final: 0.9035 (tp) REVERT: O 64 THR cc_start: 0.9232 (p) cc_final: 0.9017 (p) REVERT: O 77 ASN cc_start: 0.8209 (t0) cc_final: 0.7880 (t0) REVERT: P 12 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8166 (mtm-85) REVERT: P 21 LEU cc_start: 0.9294 (tp) cc_final: 0.8974 (tp) REVERT: P 58 PHE cc_start: 0.9421 (m-80) cc_final: 0.9157 (m-80) REVERT: P 74 PHE cc_start: 0.8350 (m-10) cc_final: 0.7817 (t80) REVERT: Q 19 MET cc_start: 0.8772 (mtm) cc_final: 0.8459 (mtm) REVERT: Q 65 LEU cc_start: 0.9448 (mm) cc_final: 0.9220 (mm) REVERT: R 60 LEU cc_start: 0.9257 (mt) cc_final: 0.8460 (mm) REVERT: R 63 GLU cc_start: 0.8591 (mp0) cc_final: 0.8307 (mp0) REVERT: R 68 PHE cc_start: 0.8926 (m-10) cc_final: 0.8585 (m-10) REVERT: S 34 GLN cc_start: 0.8469 (mt0) cc_final: 0.7926 (mt0) REVERT: S 52 PHE cc_start: 0.8254 (t80) cc_final: 0.7989 (t80) REVERT: T 32 VAL cc_start: 0.8831 (m) cc_final: 0.8627 (p) REVERT: U 56 LEU cc_start: 0.9134 (mm) cc_final: 0.8750 (mm) REVERT: V 19 MET cc_start: 0.8548 (ptp) cc_final: 0.8339 (ptm) REVERT: V 68 PHE cc_start: 0.8730 (m-80) cc_final: 0.8320 (m-80) REVERT: W 15 ILE cc_start: 0.9583 (mt) cc_final: 0.9381 (mm) REVERT: W 61 LEU cc_start: 0.8405 (tp) cc_final: 0.8203 (tp) REVERT: X 11 ASP cc_start: 0.8347 (m-30) cc_final: 0.7883 (m-30) REVERT: X 19 MET cc_start: 0.8784 (ptm) cc_final: 0.8522 (ptp) REVERT: Y 12 ARG cc_start: 0.8252 (ttm110) cc_final: 0.8013 (mtp-110) REVERT: Y 47 GLU cc_start: 0.8472 (tp30) cc_final: 0.8044 (tp30) REVERT: Z 79 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8094 (tpt90) REVERT: M 23 SER cc_start: 0.9092 (p) cc_final: 0.8807 (p) REVERT: M 94 HIS cc_start: 0.8673 (t70) cc_final: 0.8428 (t70) REVERT: M 128 TYR cc_start: 0.8592 (t80) cc_final: 0.8324 (t80) REVERT: M 301 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7798 (mmm160) outliers start: 14 outliers final: 10 residues processed: 467 average time/residue: 0.1220 time to fit residues: 82.7518 Evaluate side-chains 393 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 383 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain M residue 252 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 95 GLN N 104 GLN N 106 GLN N 116 GLN N 183 HIS ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 237 HIS N 554 GLN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 652 GLN R 34 GLN R 51 ASN Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089380 restraints weight = 33113.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092008 restraints weight = 19081.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093760 restraints weight = 12976.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094831 restraints weight = 9933.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095736 restraints weight = 8327.256| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14106 Z= 0.160 Angle : 0.702 10.550 19087 Z= 0.346 Chirality : 0.041 0.158 2254 Planarity : 0.005 0.050 2456 Dihedral : 5.896 53.002 2045 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.48 % Allowed : 20.10 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1862 helix: -0.10 (0.13), residues: 1457 sheet: -3.77 (0.70), residues: 40 loop : -2.73 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 158 TYR 0.018 0.002 TYR N 373 PHE 0.034 0.002 PHE S 68 TRP 0.012 0.001 TRP N 545 HIS 0.006 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00351 (14105) covalent geometry : angle 0.70232 (19085) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.67952 ( 2) hydrogen bonds : bond 0.05037 ( 1133) hydrogen bonds : angle 4.47870 ( 3375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 449 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 164 ARG cc_start: 0.7112 (mtp180) cc_final: 0.6479 (mmp80) REVERT: N 183 HIS cc_start: 0.6877 (t-90) cc_final: 0.6613 (t-90) REVERT: N 222 GLU cc_start: 0.8227 (pt0) cc_final: 0.7762 (pt0) REVERT: N 435 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6608 (mm) REVERT: N 476 PHE cc_start: 0.8701 (m-10) cc_final: 0.8421 (m-80) REVERT: N 580 ASP cc_start: 0.8127 (t70) cc_final: 0.7761 (t0) REVERT: N 585 LEU cc_start: 0.8325 (tp) cc_final: 0.8106 (tp) REVERT: N 618 LEU cc_start: 0.9299 (tp) cc_final: 0.8971 (tp) REVERT: N 622 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8048 (ptt90) REVERT: O 11 ASP cc_start: 0.8047 (p0) cc_final: 0.7782 (p0) REVERT: O 77 ASN cc_start: 0.8502 (t0) cc_final: 0.7751 (t0) REVERT: P 12 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7825 (mtm-85) REVERT: P 21 LEU cc_start: 0.9114 (tp) cc_final: 0.8832 (tp) REVERT: P 58 PHE cc_start: 0.9369 (m-80) cc_final: 0.9074 (m-80) REVERT: P 74 PHE cc_start: 0.8194 (m-10) cc_final: 0.7699 (t80) REVERT: R 51 ASN cc_start: 0.8984 (m-40) cc_final: 0.8716 (m110) REVERT: R 60 LEU cc_start: 0.9121 (mt) cc_final: 0.8613 (mm) REVERT: R 68 PHE cc_start: 0.8921 (m-10) cc_final: 0.8639 (m-10) REVERT: S 63 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: S 79 ARG cc_start: 0.6850 (mpt180) cc_final: 0.6431 (mtt180) REVERT: T 63 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8109 (mm-30) REVERT: W 15 ILE cc_start: 0.9489 (mt) cc_final: 0.9232 (mm) REVERT: W 68 PHE cc_start: 0.8430 (m-10) cc_final: 0.7893 (m-80) REVERT: X 11 ASP cc_start: 0.8236 (m-30) cc_final: 0.8030 (m-30) REVERT: Z 51 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8059 (t0) REVERT: M 94 HIS cc_start: 0.8647 (t70) cc_final: 0.8411 (t-90) REVERT: M 132 ASP cc_start: 0.8139 (m-30) cc_final: 0.7877 (m-30) REVERT: M 234 MET cc_start: 0.8200 (mmt) cc_final: 0.7976 (tpt) REVERT: M 283 VAL cc_start: 0.8701 (t) cc_final: 0.8369 (p) REVERT: M 301 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7783 (mmm160) outliers start: 60 outliers final: 31 residues processed: 471 average time/residue: 0.1198 time to fit residues: 82.8098 Evaluate side-chains 424 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 389 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 308 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 621 ILE Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 63 GLU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 51 ASN Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 136 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 126 GLN M 200 ASN ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090034 restraints weight = 33357.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092712 restraints weight = 19275.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094479 restraints weight = 13045.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095376 restraints weight = 9933.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096439 restraints weight = 8421.243| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14106 Z= 0.164 Angle : 0.697 9.843 19087 Z= 0.343 Chirality : 0.042 0.211 2254 Planarity : 0.005 0.052 2456 Dihedral : 5.357 49.478 2038 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.61 % Allowed : 22.20 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1862 helix: 0.53 (0.13), residues: 1443 sheet: -3.42 (0.76), residues: 38 loop : -2.43 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 158 TYR 0.024 0.002 TYR M 191 PHE 0.047 0.002 PHE S 68 TRP 0.037 0.002 TRP N 625 HIS 0.008 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00368 (14105) covalent geometry : angle 0.69697 (19085) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.71383 ( 2) hydrogen bonds : bond 0.04809 ( 1133) hydrogen bonds : angle 4.39512 ( 3375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 421 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 6 GLU cc_start: 0.7712 (pt0) cc_final: 0.7300 (pt0) REVERT: N 218 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7332 (ttp80) REVERT: N 435 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6473 (mm) REVERT: N 580 ASP cc_start: 0.8093 (t70) cc_final: 0.7713 (t0) REVERT: N 618 LEU cc_start: 0.9351 (tp) cc_final: 0.9064 (tp) REVERT: O 77 ASN cc_start: 0.8142 (t0) cc_final: 0.7771 (t0) REVERT: P 21 LEU cc_start: 0.9072 (tp) cc_final: 0.8751 (tp) REVERT: P 58 PHE cc_start: 0.9383 (m-80) cc_final: 0.9093 (m-80) REVERT: P 74 PHE cc_start: 0.8286 (m-10) cc_final: 0.7700 (t80) REVERT: Q 19 MET cc_start: 0.8520 (mtm) cc_final: 0.8071 (mtm) REVERT: Q 66 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7380 (p) REVERT: R 21 LEU cc_start: 0.9248 (tt) cc_final: 0.8883 (tp) REVERT: R 34 GLN cc_start: 0.8396 (tt0) cc_final: 0.8061 (mt0) REVERT: R 51 ASN cc_start: 0.9005 (m-40) cc_final: 0.8749 (m110) REVERT: S 21 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8857 (tp) REVERT: T 28 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8835 (pt) REVERT: U 56 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8538 (mm) REVERT: W 15 ILE cc_start: 0.9441 (mt) cc_final: 0.9153 (mm) REVERT: Y 12 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7930 (mtm110) REVERT: Y 21 LEU cc_start: 0.9092 (tp) cc_final: 0.8830 (tp) REVERT: Z 19 MET cc_start: 0.8976 (ptm) cc_final: 0.8702 (ptp) REVERT: Z 51 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7349 (t0) REVERT: M 85 ARG cc_start: 0.8976 (tpp80) cc_final: 0.8759 (tpp80) REVERT: M 94 HIS cc_start: 0.8651 (t70) cc_final: 0.8414 (t-90) REVERT: M 301 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7784 (mmm160) outliers start: 75 outliers final: 41 residues processed: 460 average time/residue: 0.1139 time to fit residues: 78.0891 Evaluate side-chains 429 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 382 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 51 ASN Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 163 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 HIS ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN S 77 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 ASN Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084430 restraints weight = 33435.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086981 restraints weight = 19298.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088671 restraints weight = 13091.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089764 restraints weight = 10009.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090581 restraints weight = 8338.685| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14106 Z= 0.253 Angle : 0.748 12.132 19087 Z= 0.372 Chirality : 0.043 0.167 2254 Planarity : 0.005 0.062 2456 Dihedral : 5.332 47.814 2036 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.95 % Allowed : 23.77 % Favored : 69.28 % 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: -0.14 (0.19), residues: 1862 helix: 0.59 (0.13), residues: 1455 sheet: -3.34 (0.74), residues: 38 loop : -2.20 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 622 TYR 0.025 0.002 TYR M 128 PHE 0.060 0.002 PHE S 68 TRP 0.027 0.002 TRP N 625 HIS 0.007 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00579 (14105) covalent geometry : angle 0.74759 (19085) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.51710 ( 2) hydrogen bonds : bond 0.05027 ( 1133) hydrogen bonds : angle 4.53440 ( 3375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 147 GLU cc_start: 0.7834 (tt0) cc_final: 0.7622 (tt0) REVERT: N 322 ASP cc_start: 0.7937 (p0) cc_final: 0.7665 (p0) REVERT: N 354 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8386 (m-10) REVERT: N 427 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5877 (m-80) REVERT: N 435 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6426 (mm) REVERT: N 476 PHE cc_start: 0.8758 (m-10) cc_final: 0.8472 (m-80) REVERT: N 580 ASP cc_start: 0.8162 (t70) cc_final: 0.7787 (t0) REVERT: O 77 ASN cc_start: 0.8212 (t0) cc_final: 0.7930 (t0) REVERT: P 19 MET cc_start: 0.8872 (ttm) cc_final: 0.8660 (mtp) REVERT: P 21 LEU cc_start: 0.9140 (tp) cc_final: 0.8835 (tp) REVERT: P 58 PHE cc_start: 0.9437 (m-80) cc_final: 0.9158 (m-80) REVERT: P 74 PHE cc_start: 0.8380 (m-10) cc_final: 0.7697 (t80) REVERT: Q 19 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8031 (mtm) REVERT: R 10 LEU cc_start: 0.9125 (pp) cc_final: 0.8630 (pp) REVERT: R 21 LEU cc_start: 0.9245 (tt) cc_final: 0.8872 (tt) REVERT: R 51 ASN cc_start: 0.9122 (m-40) cc_final: 0.8765 (m110) REVERT: R 65 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8256 (mt) REVERT: R 68 PHE cc_start: 0.8912 (m-80) cc_final: 0.8367 (m-80) REVERT: S 21 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8976 (tp) REVERT: S 63 GLU cc_start: 0.8721 (mp0) cc_final: 0.8398 (mp0) REVERT: T 28 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8868 (pt) REVERT: U 56 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8444 (mm) REVERT: W 15 ILE cc_start: 0.9433 (mt) cc_final: 0.9143 (mm) REVERT: Z 51 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7509 (t0) REVERT: M 94 HIS cc_start: 0.8824 (t70) cc_final: 0.8591 (t-90) REVERT: M 301 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7744 (mmm160) outliers start: 93 outliers final: 60 residues processed: 444 average time/residue: 0.1135 time to fit residues: 75.6012 Evaluate side-chains 424 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 427 PHE Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 621 ILE Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 19 MET Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 51 ASN Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 15 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086753 restraints weight = 33205.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.089417 restraints weight = 18934.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091082 restraints weight = 12709.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092380 restraints weight = 9701.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093165 restraints weight = 7937.506| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14106 Z= 0.178 Angle : 0.711 10.956 19087 Z= 0.351 Chirality : 0.042 0.184 2254 Planarity : 0.005 0.095 2456 Dihedral : 5.331 49.156 2036 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.88 % Allowed : 26.01 % Favored : 67.12 % 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: 0.10 (0.20), residues: 1862 helix: 0.74 (0.13), residues: 1459 sheet: -3.41 (0.74), residues: 38 loop : -2.06 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 158 TYR 0.025 0.002 TYR M 191 PHE 0.082 0.002 PHE S 68 TRP 0.020 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00413 (14105) covalent geometry : angle 0.71085 (19085) SS BOND : bond 0.00018 ( 1) SS BOND : angle 1.57143 ( 2) hydrogen bonds : bond 0.04841 ( 1133) hydrogen bonds : angle 4.39766 ( 3375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 404 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 150 LEU cc_start: 0.9098 (mp) cc_final: 0.8868 (mm) REVERT: N 354 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: N 435 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6512 (mm) REVERT: N 580 ASP cc_start: 0.8127 (t70) cc_final: 0.7782 (t0) REVERT: N 625 TRP cc_start: 0.8967 (m-10) cc_final: 0.8720 (m-90) REVERT: O 77 ASN cc_start: 0.8323 (t0) cc_final: 0.7921 (t0) REVERT: P 19 MET cc_start: 0.8900 (mtm) cc_final: 0.8361 (ttm) REVERT: P 58 PHE cc_start: 0.9400 (m-80) cc_final: 0.9102 (m-80) REVERT: P 74 PHE cc_start: 0.8370 (m-10) cc_final: 0.7696 (t80) REVERT: R 10 LEU cc_start: 0.9097 (pp) cc_final: 0.8678 (pp) REVERT: R 21 LEU cc_start: 0.9232 (tt) cc_final: 0.8851 (tp) REVERT: R 34 GLN cc_start: 0.8466 (tt0) cc_final: 0.7860 (mt0) REVERT: R 51 ASN cc_start: 0.9094 (m-40) cc_final: 0.8736 (m110) REVERT: R 68 PHE cc_start: 0.8954 (m-80) cc_final: 0.8731 (m-10) REVERT: S 21 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8987 (tp) REVERT: S 61 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8796 (tt) REVERT: T 28 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8859 (pt) REVERT: U 56 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8480 (mm) REVERT: W 15 ILE cc_start: 0.9399 (mt) cc_final: 0.9143 (mm) REVERT: Z 51 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7245 (t0) REVERT: M 131 GLN cc_start: 0.8098 (pt0) cc_final: 0.7871 (pm20) REVERT: M 283 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8503 (p) REVERT: M 301 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7741 (mmm160) outliers start: 92 outliers final: 51 residues processed: 445 average time/residue: 0.1097 time to fit residues: 73.2045 Evaluate side-chains 434 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 375 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 621 ILE Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 51 ASN Chi-restraints excluded: chain Z residue 67 ILE Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 94 HIS ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086955 restraints weight = 33055.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.089611 restraints weight = 18928.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091335 restraints weight = 12758.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092510 restraints weight = 9694.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093067 restraints weight = 8015.928| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14106 Z= 0.180 Angle : 0.719 10.648 19087 Z= 0.353 Chirality : 0.042 0.154 2254 Planarity : 0.005 0.062 2456 Dihedral : 5.325 49.861 2036 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.05 % Allowed : 28.55 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1862 helix: 0.78 (0.13), residues: 1463 sheet: -3.28 (0.84), residues: 31 loop : -2.04 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 158 TYR 0.021 0.002 TYR M 128 PHE 0.056 0.002 PHE S 68 TRP 0.015 0.001 TRP N 625 HIS 0.009 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00418 (14105) covalent geometry : angle 0.71913 (19085) SS BOND : bond 0.00062 ( 1) SS BOND : angle 1.70814 ( 2) hydrogen bonds : bond 0.04819 ( 1133) hydrogen bonds : angle 4.39838 ( 3375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 394 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 354 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8387 (m-10) REVERT: N 435 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6501 (mm) REVERT: N 528 MET cc_start: 0.8123 (mtm) cc_final: 0.7909 (mtt) REVERT: N 580 ASP cc_start: 0.8146 (t70) cc_final: 0.7768 (t0) REVERT: N 625 TRP cc_start: 0.8960 (m-10) cc_final: 0.8737 (m-90) REVERT: O 77 ASN cc_start: 0.8328 (t0) cc_final: 0.7850 (t0) REVERT: P 58 PHE cc_start: 0.9405 (m-80) cc_final: 0.9106 (m-80) REVERT: P 74 PHE cc_start: 0.8390 (m-10) cc_final: 0.7680 (t80) REVERT: Q 49 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6484 (mtp85) REVERT: R 10 LEU cc_start: 0.9010 (pp) cc_final: 0.8551 (pp) REVERT: R 21 LEU cc_start: 0.9239 (tt) cc_final: 0.8855 (tp) REVERT: R 34 GLN cc_start: 0.8440 (tt0) cc_final: 0.7998 (mt0) REVERT: R 51 ASN cc_start: 0.9034 (m-40) cc_final: 0.8723 (m110) REVERT: R 68 PHE cc_start: 0.8986 (m-80) cc_final: 0.8758 (m-10) REVERT: S 21 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (tp) REVERT: T 28 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8866 (pt) REVERT: U 56 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8422 (mm) REVERT: W 15 ILE cc_start: 0.9449 (mt) cc_final: 0.9134 (mm) REVERT: W 70 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9078 (mm) REVERT: Y 21 LEU cc_start: 0.9116 (tp) cc_final: 0.8861 (tp) REVERT: M 283 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8502 (p) REVERT: M 301 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7737 (mmm160) outliers start: 81 outliers final: 61 residues processed: 434 average time/residue: 0.1073 time to fit residues: 70.2668 Evaluate side-chains 440 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 621 ILE Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 97 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.089733 restraints weight = 33088.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092381 restraints weight = 19051.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094027 restraints weight = 12839.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095322 restraints weight = 9832.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096060 restraints weight = 8067.616| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14106 Z= 0.173 Angle : 0.739 10.810 19087 Z= 0.359 Chirality : 0.042 0.158 2254 Planarity : 0.005 0.059 2456 Dihedral : 5.286 49.647 2036 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.83 % Allowed : 29.67 % Favored : 64.50 % 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: 0.24 (0.20), residues: 1862 helix: 0.81 (0.13), residues: 1464 sheet: -3.21 (0.85), residues: 31 loop : -1.98 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 158 TYR 0.027 0.001 TYR M 191 PHE 0.078 0.002 PHE S 68 TRP 0.013 0.001 TRP N 625 HIS 0.009 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00402 (14105) covalent geometry : angle 0.73854 (19085) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.78564 ( 2) hydrogen bonds : bond 0.04805 ( 1133) hydrogen bonds : angle 4.37649 ( 3375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 354 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: N 435 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6510 (mm) REVERT: N 580 ASP cc_start: 0.8113 (t70) cc_final: 0.7740 (t0) REVERT: O 77 ASN cc_start: 0.8141 (t0) cc_final: 0.7681 (t0) REVERT: P 19 MET cc_start: 0.8692 (mtm) cc_final: 0.8437 (mtp) REVERT: P 58 PHE cc_start: 0.9392 (m-80) cc_final: 0.9079 (m-80) REVERT: P 74 PHE cc_start: 0.8293 (m-10) cc_final: 0.7628 (t80) REVERT: Q 49 ARG cc_start: 0.6724 (ttm110) cc_final: 0.6370 (mtp85) REVERT: R 10 LEU cc_start: 0.9043 (pp) cc_final: 0.8443 (pp) REVERT: R 14 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9143 (mp) REVERT: R 21 LEU cc_start: 0.9224 (tt) cc_final: 0.8648 (tp) REVERT: R 34 GLN cc_start: 0.8319 (tt0) cc_final: 0.8039 (mt0) REVERT: R 51 ASN cc_start: 0.8959 (m-40) cc_final: 0.8700 (m110) REVERT: R 68 PHE cc_start: 0.9004 (m-80) cc_final: 0.8766 (m-10) REVERT: S 21 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9000 (tp) REVERT: T 28 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8869 (pt) REVERT: T 45 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9090 (mp) REVERT: U 56 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8446 (mm) REVERT: W 15 ILE cc_start: 0.9469 (mt) cc_final: 0.9163 (mm) REVERT: M 226 ASP cc_start: 0.7006 (p0) cc_final: 0.6629 (p0) REVERT: M 301 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7742 (mmm160) outliers start: 78 outliers final: 57 residues processed: 428 average time/residue: 0.1096 time to fit residues: 71.0181 Evaluate side-chains 437 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 621 ILE Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.087020 restraints weight = 33491.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089559 restraints weight = 19696.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091109 restraints weight = 13546.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092342 restraints weight = 10600.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093065 restraints weight = 8857.591| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 14106 Z= 0.244 Angle : 0.782 10.854 19087 Z= 0.385 Chirality : 0.044 0.170 2254 Planarity : 0.005 0.062 2456 Dihedral : 5.359 51.911 2036 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.90 % Allowed : 30.34 % Favored : 63.75 % 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: 0.06 (0.19), residues: 1862 helix: 0.66 (0.13), residues: 1466 sheet: -3.24 (0.82), residues: 31 loop : -1.92 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 158 TYR 0.025 0.002 TYR M 191 PHE 0.071 0.002 PHE S 68 TRP 0.088 0.002 TRP N 625 HIS 0.007 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00569 (14105) covalent geometry : angle 0.78147 (19085) SS BOND : bond 0.00018 ( 1) SS BOND : angle 1.58251 ( 2) hydrogen bonds : bond 0.05043 ( 1133) hydrogen bonds : angle 4.53928 ( 3375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 354 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: N 435 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6373 (mm) REVERT: N 494 HIS cc_start: 0.8749 (OUTLIER) cc_final: 0.7788 (m170) REVERT: N 511 LEU cc_start: 0.9236 (tp) cc_final: 0.8990 (tt) REVERT: N 528 MET cc_start: 0.8249 (mtt) cc_final: 0.7966 (ttt) REVERT: N 580 ASP cc_start: 0.8152 (t70) cc_final: 0.7780 (t0) REVERT: O 77 ASN cc_start: 0.8138 (t0) cc_final: 0.7802 (t0) REVERT: P 58 PHE cc_start: 0.9398 (m-80) cc_final: 0.9094 (m-80) REVERT: P 74 PHE cc_start: 0.8261 (m-10) cc_final: 0.7634 (t80) REVERT: Q 49 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6421 (mtp85) REVERT: R 10 LEU cc_start: 0.9056 (pp) cc_final: 0.8483 (pp) REVERT: R 14 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9233 (mp) REVERT: R 21 LEU cc_start: 0.9382 (tt) cc_final: 0.8933 (tt) REVERT: R 34 GLN cc_start: 0.8343 (tt0) cc_final: 0.7976 (mt0) REVERT: R 51 ASN cc_start: 0.9005 (m-40) cc_final: 0.8699 (m110) REVERT: R 68 PHE cc_start: 0.8974 (m-80) cc_final: 0.8712 (m-10) REVERT: S 21 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8957 (tp) REVERT: S 61 LEU cc_start: 0.8789 (tt) cc_final: 0.8550 (tt) REVERT: T 28 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (pt) REVERT: U 56 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8519 (mm) REVERT: W 15 ILE cc_start: 0.9485 (mt) cc_final: 0.9184 (mm) REVERT: M 128 TYR cc_start: 0.8356 (t80) cc_final: 0.8137 (t80) REVERT: M 283 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8592 (p) REVERT: M 301 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7766 (mmm160) outliers start: 79 outliers final: 59 residues processed: 422 average time/residue: 0.1063 time to fit residues: 68.1786 Evaluate side-chains 427 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 360 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 149 GLU Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 494 HIS Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 135 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 51 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN Y 77 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091033 restraints weight = 33237.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.093764 restraints weight = 19290.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095556 restraints weight = 13106.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096636 restraints weight = 10064.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097520 restraints weight = 8453.314| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14106 Z= 0.162 Angle : 0.771 10.797 19087 Z= 0.369 Chirality : 0.043 0.166 2254 Planarity : 0.005 0.062 2456 Dihedral : 5.361 52.435 2036 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.08 % Allowed : 31.69 % Favored : 63.23 % 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: 0.29 (0.20), residues: 1862 helix: 0.83 (0.13), residues: 1466 sheet: -3.14 (0.86), residues: 31 loop : -1.89 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 158 TYR 0.022 0.001 TYR M 191 PHE 0.068 0.002 PHE S 68 TRP 0.065 0.002 TRP N 625 HIS 0.010 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00368 (14105) covalent geometry : angle 0.77060 (19085) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.63879 ( 2) hydrogen bonds : bond 0.04781 ( 1133) hydrogen bonds : angle 4.39867 ( 3375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 435 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6492 (mm) REVERT: N 476 PHE cc_start: 0.8583 (m-10) cc_final: 0.8373 (m-10) REVERT: N 580 ASP cc_start: 0.8133 (t70) cc_final: 0.7765 (t0) REVERT: O 77 ASN cc_start: 0.7846 (t0) cc_final: 0.7404 (t0) REVERT: P 19 MET cc_start: 0.7927 (mtp) cc_final: 0.7649 (ttm) REVERT: P 58 PHE cc_start: 0.9297 (m-80) cc_final: 0.8948 (m-80) REVERT: P 74 PHE cc_start: 0.8232 (m-10) cc_final: 0.7619 (t80) REVERT: Q 49 ARG cc_start: 0.6656 (ttm110) cc_final: 0.6431 (mtp85) REVERT: R 10 LEU cc_start: 0.8791 (pp) cc_final: 0.8202 (pp) REVERT: R 14 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9099 (mp) REVERT: R 21 LEU cc_start: 0.9380 (tt) cc_final: 0.8923 (tt) REVERT: R 34 GLN cc_start: 0.8237 (tt0) cc_final: 0.8033 (mt0) REVERT: R 51 ASN cc_start: 0.8952 (m-40) cc_final: 0.8680 (m110) REVERT: R 60 LEU cc_start: 0.9044 (mm) cc_final: 0.7948 (mm) REVERT: R 68 PHE cc_start: 0.8967 (m-80) cc_final: 0.8684 (m-10) REVERT: S 21 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8905 (tp) REVERT: T 28 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8886 (pt) REVERT: U 56 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8165 (mt) REVERT: V 68 PHE cc_start: 0.8156 (m-80) cc_final: 0.7751 (m-80) REVERT: W 15 ILE cc_start: 0.9455 (mt) cc_final: 0.9154 (mm) REVERT: M 226 ASP cc_start: 0.7019 (p0) cc_final: 0.6694 (p0) REVERT: M 301 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7677 (mmm160) outliers start: 68 outliers final: 56 residues processed: 439 average time/residue: 0.1071 time to fit residues: 70.9465 Evaluate side-chains 449 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 388 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 149 GLU Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 180 optimal weight: 50.0000 chunk 139 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 77 ASN Y 77 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092160 restraints weight = 33113.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094865 restraints weight = 19273.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096663 restraints weight = 13162.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097698 restraints weight = 10084.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098691 restraints weight = 8466.787| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14106 Z= 0.166 Angle : 0.785 11.667 19087 Z= 0.378 Chirality : 0.044 0.190 2254 Planarity : 0.005 0.063 2456 Dihedral : 5.363 53.169 2036 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.86 % Allowed : 32.44 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1862 helix: 0.77 (0.13), residues: 1466 sheet: -3.06 (0.88), residues: 31 loop : -1.93 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 158 TYR 0.035 0.001 TYR M 191 PHE 0.085 0.002 PHE S 68 TRP 0.061 0.002 TRP N 625 HIS 0.009 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00382 (14105) covalent geometry : angle 0.78490 (19085) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.65712 ( 2) hydrogen bonds : bond 0.04761 ( 1133) hydrogen bonds : angle 4.44341 ( 3375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 354 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: N 435 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6438 (mm) REVERT: N 580 ASP cc_start: 0.8127 (t70) cc_final: 0.7713 (t0) REVERT: O 77 ASN cc_start: 0.7883 (t0) cc_final: 0.7412 (t0) REVERT: P 51 ASN cc_start: 0.7916 (p0) cc_final: 0.7588 (p0) REVERT: P 58 PHE cc_start: 0.9272 (m-80) cc_final: 0.8929 (m-80) REVERT: P 74 PHE cc_start: 0.8173 (m-10) cc_final: 0.7551 (t80) REVERT: R 34 GLN cc_start: 0.8271 (tt0) cc_final: 0.8018 (mt0) REVERT: R 68 PHE cc_start: 0.8950 (m-80) cc_final: 0.8715 (m-10) REVERT: S 21 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9008 (tp) REVERT: T 28 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8887 (pt) REVERT: T 45 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9134 (mp) REVERT: U 56 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8157 (mt) REVERT: V 68 PHE cc_start: 0.8062 (m-80) cc_final: 0.7702 (m-80) REVERT: W 15 ILE cc_start: 0.9459 (mt) cc_final: 0.9134 (mm) REVERT: W 68 PHE cc_start: 0.8137 (m-10) cc_final: 0.7765 (m-80) REVERT: M 226 ASP cc_start: 0.6982 (p0) cc_final: 0.6670 (p0) REVERT: M 301 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7680 (mmm160) outliers start: 65 outliers final: 52 residues processed: 429 average time/residue: 0.1053 time to fit residues: 68.6042 Evaluate side-chains 437 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 379 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 149 GLU Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 77 ASN Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092834 restraints weight = 33270.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095516 restraints weight = 19405.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097162 restraints weight = 13235.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098478 restraints weight = 10227.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099025 restraints weight = 8459.415| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14106 Z= 0.165 Angle : 0.789 13.761 19087 Z= 0.379 Chirality : 0.044 0.396 2254 Planarity : 0.005 0.062 2456 Dihedral : 5.330 51.950 2036 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.93 % Allowed : 32.81 % Favored : 62.26 % 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: 0.25 (0.20), residues: 1862 helix: 0.80 (0.13), residues: 1469 sheet: -3.06 (0.88), residues: 31 loop : -1.94 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 158 TYR 0.035 0.002 TYR M 191 PHE 0.082 0.002 PHE S 68 TRP 0.059 0.002 TRP N 625 HIS 0.010 0.001 HIS N 65 Details of bonding type rmsd covalent geometry : bond 0.00378 (14105) covalent geometry : angle 0.78875 (19085) SS BOND : bond 0.00096 ( 1) SS BOND : angle 1.69045 ( 2) hydrogen bonds : bond 0.04737 ( 1133) hydrogen bonds : angle 4.45392 ( 3375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.02 seconds wall clock time: 41 minutes 59.25 seconds (2519.25 seconds total)