Starting phenix.real_space_refine on Thu Jul 31 15:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_30015.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_30015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_30015.map" model { file = "/net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_30015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ly9_30015/07_2025/6ly9_30015.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, '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: {'GLN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 9.79, per 1000 atoms: 0.70 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: 4.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.28 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: 4.40 Time building geometry restraints manager: 4.94 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: 0.700 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: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.450 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP N 545 HIS 0.007 0.001 HIS M 94 PHE 0.028 0.002 PHE N 427 TYR 0.014 0.002 TYR N 373 ARG 0.006 0.000 ARG N 622 Details of bonding type rmsd hydrogen bonds : bond 0.10166 ( 1133) hydrogen bonds : angle 5.43106 ( 3375) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.51947 ( 2) covalent geometry : bond 0.00584 (14105) covalent geometry : angle 0.74552 (19085) *********************** 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 : 1.565 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 155 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8151 (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: 0.9013 (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: 0.8167 (mtm-85) REVERT: P 21 LEU cc_start: 0.9294 (tp) cc_final: 0.8968 (tp) REVERT: P 74 PHE cc_start: 0.8350 (m-10) cc_final: 0.7816 (t80) REVERT: Q 19 MET cc_start: 0.8772 (mtm) cc_final: 0.8467 (mtm) REVERT: Q 65 LEU cc_start: 0.9448 (mm) cc_final: 0.9199 (mm) REVERT: R 60 LEU cc_start: 0.9257 (mt) cc_final: 0.8459 (mm) REVERT: R 63 GLU cc_start: 0.8591 (mp0) cc_final: 0.8306 (mp0) REVERT: R 68 PHE cc_start: 0.8926 (m-10) cc_final: 0.8586 (m-10) REVERT: S 34 GLN cc_start: 0.8469 (mt0) cc_final: 0.7915 (mt0) REVERT: S 52 PHE cc_start: 0.8254 (t80) cc_final: 0.7990 (t80) REVERT: T 32 VAL cc_start: 0.8831 (m) cc_final: 0.8609 (p) REVERT: U 30 THR cc_start: 0.9347 (t) cc_final: 0.9120 (t) REVERT: U 56 LEU cc_start: 0.9134 (mm) cc_final: 0.8754 (mm) REVERT: V 19 MET cc_start: 0.8548 (ptp) cc_final: 0.8341 (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: 0.9382 (mm) REVERT: W 61 LEU cc_start: 0.8405 (tp) cc_final: 0.8202 (tp) REVERT: X 11 ASP cc_start: 0.8347 (m-30) cc_final: 0.7879 (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: 0.8012 (mtp-110) REVERT: Y 47 GLU cc_start: 0.8472 (tp30) cc_final: 0.8046 (tp30) REVERT: Z 79 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8093 (tpt90) REVERT: M 23 SER cc_start: 0.9092 (p) cc_final: 0.8822 (p) REVERT: M 94 HIS cc_start: 0.8673 (t70) cc_final: 0.8341 (t-90) REVERT: M 128 TYR cc_start: 0.8592 (t80) cc_final: 0.8323 (t80) REVERT: M 301 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7792 (mmm160) outliers start: 14 outliers final: 10 residues processed: 467 average time/residue: 0.2673 time to fit residues: 181.2363 Evaluate side-chains 395 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 385 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.109170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089334 restraints weight = 33000.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091953 restraints weight = 19074.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093561 restraints weight = 12932.738| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14106 Z= 0.162 Angle : 0.703 10.636 19087 Z= 0.347 Chirality : 0.042 0.156 2254 Planarity : 0.005 0.049 2456 Dihedral : 5.908 52.800 2045 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.56 % Allowed : 20.33 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 1862 helix: -0.05 (0.13), residues: 1454 sheet: -3.75 (0.71), residues: 40 loop : -2.69 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 545 HIS 0.006 0.001 HIS N 169 PHE 0.029 0.002 PHE S 68 TYR 0.025 0.002 TYR M 191 ARG 0.007 0.001 ARG M 299 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 1133) hydrogen bonds : angle 4.48097 ( 3375) SS BOND : bond 0.00012 ( 1) SS BOND : angle 1.37451 ( 2) covalent geometry : bond 0.00354 (14105) covalent geometry : angle 0.70326 (19085) *********************** 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 508 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 447 time to evaluate : 1.656 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: N 150 LEU cc_start: 0.9058 (mp) cc_final: 0.8811 (mm) REVERT: N 164 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6504 (mmp80) REVERT: N 183 HIS cc_start: 0.7035 (t-90) cc_final: 0.6733 (t-90) REVERT: N 215 GLU cc_start: 0.7830 (tp30) cc_final: 0.7364 (tp30) REVERT: N 218 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7022 (ttp80) REVERT: N 435 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6461 (mm) REVERT: N 476 PHE cc_start: 0.8698 (m-10) cc_final: 0.8424 (m-80) REVERT: N 580 ASP cc_start: 0.8191 (t70) cc_final: 0.7822 (t0) REVERT: N 585 LEU cc_start: 0.8214 (tp) cc_final: 0.7991 (tp) REVERT: N 618 LEU cc_start: 0.9294 (tp) cc_final: 0.8974 (tp) REVERT: N 622 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8083 (ptt90) REVERT: O 77 ASN cc_start: 0.8511 (t0) cc_final: 0.7859 (t0) REVERT: P 12 ARG cc_start: 0.8252 (mtm180) cc_final: 0.8031 (mtm-85) REVERT: P 19 MET cc_start: 0.8697 (ttm) cc_final: 0.8373 (ttm) REVERT: P 21 LEU cc_start: 0.9153 (tp) cc_final: 0.8850 (tp) REVERT: P 48 ASP cc_start: 0.7091 (p0) cc_final: 0.6545 (p0) REVERT: P 74 PHE cc_start: 0.8256 (m-10) cc_final: 0.7691 (t80) REVERT: R 51 ASN cc_start: 0.9027 (m-40) cc_final: 0.8728 (m110) REVERT: R 60 LEU cc_start: 0.9142 (mt) cc_final: 0.8614 (mm) REVERT: R 61 LEU cc_start: 0.8712 (mm) cc_final: 0.8499 (mm) REVERT: R 68 PHE cc_start: 0.8920 (m-10) cc_final: 0.8641 (m-10) REVERT: U 30 THR cc_start: 0.9279 (t) cc_final: 0.9052 (t) REVERT: V 75 ILE cc_start: 0.9057 (mm) cc_final: 0.8857 (mm) REVERT: W 15 ILE cc_start: 0.9483 (mt) cc_final: 0.9228 (mm) REVERT: W 68 PHE cc_start: 0.8465 (m-10) cc_final: 0.7898 (m-80) REVERT: X 11 ASP cc_start: 0.8255 (m-30) cc_final: 0.8051 (m-30) REVERT: Z 51 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8082 (t0) REVERT: M 94 HIS cc_start: 0.8604 (t70) cc_final: 0.8384 (t-90) REVERT: M 132 ASP cc_start: 0.8155 (m-30) cc_final: 0.7899 (m-30) REVERT: M 283 VAL cc_start: 0.8717 (t) cc_final: 0.8384 (p) REVERT: M 301 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7680 (mmm160) outliers start: 61 outliers final: 34 residues processed: 469 average time/residue: 0.2762 time to fit residues: 191.4472 Evaluate side-chains 430 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 393 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 O residue 71 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 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 T residue 11 ASP Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 66 VAL 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 183 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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** V 51 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085074 restraints weight = 33292.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087655 restraints weight = 19256.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089233 restraints weight = 13080.249| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14106 Z= 0.214 Angle : 0.722 11.913 19087 Z= 0.359 Chirality : 0.042 0.176 2254 Planarity : 0.005 0.047 2456 Dihedral : 5.433 48.120 2038 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.05 % Allowed : 22.27 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1862 helix: 0.39 (0.13), residues: 1453 sheet: -3.37 (0.77), residues: 38 loop : -2.41 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 625 HIS 0.007 0.001 HIS N 97 PHE 0.050 0.002 PHE S 68 TYR 0.025 0.002 TYR M 191 ARG 0.008 0.001 ARG N 139 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 1133) hydrogen bonds : angle 4.50477 ( 3375) SS BOND : bond 0.00004 ( 1) SS BOND : angle 1.63635 ( 2) covalent geometry : bond 0.00492 (14105) covalent geometry : angle 0.72137 (19085) *********************** 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 481 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 400 time to evaluate : 1.523 Fit side-chains 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 6 GLU cc_start: 0.7840 (pt0) cc_final: 0.7361 (pt0) REVERT: N 215 GLU cc_start: 0.7889 (tp30) cc_final: 0.7377 (tp30) REVERT: N 218 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7605 (ttp80) REVERT: N 435 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6404 (mm) REVERT: N 580 ASP cc_start: 0.8146 (t70) cc_final: 0.7802 (t0) REVERT: N 618 LEU cc_start: 0.9377 (tp) cc_final: 0.9093 (tp) REVERT: O 11 ASP cc_start: 0.8161 (p0) cc_final: 0.7713 (p0) REVERT: O 77 ASN cc_start: 0.8245 (t0) cc_final: 0.7906 (t0) REVERT: P 12 ARG cc_start: 0.8399 (mtm180) cc_final: 0.7993 (mtm-85) REVERT: P 19 MET cc_start: 0.8848 (ttm) cc_final: 0.8577 (ttm) REVERT: P 74 PHE cc_start: 0.8355 (m-10) cc_final: 0.7717 (t80) REVERT: Q 19 MET cc_start: 0.8706 (mtm) cc_final: 0.8373 (mtm) REVERT: R 21 LEU cc_start: 0.9261 (tt) cc_final: 0.8940 (tt) REVERT: R 51 ASN cc_start: 0.9130 (m-40) cc_final: 0.8797 (m110) REVERT: R 65 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8609 (mt) REVERT: R 68 PHE cc_start: 0.8945 (m-10) cc_final: 0.8697 (m-10) REVERT: S 21 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9061 (tp) REVERT: T 28 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8859 (pt) REVERT: U 56 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8495 (mm) REVERT: U 59 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8361 (tt) REVERT: W 15 ILE cc_start: 0.9438 (mt) cc_final: 0.9156 (mm) REVERT: Y 12 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.8003 (mtm110) REVERT: Z 51 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7503 (t0) REVERT: M 94 HIS cc_start: 0.8756 (t70) cc_final: 0.8550 (t-90) REVERT: M 283 VAL cc_start: 0.8793 (t) cc_final: 0.8465 (p) REVERT: M 301 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7811 (mmm160) outliers start: 81 outliers final: 45 residues processed: 443 average time/residue: 0.2432 time to fit residues: 158.5697 Evaluate side-chains 429 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 308 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 573 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 56 LEU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain R residue 65 LEU 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 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 66 VAL 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 72 ILE 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 43 THR 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 219 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 61 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.3538 r_free = 0.3538 target = 0.108991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090061 restraints weight = 32740.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092703 restraints weight = 18512.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094310 restraints weight = 12349.969| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14106 Z= 0.162 Angle : 0.693 11.415 19087 Z= 0.341 Chirality : 0.041 0.187 2254 Planarity : 0.005 0.061 2456 Dihedral : 5.317 48.605 2036 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.13 % Allowed : 23.84 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1862 helix: 0.74 (0.13), residues: 1446 sheet: -3.33 (0.76), residues: 38 loop : -2.21 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.055 0.002 PHE S 68 TYR 0.030 0.002 TYR M 128 ARG 0.016 0.001 ARG N 622 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 1133) hydrogen bonds : angle 4.35140 ( 3375) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.78191 ( 2) covalent geometry : bond 0.00362 (14105) covalent geometry : angle 0.69251 (19085) *********************** 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 507 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 425 time to evaluate : 1.494 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 215 GLU cc_start: 0.7846 (tp30) cc_final: 0.7114 (tp30) REVERT: N 322 ASP cc_start: 0.7693 (p0) cc_final: 0.7491 (p0) REVERT: N 435 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6496 (mm) REVERT: N 472 VAL cc_start: 0.9273 (t) cc_final: 0.8882 (p) REVERT: N 476 PHE cc_start: 0.8636 (m-10) cc_final: 0.8357 (m-80) REVERT: N 580 ASP cc_start: 0.8152 (t70) cc_final: 0.7801 (t0) REVERT: N 618 LEU cc_start: 0.9379 (tp) cc_final: 0.9016 (tp) REVERT: O 77 ASN cc_start: 0.8241 (t0) cc_final: 0.7889 (t0) REVERT: P 12 ARG cc_start: 0.8382 (mtm180) cc_final: 0.8107 (mtm-85) REVERT: P 19 MET cc_start: 0.8801 (ttm) cc_final: 0.8466 (ttm) REVERT: P 74 PHE cc_start: 0.8286 (m-10) cc_final: 0.7690 (t80) REVERT: Q 19 MET cc_start: 0.8482 (mtm) cc_final: 0.7972 (mtm) REVERT: R 10 LEU cc_start: 0.9096 (pp) cc_final: 0.8638 (pp) REVERT: R 21 LEU cc_start: 0.9230 (tt) cc_final: 0.8875 (tp) REVERT: R 51 ASN cc_start: 0.9049 (m-40) cc_final: 0.8766 (m110) REVERT: R 68 PHE cc_start: 0.8875 (m-10) cc_final: 0.8635 (m-10) REVERT: S 21 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9054 (tp) REVERT: S 61 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8648 (tt) REVERT: T 28 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8860 (pt) REVERT: U 56 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8530 (mm) REVERT: W 15 ILE cc_start: 0.9409 (mt) cc_final: 0.9160 (mm) REVERT: Z 51 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7357 (t0) REVERT: M 94 HIS cc_start: 0.8675 (t70) cc_final: 0.8399 (t-90) REVERT: M 283 VAL cc_start: 0.8764 (t) cc_final: 0.8444 (p) REVERT: M 301 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7710 (mmm160) outliers start: 82 outliers final: 48 residues processed: 462 average time/residue: 0.2457 time to fit residues: 167.6582 Evaluate side-chains 434 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 380 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 407 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 30 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 71 LEU 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 56 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 66 VAL 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 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 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL 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 80 LEU Chi-restraints excluded: chain Y residue 72 ILE 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 54 LEU Chi-restraints excluded: chain M residue 71 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 135 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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** S 34 GLN ** 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 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 = 0.3568 r_free = 0.3568 target = 0.110901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090921 restraints weight = 33130.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093618 restraints weight = 19073.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095438 restraints weight = 12898.341| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14106 Z= 0.158 Angle : 0.712 11.480 19087 Z= 0.346 Chirality : 0.042 0.177 2254 Planarity : 0.005 0.047 2456 Dihedral : 5.310 48.767 2036 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.46 % Allowed : 27.73 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1862 helix: 0.87 (0.13), residues: 1446 sheet: -3.20 (0.87), residues: 31 loop : -2.19 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP N 625 HIS 0.010 0.001 HIS N 65 PHE 0.068 0.002 PHE S 68 TYR 0.023 0.001 TYR M 191 ARG 0.010 0.001 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 1133) hydrogen bonds : angle 4.34131 ( 3375) SS BOND : bond 0.00066 ( 1) SS BOND : angle 1.57164 ( 2) covalent geometry : bond 0.00352 (14105) covalent geometry : angle 0.71157 (19085) *********************** 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 484 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 411 time to evaluate : 1.550 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: N 150 LEU cc_start: 0.9103 (mp) cc_final: 0.8855 (mm) REVERT: N 243 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8104 (ptt90) REVERT: N 354 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: N 435 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6430 (mm) REVERT: N 560 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8422 (t) REVERT: N 563 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7221 (ptt-90) REVERT: N 580 ASP cc_start: 0.8164 (t70) cc_final: 0.7806 (t0) REVERT: N 618 LEU cc_start: 0.9339 (tp) cc_final: 0.9014 (tp) REVERT: O 77 ASN cc_start: 0.8206 (t0) cc_final: 0.7724 (t0) REVERT: P 12 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8102 (mtm-85) REVERT: P 74 PHE cc_start: 0.8284 (m-10) cc_final: 0.7687 (t80) REVERT: Q 34 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8740 (mm-40) REVERT: Q 65 LEU cc_start: 0.9099 (mp) cc_final: 0.8866 (mm) REVERT: R 10 LEU cc_start: 0.9097 (pp) cc_final: 0.8649 (pp) REVERT: R 21 LEU cc_start: 0.9199 (tt) cc_final: 0.8788 (tt) REVERT: R 34 GLN cc_start: 0.8314 (tt0) cc_final: 0.8040 (mt0) REVERT: R 51 ASN cc_start: 0.9003 (m-40) cc_final: 0.8771 (m110) REVERT: R 68 PHE cc_start: 0.8856 (m-10) cc_final: 0.8593 (m-10) REVERT: S 21 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9016 (tp) REVERT: S 61 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8528 (tt) REVERT: T 28 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8834 (pt) REVERT: U 56 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8392 (mm) REVERT: U 63 GLU cc_start: 0.9006 (mp0) cc_final: 0.8774 (mp0) REVERT: W 15 ILE cc_start: 0.9461 (mt) cc_final: 0.9152 (mm) REVERT: W 70 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9067 (mm) REVERT: X 79 ARG cc_start: 0.7172 (mpp80) cc_final: 0.6137 (tpm170) REVERT: Z 51 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7203 (t0) REVERT: M 131 GLN cc_start: 0.8027 (pt0) cc_final: 0.7822 (pm20) REVERT: M 301 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7647 (mmm160) outliers start: 73 outliers final: 45 residues processed: 443 average time/residue: 0.2452 time to fit residues: 161.5579 Evaluate side-chains 439 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 384 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG 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 463 LEU Chi-restraints excluded: chain N residue 497 GLU Chi-restraints excluded: chain N residue 560 SER Chi-restraints excluded: chain N residue 563 ARG 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 O residue 72 ILE Chi-restraints excluded: chain P residue 71 LEU 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 56 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 61 LEU 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 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL 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 70 LEU 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 72 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 312 HIS ** 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 = 0.3568 r_free = 0.3568 target = 0.110787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090592 restraints weight = 33601.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093296 restraints weight = 19422.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095119 restraints weight = 13217.668| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14106 Z= 0.167 Angle : 0.721 13.240 19087 Z= 0.349 Chirality : 0.042 0.259 2254 Planarity : 0.005 0.064 2456 Dihedral : 5.263 49.293 2036 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.83 % Allowed : 28.62 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1862 helix: 0.94 (0.13), residues: 1448 sheet: -3.15 (0.86), residues: 31 loop : -2.14 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.077 0.002 PHE S 68 TYR 0.021 0.002 TYR M 128 ARG 0.010 0.001 ARG N 158 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 1133) hydrogen bonds : angle 4.31741 ( 3375) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.63985 ( 2) covalent geometry : bond 0.00381 (14105) covalent geometry : angle 0.72109 (19085) *********************** 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 484 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 1.419 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 354 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: N 435 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6488 (mm) REVERT: N 560 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8394 (t) REVERT: N 563 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7340 (ptt-90) REVERT: N 580 ASP cc_start: 0.8167 (t70) cc_final: 0.7780 (t0) REVERT: N 618 LEU cc_start: 0.9382 (tp) cc_final: 0.9174 (tp) REVERT: O 77 ASN cc_start: 0.8119 (t0) cc_final: 0.7657 (t0) REVERT: P 12 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8083 (mtm-85) REVERT: P 19 MET cc_start: 0.8541 (ttm) cc_final: 0.8220 (ttm) REVERT: P 74 PHE cc_start: 0.8256 (m-10) cc_final: 0.7689 (t80) REVERT: R 10 LEU cc_start: 0.9004 (pp) cc_final: 0.8563 (pp) REVERT: R 21 LEU cc_start: 0.9219 (tt) cc_final: 0.8798 (tt) REVERT: R 34 GLN cc_start: 0.8324 (tt0) cc_final: 0.8102 (mt0) REVERT: R 51 ASN cc_start: 0.9004 (m-40) cc_final: 0.8724 (m110) REVERT: R 68 PHE cc_start: 0.8868 (m-10) cc_final: 0.8661 (m-10) REVERT: S 21 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8963 (tp) REVERT: S 61 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8636 (tt) REVERT: T 28 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8921 (pt) REVERT: U 56 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8495 (mm) REVERT: W 15 ILE cc_start: 0.9460 (mt) cc_final: 0.9156 (mm) REVERT: Y 21 LEU cc_start: 0.9117 (tp) cc_final: 0.8852 (tp) REVERT: Z 51 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7067 (t0) REVERT: M 301 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7780 (mmm160) outliers start: 78 outliers final: 53 residues processed: 446 average time/residue: 0.2411 time to fit residues: 160.5361 Evaluate side-chains 452 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 390 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 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 560 SER Chi-restraints excluded: chain N residue 563 ARG 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 O residue 72 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 61 LEU 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 72 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 ILE 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 67 ILE Chi-restraints excluded: chain Y residue 72 ILE Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 51 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 0.0010 chunk 69 optimal weight: 0.0970 chunk 144 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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** S 34 GLN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.112003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091891 restraints weight = 33244.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094559 restraints weight = 19235.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096350 restraints weight = 13062.969| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14106 Z= 0.155 Angle : 0.726 11.259 19087 Z= 0.351 Chirality : 0.042 0.320 2254 Planarity : 0.005 0.089 2456 Dihedral : 5.248 50.893 2036 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.83 % Allowed : 29.22 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1862 helix: 0.94 (0.13), residues: 1457 sheet: -3.15 (0.86), residues: 31 loop : -2.13 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.066 0.002 PHE S 68 TYR 0.024 0.001 TYR M 191 ARG 0.012 0.000 ARG N 158 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1133) hydrogen bonds : angle 4.28763 ( 3375) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.69504 ( 2) covalent geometry : bond 0.00349 (14105) covalent geometry : angle 0.72621 (19085) *********************** 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 485 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 407 time to evaluate : 1.499 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 155 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8180 (tm-30) REVERT: N 354 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8400 (m-10) REVERT: N 368 TYR cc_start: 0.8399 (m-10) cc_final: 0.8140 (m-80) REVERT: N 435 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6469 (mm) REVERT: N 470 PHE cc_start: 0.8204 (m-80) cc_final: 0.7880 (m-80) REVERT: N 560 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8340 (t) REVERT: N 563 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7201 (ptt-90) REVERT: N 580 ASP cc_start: 0.8150 (t70) cc_final: 0.7767 (t0) REVERT: N 643 ARG cc_start: 0.6963 (mmm160) cc_final: 0.6705 (mmp80) REVERT: O 77 ASN cc_start: 0.7901 (t0) cc_final: 0.7461 (t0) REVERT: P 19 MET cc_start: 0.8538 (ttm) cc_final: 0.8301 (ttm) REVERT: P 71 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8878 (tp) REVERT: P 74 PHE cc_start: 0.8277 (m-10) cc_final: 0.7631 (t80) REVERT: R 10 LEU cc_start: 0.9032 (pp) cc_final: 0.8453 (pp) REVERT: R 14 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9164 (mp) REVERT: R 21 LEU cc_start: 0.9213 (tt) cc_final: 0.8625 (tt) REVERT: R 65 LEU cc_start: 0.8537 (mt) cc_final: 0.7807 (mt) REVERT: S 21 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8928 (tp) REVERT: S 61 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8607 (tt) REVERT: T 28 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8869 (pt) REVERT: T 45 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9091 (mp) REVERT: U 56 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8508 (mm) REVERT: W 15 ILE cc_start: 0.9438 (mt) cc_final: 0.9143 (mm) REVERT: W 68 PHE cc_start: 0.8069 (m-10) cc_final: 0.7710 (m-80) REVERT: Z 17 VAL cc_start: 0.9053 (p) cc_final: 0.8851 (p) REVERT: M 226 ASP cc_start: 0.7065 (p0) cc_final: 0.6735 (p0) REVERT: M 301 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7768 (mmm160) outliers start: 78 outliers final: 51 residues processed: 445 average time/residue: 0.2322 time to fit residues: 155.8398 Evaluate side-chains 445 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 383 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 144 LEU 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 560 SER Chi-restraints excluded: chain N residue 563 ARG 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 O residue 72 ILE Chi-restraints excluded: chain P residue 71 LEU 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 56 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 61 LEU 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 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 ILE 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 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 40 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3593 r_free = 0.3593 target = 0.112583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092408 restraints weight = 33093.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095102 restraints weight = 19222.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096818 restraints weight = 13098.068| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14106 Z= 0.157 Angle : 0.747 11.186 19087 Z= 0.359 Chirality : 0.043 0.323 2254 Planarity : 0.005 0.057 2456 Dihedral : 5.221 51.964 2036 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.61 % Allowed : 30.72 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1862 helix: 0.94 (0.13), residues: 1457 sheet: -3.10 (0.88), residues: 31 loop : -2.10 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.080 0.002 PHE S 68 TYR 0.021 0.001 TYR M 191 ARG 0.013 0.001 ARG N 158 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1133) hydrogen bonds : angle 4.29775 ( 3375) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.74646 ( 2) covalent geometry : bond 0.00356 (14105) covalent geometry : angle 0.74663 (19085) *********************** 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 476 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 401 time to evaluate : 1.577 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 X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 155 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8196 (tm-30) REVERT: N 354 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: N 368 TYR cc_start: 0.8366 (m-10) cc_final: 0.8082 (m-80) REVERT: N 435 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6483 (mm) REVERT: N 470 PHE cc_start: 0.8122 (m-80) cc_final: 0.7821 (m-80) REVERT: N 560 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8974 (t) REVERT: N 580 ASP cc_start: 0.8159 (t70) cc_final: 0.7788 (t0) REVERT: O 77 ASN cc_start: 0.7874 (t0) cc_final: 0.7403 (t0) REVERT: P 19 MET cc_start: 0.8487 (ttm) cc_final: 0.8244 (ttm) REVERT: P 74 PHE cc_start: 0.8277 (m-10) cc_final: 0.7529 (t80) REVERT: R 10 LEU cc_start: 0.8929 (pp) cc_final: 0.8360 (pp) REVERT: R 14 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9148 (mp) REVERT: R 21 LEU cc_start: 0.9317 (tt) cc_final: 0.8877 (tt) REVERT: R 68 PHE cc_start: 0.8745 (m-80) cc_final: 0.8318 (m-80) REVERT: S 21 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8911 (tp) REVERT: S 61 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8546 (tt) REVERT: T 28 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8916 (pt) REVERT: T 45 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9085 (mp) REVERT: U 56 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8496 (mm) REVERT: V 68 PHE cc_start: 0.8203 (m-80) cc_final: 0.7847 (m-80) REVERT: W 15 ILE cc_start: 0.9429 (mt) cc_final: 0.9106 (mm) REVERT: W 65 LEU cc_start: 0.8880 (mp) cc_final: 0.8427 (mt) REVERT: W 68 PHE cc_start: 0.8046 (m-10) cc_final: 0.7687 (m-80) REVERT: Z 17 VAL cc_start: 0.9059 (p) cc_final: 0.8836 (p) REVERT: M 226 ASP cc_start: 0.7007 (p0) cc_final: 0.6679 (p0) REVERT: M 301 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7782 (mmm160) outliers start: 75 outliers final: 55 residues processed: 439 average time/residue: 0.2308 time to fit residues: 151.9551 Evaluate side-chains 445 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 144 LEU 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 560 SER 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 O residue 72 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 66 VAL 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 56 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 61 LEU 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 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 ILE 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 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 40 LEU Chi-restraints excluded: chain M residue 112 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 S 34 GLN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3609 r_free = 0.3609 target = 0.113463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093488 restraints weight = 33021.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096150 restraints weight = 19338.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097952 restraints weight = 13192.398| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3441 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= 0.157 Angle : 0.772 11.267 19087 Z= 0.365 Chirality : 0.045 0.439 2254 Planarity : 0.005 0.057 2456 Dihedral : 5.187 53.285 2036 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.31 % Allowed : 31.54 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1862 helix: 0.91 (0.13), residues: 1470 sheet: -3.04 (0.89), residues: 31 loop : -1.93 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.077 0.002 PHE S 68 TYR 0.024 0.001 TYR M 191 ARG 0.014 0.001 ARG N 158 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 1133) hydrogen bonds : angle 4.26956 ( 3375) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.76252 ( 2) covalent geometry : bond 0.00354 (14105) covalent geometry : angle 0.77144 (19085) *********************** 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 479 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 408 time to evaluate : 1.601 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 155 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8194 (tm-30) REVERT: N 354 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8302 (m-10) REVERT: N 368 TYR cc_start: 0.8351 (m-10) cc_final: 0.7947 (m-80) REVERT: N 435 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6453 (mm) REVERT: N 470 PHE cc_start: 0.8072 (m-80) cc_final: 0.7787 (m-80) REVERT: N 580 ASP cc_start: 0.8191 (t70) cc_final: 0.7759 (t0) REVERT: N 627 GLU cc_start: 0.7308 (mp0) cc_final: 0.7095 (mp0) REVERT: O 77 ASN cc_start: 0.7863 (t0) cc_final: 0.7387 (t0) REVERT: P 19 MET cc_start: 0.8445 (ttm) cc_final: 0.8165 (ttm) REVERT: P 28 LEU cc_start: 0.9113 (tp) cc_final: 0.8884 (tt) REVERT: P 74 PHE cc_start: 0.8230 (m-10) cc_final: 0.7525 (t80) REVERT: R 10 LEU cc_start: 0.8928 (pp) cc_final: 0.8200 (pp) REVERT: R 14 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9023 (mp) REVERT: R 15 ILE cc_start: 0.9590 (mt) cc_final: 0.9316 (mt) REVERT: R 19 MET cc_start: 0.8460 (mtt) cc_final: 0.8093 (mmm) REVERT: R 21 LEU cc_start: 0.9261 (tt) cc_final: 0.8761 (tt) REVERT: R 65 LEU cc_start: 0.8499 (mt) cc_final: 0.8150 (mt) REVERT: R 68 PHE cc_start: 0.8829 (m-80) cc_final: 0.8462 (m-80) REVERT: S 21 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8902 (tp) REVERT: T 28 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8923 (pt) REVERT: T 45 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9074 (mp) REVERT: U 56 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8445 (mm) REVERT: W 15 ILE cc_start: 0.9420 (mt) cc_final: 0.9101 (mm) REVERT: W 68 PHE cc_start: 0.8054 (m-10) cc_final: 0.7694 (m-80) REVERT: W 79 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.6971 (mmm-85) REVERT: Z 17 VAL cc_start: 0.9048 (p) cc_final: 0.8806 (p) REVERT: M 226 ASP cc_start: 0.6926 (p0) cc_final: 0.6625 (p0) REVERT: M 301 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7647 (mmm160) outliers start: 71 outliers final: 51 residues processed: 444 average time/residue: 0.2354 time to fit residues: 156.3534 Evaluate side-chains 445 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 149 GLU 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 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 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 61 LEU Chi-restraints excluded: chain S residue 21 LEU 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 80 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 ILE 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 Y residue 67 ILE Chi-restraints excluded: chain Y residue 71 LEU 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 40 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 112 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 143 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN ** T 51 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 = 0.3631 r_free = 0.3631 target = 0.114793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094890 restraints weight = 32891.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097615 restraints weight = 19179.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099314 restraints weight = 13043.759| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14106 Z= 0.156 Angle : 0.782 11.031 19087 Z= 0.372 Chirality : 0.044 0.381 2254 Planarity : 0.005 0.060 2456 Dihedral : 5.240 55.291 2036 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.26 % Allowed : 32.66 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1862 helix: 0.92 (0.13), residues: 1470 sheet: -2.96 (0.93), residues: 31 loop : -1.92 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.074 0.002 PHE S 68 TYR 0.030 0.001 TYR M 191 ARG 0.016 0.001 ARG Q 49 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1133) hydrogen bonds : angle 4.28626 ( 3375) SS BOND : bond 0.00117 ( 1) SS BOND : angle 1.80985 ( 2) covalent geometry : bond 0.00353 (14105) covalent geometry : angle 0.78167 (19085) ********************** 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 466 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 409 time to evaluate : 1.434 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 Y 80 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 155 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8205 (tm-30) REVERT: N 354 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: N 435 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6402 (mm) REVERT: N 470 PHE cc_start: 0.8032 (m-80) cc_final: 0.7813 (m-80) REVERT: N 580 ASP cc_start: 0.8193 (t70) cc_final: 0.7766 (t0) REVERT: O 77 ASN cc_start: 0.7863 (t0) cc_final: 0.7399 (t0) REVERT: P 19 MET cc_start: 0.8405 (ttm) cc_final: 0.8056 (ttm) REVERT: P 74 PHE cc_start: 0.8199 (m-10) cc_final: 0.7474 (t80) REVERT: R 10 LEU cc_start: 0.8912 (pp) cc_final: 0.8203 (pp) REVERT: R 14 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9065 (mp) REVERT: R 21 LEU cc_start: 0.9259 (tt) cc_final: 0.8817 (tt) REVERT: R 65 LEU cc_start: 0.8538 (mt) cc_final: 0.8183 (mt) REVERT: R 68 PHE cc_start: 0.8818 (m-80) cc_final: 0.8511 (m-80) REVERT: S 21 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8913 (tp) REVERT: T 28 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8885 (pt) REVERT: T 45 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9042 (mp) REVERT: U 56 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (mm) REVERT: V 14 LEU cc_start: 0.8562 (mm) cc_final: 0.8348 (mm) REVERT: W 15 ILE cc_start: 0.9411 (mt) cc_final: 0.9067 (mm) REVERT: W 68 PHE cc_start: 0.8003 (m-10) cc_final: 0.7759 (m-80) REVERT: W 79 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.7082 (mmm-85) REVERT: X 79 ARG cc_start: 0.6788 (mpp80) cc_final: 0.5818 (tpm170) REVERT: Z 17 VAL cc_start: 0.9094 (p) cc_final: 0.8849 (p) REVERT: M 35 ASP cc_start: 0.7862 (p0) cc_final: 0.7485 (p0) REVERT: M 88 LEU cc_start: 0.9209 (mt) cc_final: 0.8848 (mm) REVERT: M 226 ASP cc_start: 0.6862 (p0) cc_final: 0.6565 (p0) REVERT: M 301 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7588 (mmm160) outliers start: 57 outliers final: 47 residues processed: 438 average time/residue: 0.2361 time to fit residues: 153.3580 Evaluate side-chains 443 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 149 GLU Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 282 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 497 GLU 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 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 61 LEU Chi-restraints excluded: chain S residue 21 LEU 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 80 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 ILE 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 Y residue 67 ILE Chi-restraints excluded: chain Y residue 71 LEU 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 112 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 172 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 156 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- 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** S 34 GLN S 77 ASN ** T 51 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 = 0.3592 r_free = 0.3592 target = 0.112146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092129 restraints weight = 33379.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094780 restraints weight = 19524.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096415 restraints weight = 13374.587| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14106 Z= 0.185 Angle : 0.798 12.071 19087 Z= 0.382 Chirality : 0.045 0.377 2254 Planarity : 0.005 0.061 2456 Dihedral : 5.235 55.584 2036 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.86 % Allowed : 32.74 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1862 helix: 0.92 (0.13), residues: 1466 sheet: -2.97 (0.92), residues: 31 loop : -1.83 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.074 0.002 PHE S 68 TYR 0.034 0.002 TYR M 191 ARG 0.014 0.001 ARG N 158 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 1133) hydrogen bonds : angle 4.35289 ( 3375) SS BOND : bond 0.00064 ( 1) SS BOND : angle 1.79594 ( 2) covalent geometry : bond 0.00436 (14105) covalent geometry : angle 0.79774 (19085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.45 seconds wall clock time: 84 minutes 25.58 seconds (5065.58 seconds total)