Starting phenix.real_space_refine on Fri Jul 3 12:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.map" model { file = "/net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yts_73493/07_2026/9yts_73493.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 64 5.16 5 C 8699 2.51 5 N 2343 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3436 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "F" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 405} Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 879 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "G" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 879 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.36, per 1000 atoms: 0.24 Number of scatterers: 13811 At special positions: 0 Unit cell: (119.68, 168.08, 90.64, 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 64 16.00 O 2705 8.00 N 2343 7.00 C 8699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 431 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 116 " - pdb=" SG CYS F 129 " distance=2.03 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 215 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 323 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 395 " - pdb=" SG CYS F 404 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG L 1 " - " FUC L 2 " NAG-ASN " NAG L 1 " - " ASN A 389 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 608.6 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 43 sheets defined 5.5% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.511A pdb=" N CYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 6.934A pdb=" N TRP A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 238 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 219 through 227 removed outlier: 3.511A pdb=" N CYS F 223 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 6.914A pdb=" N TRP F 231 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE F 232 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.938A pdb=" N PHE E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.950A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.700A pdb=" N SER C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.935A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.595A pdb=" N LYS A 15 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 394 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN A 417 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR A 396 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.538A pdb=" N SER A 436 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 64 removed outlier: 6.588A pdb=" N THR A 72 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A 62 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 70 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 56 through 64 removed outlier: 6.588A pdb=" N THR A 72 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A 62 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 70 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 69 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 93 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 92 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.525A pdb=" N SER A 166 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 281 removed outlier: 3.649A pdb=" N LEU A 281 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 285 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AB3, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.583A pdb=" N ALA F 388 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN F 411 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR F 390 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 417 " --> pdb=" O HIS F 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.539A pdb=" N SER F 430 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 50 through 58 removed outlier: 6.609A pdb=" N THR F 66 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU F 56 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 64 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 50 through 58 removed outlier: 6.609A pdb=" N THR F 66 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU F 56 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 64 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR F 63 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 87 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE F 86 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AB8, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.792A pdb=" N LYS F 255 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 242 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.792A pdb=" N LYS F 255 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 242 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 270 through 274 Processing sheet with id=AC2, first strand: chain 'F' and resid 296 through 298 Processing sheet with id=AC3, first strand: chain 'F' and resid 341 through 343 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.929A pdb=" N PHE D 80 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AC6, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.601A pdb=" N ILE D 50 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TRP D 38 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP D 52 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP D 36 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE D 54 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 34 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.514A pdb=" N ALA E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 75 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.003A pdb=" N LEU E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.365A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.911A pdb=" N PHE I 80 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AD3, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.435A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR I 112 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.435A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.580A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.030A pdb=" N LEU J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG J 45 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.771A pdb=" N ARG C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 71 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.659A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR C 117 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AE1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.522A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.694A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.568A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER G 71 " --> pdb=" O ASP G 80 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE G 69 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 34 through 36 Processing sheet with id=AE5, first strand: chain 'G' and resid 92 through 94 removed outlier: 3.575A pdb=" N ALA G 92 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR G 114 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.825A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 12 through 13 449 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.51 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: 4438 1.34 - 1.46: 3268 1.46 - 1.58: 6340 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 14130 Sorted by residual: bond pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.80e+00 bond pdb=" C THR F 29 " pdb=" N PRO F 30 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" C LYS H 39 " pdb=" N PRO H 40 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.22e+00 bond pdb=" C SER H 7 " pdb=" N PRO H 8 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" CB GLN G 112 " pdb=" CG GLN G 112 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 14125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 18721 1.55 - 3.10: 421 3.10 - 4.65: 68 4.65 - 6.20: 20 6.20 - 7.75: 4 Bond angle restraints: 19234 Sorted by residual: angle pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " pdb=" CG TYR G 32 " ideal model delta sigma weight residual 113.90 106.15 7.75 1.80e+00 3.09e-01 1.85e+01 angle pdb=" N LEU H 47 " pdb=" CA LEU H 47 " pdb=" C LEU H 47 " ideal model delta sigma weight residual 111.17 116.31 -5.14 1.41e+00 5.03e-01 1.33e+01 angle pdb=" C GLY G 26 " pdb=" N PHE G 27 " pdb=" CA PHE G 27 " ideal model delta sigma weight residual 121.58 126.88 -5.30 1.62e+00 3.81e-01 1.07e+01 angle pdb=" CA PRO H 8 " pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 112.00 107.59 4.41 1.40e+00 5.10e-01 9.94e+00 angle pdb=" CA LEU H 47 " pdb=" C LEU H 47 " pdb=" N ILE H 48 " ideal model delta sigma weight residual 114.81 119.03 -4.22 1.42e+00 4.96e-01 8.83e+00 ... (remaining 19229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7232 17.33 - 34.66: 968 34.66 - 51.98: 247 51.98 - 69.31: 60 69.31 - 86.64: 7 Dihedral angle restraints: 8514 sinusoidal: 3390 harmonic: 5124 Sorted by residual: dihedral pdb=" CA THR A 35 " pdb=" C THR A 35 " pdb=" N PRO A 36 " pdb=" CA PRO A 36 " ideal model delta harmonic sigma weight residual 180.00 127.37 52.63 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA THR F 29 " pdb=" C THR F 29 " pdb=" N PRO F 30 " pdb=" CA PRO F 30 " ideal model delta harmonic sigma weight residual -180.00 -139.37 -40.63 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CA PRO H 40 " pdb=" C PRO H 40 " pdb=" N GLY H 41 " pdb=" CA GLY H 41 " ideal model delta harmonic sigma weight residual -180.00 -144.73 -35.27 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 8511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1655 0.042 - 0.084: 325 0.084 - 0.127: 179 0.127 - 0.169: 13 0.169 - 0.211: 4 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB ILE H 48 " pdb=" CA ILE H 48 " pdb=" CG1 ILE H 48 " pdb=" CG2 ILE H 48 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO H 8 " pdb=" N PRO H 8 " pdb=" C PRO H 8 " pdb=" CB PRO H 8 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 2173 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 39 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO H 40 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO H 8 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 29 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO F 30 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 30 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 30 " 0.035 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6695 2.98 - 3.46: 12319 3.46 - 3.94: 21197 3.94 - 4.42: 23597 4.42 - 4.90: 42539 Nonbonded interactions: 106347 Sorted by model distance: nonbonded pdb=" N GLN G 112 " pdb=" OE1 GLN G 112 " model vdw 2.498 3.120 nonbonded pdb=" O LYS H 39 " pdb=" O PRO H 40 " model vdw 2.540 3.040 nonbonded pdb=" N GLN D 115 " pdb=" OE1 GLN D 115 " model vdw 2.562 3.120 nonbonded pdb=" N GLY G 100 " pdb=" N ALA G 101 " model vdw 2.567 2.560 nonbonded pdb=" N PRO A 36 " pdb=" O PRO A 36 " model vdw 2.580 2.496 ... (remaining 106342 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 'A' and resid 7 through 438) selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.084 14157 Z= 0.126 Angle : 0.588 7.746 19290 Z= 0.308 Chirality : 0.044 0.211 2176 Planarity : 0.005 0.120 2451 Dihedral : 16.444 86.641 5184 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.73 % Favored : 90.82 % Rotamer: Outliers : 3.94 % Allowed : 25.78 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1764 helix: -0.21 (0.93), residues: 32 sheet: -0.51 (0.21), residues: 665 loop : -1.68 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 18 TYR 0.031 0.001 TYR G 32 PHE 0.018 0.001 PHE H 71 TRP 0.016 0.001 TRP D 102 HIS 0.003 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14130) covalent geometry : angle 0.58522 / 0.31 (19234) SS BOND : bond 0.00178 / 0.12 ( 22) SS BOND : angle 0.65550 / 0.47 ( 44) hydrogen bonds : bond 0.26715 / 17.57 ( 405) hydrogen bonds : angle 10.39892 / 7.16 ( 1080) Misc. bond : bond 0.00209 / 0.11 ( 1) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 0.90870 / 0.50 ( 3) link_BETA1-6 : bond 0.00387 / 0.19 ( 2) link_BETA1-6 : angle 1.37334 / 0.90 ( 6) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 3.80653 / 1.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7043 (pttp) REVERT: A 81 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: A 128 ASN cc_start: 0.7330 (m-40) cc_final: 0.7087 (m-40) REVERT: A 243 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: A 427 MET cc_start: 0.7486 (mtt) cc_final: 0.6959 (mmm) REVERT: F 72 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7595 (mtt90) REVERT: F 122 ASN cc_start: 0.7320 (m-40) cc_final: 0.7020 (m-40) REVERT: F 200 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7804 (tt) REVERT: F 421 MET cc_start: 0.7514 (mtt) cc_final: 0.6858 (mmm) REVERT: D 103 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 79 GLU cc_start: 0.5445 (mp0) cc_final: 0.5234 (mp0) REVERT: I 115 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: J 97 THR cc_start: 0.9241 (m) cc_final: 0.8930 (p) REVERT: B 7 SER cc_start: 0.8317 (t) cc_final: 0.7868 (p) REVERT: B 82 ASP cc_start: 0.6701 (m-30) cc_final: 0.6256 (t70) REVERT: G 56 GLU cc_start: 0.2349 (OUTLIER) cc_final: 0.1556 (pt0) REVERT: G 90 ASP cc_start: 0.6774 (m-30) cc_final: 0.6453 (t70) REVERT: G 107 MET cc_start: 0.4726 (tmm) cc_final: 0.3669 (mmt) REVERT: H 19 VAL cc_start: 0.5954 (OUTLIER) cc_final: 0.5691 (p) REVERT: H 49 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6321 (t80) REVERT: H 90 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.5371 (mp10) outliers start: 61 outliers final: 47 residues processed: 202 average time/residue: 0.1204 time to fit residues: 36.0916 Evaluate side-chains 211 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN H 24 GLN ** H 89 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 = 0.4203 r_free = 0.4203 target = 0.193073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149654 restraints weight = 16079.331| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.25 r_work: 0.3648 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14157 Z= 0.112 Angle : 0.587 7.410 19290 Z= 0.307 Chirality : 0.045 0.208 2176 Planarity : 0.005 0.122 2451 Dihedral : 8.186 71.188 2144 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.28 % Favored : 91.27 % Rotamer: Outliers : 4.46 % Allowed : 25.19 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.20), residues: 1764 helix: 0.40 (0.93), residues: 32 sheet: -0.50 (0.20), residues: 715 loop : -1.48 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 18 TYR 0.031 0.001 TYR G 32 PHE 0.011 0.001 PHE D 80 TRP 0.011 0.001 TRP D 102 HIS 0.004 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14130) covalent geometry : angle 0.58441 / 0.31 (19234) SS BOND : bond 0.00320 / 0.25 ( 22) SS BOND : angle 0.77095 / 0.55 ( 44) hydrogen bonds : bond 0.04212 / 2.72 ( 405) hydrogen bonds : angle 7.02420 / 4.84 ( 1080) Misc. bond : bond 0.00133 / 0.07 ( 1) link_BETA1-4 : bond 0.00287 / 0.15 ( 1) link_BETA1-4 : angle 0.79797 / 0.43 ( 3) link_BETA1-6 : bond 0.00287 / 0.14 ( 2) link_BETA1-6 : angle 1.39378 / 0.92 ( 6) link_NAG-ASN : bond 0.00121 / 0.06 ( 1) link_NAG-ASN : angle 3.88906 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7826 (mm) cc_final: 0.7517 (mt) REVERT: A 41 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6745 (mmp) REVERT: A 128 ASN cc_start: 0.7324 (m-40) cc_final: 0.7092 (m-40) REVERT: A 419 LYS cc_start: 0.7426 (tttt) cc_final: 0.6795 (tppt) REVERT: A 427 MET cc_start: 0.7409 (mtt) cc_final: 0.6858 (mmm) REVERT: F 72 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7593 (mtt90) REVERT: F 122 ASN cc_start: 0.7288 (m-40) cc_final: 0.6988 (m-40) REVERT: F 124 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6945 (t0) REVERT: F 421 MET cc_start: 0.7337 (mtt) cc_final: 0.6759 (mmm) REVERT: D 103 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7897 (mt-10) REVERT: D 106 TYR cc_start: 0.7003 (m-80) cc_final: 0.6741 (m-80) REVERT: D 111 ASP cc_start: 0.7277 (t0) cc_final: 0.7061 (t0) REVERT: I 11 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7328 (mt) REVERT: I 115 GLN cc_start: 0.8473 (mp10) cc_final: 0.8120 (mp10) REVERT: J 78 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.2906 (tt) REVERT: J 97 THR cc_start: 0.9246 (m) cc_final: 0.8974 (p) REVERT: C 67 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6014 (ptm-80) REVERT: B 82 ASP cc_start: 0.6536 (m-30) cc_final: 0.6148 (t70) REVERT: G 25 SER cc_start: 0.7810 (t) cc_final: 0.7493 (m) REVERT: G 56 GLU cc_start: 0.2421 (OUTLIER) cc_final: 0.1646 (pt0) REVERT: G 107 MET cc_start: 0.4900 (tmm) cc_final: 0.3981 (mmt) REVERT: H 5 THR cc_start: 0.7798 (t) cc_final: 0.7168 (m) REVERT: H 49 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6350 (t80) outliers start: 69 outliers final: 39 residues processed: 215 average time/residue: 0.1193 time to fit residues: 38.0948 Evaluate side-chains 192 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 92 optimal weight: 0.2980 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN B 53 ASN B 90 GLN ** H 89 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 = 0.4194 r_free = 0.4194 target = 0.191980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148313 restraints weight = 16265.643| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.20 r_work: 0.3632 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14157 Z= 0.132 Angle : 0.600 8.374 19290 Z= 0.311 Chirality : 0.045 0.235 2176 Planarity : 0.005 0.122 2451 Dihedral : 6.785 58.602 2081 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.01 % Favored : 90.53 % Rotamer: Outliers : 6.59 % Allowed : 23.77 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.20), residues: 1764 helix: 0.66 (0.94), residues: 32 sheet: -0.41 (0.20), residues: 704 loop : -1.57 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 18 TYR 0.038 0.002 TYR G 32 PHE 0.011 0.001 PHE D 80 TRP 0.011 0.001 TRP D 102 HIS 0.005 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (14130) covalent geometry : angle 0.59695 / 0.31 (19234) SS BOND : bond 0.00298 / 0.22 ( 22) SS BOND : angle 0.78116 / 0.58 ( 44) hydrogen bonds : bond 0.03784 / 2.48 ( 405) hydrogen bonds : angle 6.38575 / 4.39 ( 1080) Misc. bond : bond 0.00143 / 0.08 ( 1) link_BETA1-4 : bond 0.00400 / 0.21 ( 1) link_BETA1-4 : angle 0.86086 / 0.47 ( 3) link_BETA1-6 : bond 0.00391 / 0.19 ( 2) link_BETA1-6 : angle 1.37649 / 0.89 ( 6) link_NAG-ASN : bond 0.00231 / 0.12 ( 1) link_NAG-ASN : angle 3.72175 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 156 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7817 (mm) cc_final: 0.7545 (mt) REVERT: A 41 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6723 (mmp) REVERT: A 128 ASN cc_start: 0.7328 (m-40) cc_final: 0.7103 (m-40) REVERT: A 419 LYS cc_start: 0.7445 (tttt) cc_final: 0.6800 (tppt) REVERT: A 427 MET cc_start: 0.7278 (mtt) cc_final: 0.6801 (mmm) REVERT: F 35 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6823 (mmp) REVERT: F 72 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7576 (mtt90) REVERT: F 122 ASN cc_start: 0.7328 (m-40) cc_final: 0.7047 (m-40) REVERT: F 200 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (tt) REVERT: F 237 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: F 421 MET cc_start: 0.7306 (mtt) cc_final: 0.6717 (mmm) REVERT: D 84 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4829 (tt) REVERT: D 103 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7849 (mt-10) REVERT: I 115 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: J 78 LEU cc_start: 0.3442 (OUTLIER) cc_final: 0.2885 (tt) REVERT: J 97 THR cc_start: 0.9241 (m) cc_final: 0.8925 (p) REVERT: C 67 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.6018 (ptm-80) REVERT: C 95 TYR cc_start: 0.7530 (m-80) cc_final: 0.7241 (m-80) REVERT: B 82 ASP cc_start: 0.6525 (m-30) cc_final: 0.6156 (t70) REVERT: B 90 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (pp30) REVERT: G 25 SER cc_start: 0.8017 (t) cc_final: 0.7608 (m) REVERT: G 34 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7781 (ttt) REVERT: G 56 GLU cc_start: 0.2407 (OUTLIER) cc_final: 0.1653 (pt0) REVERT: G 107 MET cc_start: 0.4796 (tmm) cc_final: 0.3928 (mmt) REVERT: H 5 THR cc_start: 0.7695 (t) cc_final: 0.7235 (m) REVERT: H 49 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6452 (t80) outliers start: 102 outliers final: 62 residues processed: 231 average time/residue: 0.1135 time to fit residues: 39.3981 Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 148 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 173 optimal weight: 0.0270 chunk 169 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.192765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149531 restraints weight = 16148.447| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.98 r_work: 0.3644 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14157 Z= 0.107 Angle : 0.574 7.968 19290 Z= 0.297 Chirality : 0.044 0.232 2176 Planarity : 0.005 0.120 2451 Dihedral : 6.589 59.709 2077 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.67 % Favored : 90.87 % Rotamer: Outliers : 5.10 % Allowed : 25.19 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1764 helix: 0.86 (0.96), residues: 32 sheet: -0.34 (0.20), residues: 710 loop : -1.47 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 18 TYR 0.031 0.001 TYR G 32 PHE 0.009 0.001 PHE D 80 TRP 0.012 0.001 TRP D 102 HIS 0.004 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14130) covalent geometry : angle 0.57000 / 0.30 (19234) SS BOND : bond 0.00257 / 0.18 ( 22) SS BOND : angle 0.91527 / 0.70 ( 44) hydrogen bonds : bond 0.03275 / 2.15 ( 405) hydrogen bonds : angle 5.97669 / 4.10 ( 1080) Misc. bond : bond 0.00121 / 0.06 ( 1) link_BETA1-4 : bond 0.00392 / 0.21 ( 1) link_BETA1-4 : angle 0.80203 / 0.43 ( 3) link_BETA1-6 : bond 0.00360 / 0.17 ( 2) link_BETA1-6 : angle 1.38704 / 0.93 ( 6) link_NAG-ASN : bond 0.00127 / 0.07 ( 1) link_NAG-ASN : angle 3.90549 / 2.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 151 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7877 (mm) cc_final: 0.7619 (mt) REVERT: A 41 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6704 (mmp) REVERT: A 128 ASN cc_start: 0.7331 (m-40) cc_final: 0.7122 (m-40) REVERT: A 419 LYS cc_start: 0.7380 (tttt) cc_final: 0.6819 (tppt) REVERT: A 427 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6846 (mmm) REVERT: F 72 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7557 (mtt90) REVERT: F 122 ASN cc_start: 0.7291 (m-40) cc_final: 0.7027 (m-40) REVERT: F 133 LYS cc_start: 0.7444 (mttt) cc_final: 0.7060 (mmtt) REVERT: F 200 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (tt) REVERT: F 421 MET cc_start: 0.7314 (mtt) cc_final: 0.6761 (mmm) REVERT: D 84 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4839 (tt) REVERT: D 103 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7811 (mt-10) REVERT: I 115 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: J 97 THR cc_start: 0.9251 (m) cc_final: 0.8963 (p) REVERT: C 67 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6006 (ptm-80) REVERT: C 95 TYR cc_start: 0.7489 (m-80) cc_final: 0.7221 (m-80) REVERT: B 82 ASP cc_start: 0.6480 (m-30) cc_final: 0.6149 (t70) REVERT: G 25 SER cc_start: 0.7938 (t) cc_final: 0.7632 (m) REVERT: G 34 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7747 (ttt) REVERT: G 56 GLU cc_start: 0.2465 (OUTLIER) cc_final: 0.1672 (pt0) REVERT: G 107 MET cc_start: 0.4921 (tmm) cc_final: 0.3939 (mmt) REVERT: H 19 VAL cc_start: 0.5864 (OUTLIER) cc_final: 0.5586 (p) REVERT: H 49 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6355 (t80) outliers start: 79 outliers final: 56 residues processed: 210 average time/residue: 0.1181 time to fit residues: 36.9712 Evaluate side-chains 213 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 147 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 166 ASN B 90 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143060 restraints weight = 15962.002| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.77 r_work: 0.3534 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 14157 Z= 0.242 Angle : 0.729 10.951 19290 Z= 0.377 Chirality : 0.049 0.271 2176 Planarity : 0.006 0.123 2451 Dihedral : 7.205 58.334 2075 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.62 % Favored : 87.87 % Rotamer: Outliers : 7.43 % Allowed : 23.97 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1764 helix: 0.48 (0.92), residues: 32 sheet: -0.43 (0.21), residues: 687 loop : -1.78 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 18 TYR 0.036 0.002 TYR G 32 PHE 0.017 0.002 PHE F 171 TRP 0.016 0.002 TRP F 266 HIS 0.006 0.002 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (14130) covalent geometry : angle 0.72600 / 0.38 (19234) SS BOND : bond 0.00386 / 0.27 ( 22) SS BOND : angle 1.09575 / 0.80 ( 44) hydrogen bonds : bond 0.04136 / 2.72 ( 405) hydrogen bonds : angle 6.27712 / 4.30 ( 1080) Misc. bond : bond 0.00243 / 0.13 ( 1) link_BETA1-4 : bond 0.00990 / 0.52 ( 1) link_BETA1-4 : angle 1.26409 / 0.70 ( 3) link_BETA1-6 : bond 0.00340 / 0.16 ( 2) link_BETA1-6 : angle 1.53823 / 0.88 ( 6) link_NAG-ASN : bond 0.00471 / 0.25 ( 1) link_NAG-ASN : angle 3.63797 / 1.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 162 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7961 (mm) cc_final: 0.7698 (mt) REVERT: A 128 ASN cc_start: 0.7396 (m-40) cc_final: 0.7165 (m-40) REVERT: A 231 GLN cc_start: 0.7217 (mt0) cc_final: 0.6734 (tt0) REVERT: A 419 LYS cc_start: 0.7529 (tttt) cc_final: 0.6910 (tppt) REVERT: A 427 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6839 (mmm) REVERT: F 35 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.6810 (mmp) REVERT: F 72 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7645 (mtt90) REVERT: F 122 ASN cc_start: 0.7358 (m-40) cc_final: 0.7076 (m-40) REVERT: F 146 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: F 200 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8021 (tp) REVERT: F 225 GLN cc_start: 0.7211 (mt0) cc_final: 0.6775 (tt0) REVERT: F 237 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7711 (mmm) REVERT: F 421 MET cc_start: 0.7266 (mtt) cc_final: 0.6778 (mmm) REVERT: D 84 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4910 (tt) REVERT: I 115 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: J 78 LEU cc_start: 0.3536 (OUTLIER) cc_final: 0.2951 (tt) REVERT: C 43 LYS cc_start: 0.8060 (tppt) cc_final: 0.7829 (tppp) REVERT: B 82 ASP cc_start: 0.6609 (m-30) cc_final: 0.6195 (t70) REVERT: B 90 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8340 (pp30) REVERT: G 25 SER cc_start: 0.8362 (t) cc_final: 0.7762 (m) REVERT: G 34 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8064 (ttt) REVERT: G 56 GLU cc_start: 0.2358 (OUTLIER) cc_final: 0.1643 (pt0) REVERT: G 80 ASP cc_start: 0.7617 (p0) cc_final: 0.7290 (p0) REVERT: G 107 MET cc_start: 0.5287 (tmm) cc_final: 0.3680 (mmt) REVERT: H 5 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7229 (m) outliers start: 115 outliers final: 77 residues processed: 253 average time/residue: 0.1123 time to fit residues: 42.7242 Evaluate side-chains 240 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 151 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN H 37 GLN ** H 89 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 = 0.4129 r_free = 0.4129 target = 0.185151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143792 restraints weight = 15853.822| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.80 r_work: 0.3561 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14157 Z= 0.169 Angle : 0.654 9.346 19290 Z= 0.339 Chirality : 0.047 0.249 2176 Planarity : 0.006 0.123 2451 Dihedral : 7.014 59.708 2073 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.69 % Favored : 89.80 % Rotamer: Outliers : 6.72 % Allowed : 24.68 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1764 helix: 0.52 (0.93), residues: 32 sheet: -0.59 (0.20), residues: 694 loop : -1.68 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 18 TYR 0.035 0.002 TYR G 32 PHE 0.012 0.002 PHE D 80 TRP 0.012 0.001 TRP F 325 HIS 0.006 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14130) covalent geometry : angle 0.65063 / 0.34 (19234) SS BOND : bond 0.00329 / 0.24 ( 22) SS BOND : angle 0.96306 / 0.74 ( 44) hydrogen bonds : bond 0.03600 / 2.35 ( 405) hydrogen bonds : angle 6.02283 / 4.13 ( 1080) Misc. bond : bond 0.00185 / 0.10 ( 1) link_BETA1-4 : bond 0.00619 / 0.33 ( 1) link_BETA1-4 : angle 0.90492 / 0.49 ( 3) link_BETA1-6 : bond 0.00447 / 0.22 ( 2) link_BETA1-6 : angle 1.51009 / 0.95 ( 6) link_NAG-ASN : bond 0.00435 / 0.23 ( 1) link_NAG-ASN : angle 4.03847 / 2.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 157 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7944 (mm) cc_final: 0.7682 (mt) REVERT: A 41 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6877 (mmp) REVERT: A 81 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: A 128 ASN cc_start: 0.7342 (m-40) cc_final: 0.7135 (m-40) REVERT: A 231 GLN cc_start: 0.7199 (mt0) cc_final: 0.6774 (tt0) REVERT: A 419 LYS cc_start: 0.7538 (tttt) cc_final: 0.6955 (tppt) REVERT: A 427 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6808 (mmm) REVERT: F 35 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6809 (mmp) REVERT: F 72 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7574 (mtt90) REVERT: F 122 ASN cc_start: 0.7337 (m-40) cc_final: 0.7079 (m-40) REVERT: F 146 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: F 200 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7969 (tt) REVERT: F 225 GLN cc_start: 0.7159 (mt0) cc_final: 0.6645 (tt0) REVERT: F 237 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7701 (mmm) REVERT: F 421 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6721 (mmm) REVERT: D 84 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4993 (tt) REVERT: I 115 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: C 43 LYS cc_start: 0.8022 (tppt) cc_final: 0.7793 (tppp) REVERT: B 82 ASP cc_start: 0.6568 (m-30) cc_final: 0.6176 (t70) REVERT: B 90 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7740 (pp30) REVERT: G 25 SER cc_start: 0.8296 (t) cc_final: 0.7770 (m) REVERT: G 34 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7923 (ttt) REVERT: G 56 GLU cc_start: 0.2382 (OUTLIER) cc_final: 0.1707 (pt0) REVERT: G 80 ASP cc_start: 0.7616 (p0) cc_final: 0.7263 (p0) REVERT: G 107 MET cc_start: 0.5293 (tmm) cc_final: 0.3600 (mmt) outliers start: 104 outliers final: 78 residues processed: 237 average time/residue: 0.1132 time to fit residues: 40.3920 Evaluate side-chains 246 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 155 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 5 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 90 GLN ** H 89 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 = 0.4152 r_free = 0.4152 target = 0.187702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146446 restraints weight = 15852.623| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.80 r_work: 0.3588 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 14157 Z= 0.116 Angle : 0.596 8.056 19290 Z= 0.309 Chirality : 0.045 0.233 2176 Planarity : 0.005 0.121 2451 Dihedral : 6.545 59.373 2071 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.41 % Favored : 90.08 % Rotamer: Outliers : 6.27 % Allowed : 25.65 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1764 helix: 0.75 (0.97), residues: 32 sheet: -0.48 (0.21), residues: 686 loop : -1.62 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 18 TYR 0.039 0.001 TYR D 109 PHE 0.009 0.001 PHE D 80 TRP 0.012 0.001 TRP D 102 HIS 0.005 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14130) covalent geometry : angle 0.59309 / 0.31 (19234) SS BOND : bond 0.00271 / 0.19 ( 22) SS BOND : angle 0.80113 / 0.62 ( 44) hydrogen bonds : bond 0.03145 / 2.05 ( 405) hydrogen bonds : angle 5.73089 / 3.93 ( 1080) Misc. bond : bond 0.00132 / 0.07 ( 1) link_BETA1-4 : bond 0.00485 / 0.26 ( 1) link_BETA1-4 : angle 0.80719 / 0.43 ( 3) link_BETA1-6 : bond 0.00360 / 0.17 ( 2) link_BETA1-6 : angle 1.47684 / 0.98 ( 6) link_NAG-ASN : bond 0.00179 / 0.09 ( 1) link_NAG-ASN : angle 4.15664 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 155 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7947 (mm) cc_final: 0.7707 (mt) REVERT: A 41 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6852 (mmp) REVERT: A 81 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: A 419 LYS cc_start: 0.7599 (tttt) cc_final: 0.6959 (tppt) REVERT: A 427 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6784 (mmm) REVERT: F 35 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6806 (mmp) REVERT: F 72 ARG cc_start: 0.7971 (tpp-160) cc_final: 0.7530 (mtt90) REVERT: F 122 ASN cc_start: 0.7263 (m-40) cc_final: 0.7040 (m-40) REVERT: F 133 LYS cc_start: 0.7497 (mttt) cc_final: 0.7070 (mmtt) REVERT: F 200 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7896 (tt) REVERT: F 237 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: F 421 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6776 (mmm) REVERT: D 84 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.5004 (tt) REVERT: I 115 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: J 78 LEU cc_start: 0.3406 (OUTLIER) cc_final: 0.2807 (tt) REVERT: C 43 LYS cc_start: 0.7944 (tppt) cc_final: 0.7735 (tppp) REVERT: C 67 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5962 (ptm-80) REVERT: B 82 ASP cc_start: 0.6518 (m-30) cc_final: 0.6129 (t70) REVERT: G 25 SER cc_start: 0.8215 (t) cc_final: 0.7779 (m) REVERT: G 56 GLU cc_start: 0.2428 (OUTLIER) cc_final: 0.1743 (pt0) REVERT: G 80 ASP cc_start: 0.7624 (p0) cc_final: 0.7279 (p0) REVERT: G 107 MET cc_start: 0.5224 (tmm) cc_final: 0.3772 (mmt) REVERT: H 19 VAL cc_start: 0.5932 (OUTLIER) cc_final: 0.5612 (p) outliers start: 97 outliers final: 69 residues processed: 229 average time/residue: 0.1093 time to fit residues: 37.2606 Evaluate side-chains 234 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 152 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 166 ASN B 90 GLN ** H 89 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 = 0.4124 r_free = 0.4124 target = 0.184594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142355 restraints weight = 16133.032| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.77 r_work: 0.3524 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 14157 Z= 0.277 Angle : 0.772 11.346 19290 Z= 0.399 Chirality : 0.050 0.256 2176 Planarity : 0.006 0.123 2451 Dihedral : 7.162 58.490 2071 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.59 % Favored : 86.85 % Rotamer: Outliers : 6.91 % Allowed : 24.87 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1764 helix: 0.21 (0.91), residues: 32 sheet: -0.55 (0.21), residues: 688 loop : -1.93 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 137 TYR 0.034 0.003 TYR D 109 PHE 0.019 0.002 PHE F 171 TRP 0.037 0.002 TRP G 110 HIS 0.005 0.002 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.28 (14130) covalent geometry : angle 0.76912 / 0.40 (19234) SS BOND : bond 0.00387 / 0.28 ( 22) SS BOND : angle 1.12275 / 0.82 ( 44) hydrogen bonds : bond 0.04199 / 2.76 ( 405) hydrogen bonds : angle 6.21940 / 4.25 ( 1080) Misc. bond : bond 0.00238 / 0.13 ( 1) link_BETA1-4 : bond 0.00477 / 0.25 ( 1) link_BETA1-4 : angle 0.96786 / 0.53 ( 3) link_BETA1-6 : bond 0.00352 / 0.18 ( 2) link_BETA1-6 : angle 1.66222 / 0.94 ( 6) link_NAG-ASN : bond 0.00675 / 0.36 ( 1) link_NAG-ASN : angle 3.83282 / 1.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 162 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8020 (mm) cc_final: 0.7760 (mt) REVERT: A 41 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6869 (mmp) REVERT: A 81 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: A 128 ASN cc_start: 0.7392 (m-40) cc_final: 0.7175 (m-40) REVERT: A 231 GLN cc_start: 0.7265 (mt0) cc_final: 0.6811 (tt0) REVERT: A 419 LYS cc_start: 0.7675 (tttt) cc_final: 0.7110 (tppt) REVERT: A 427 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6926 (mmm) REVERT: F 35 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.6850 (mmp) REVERT: F 122 ASN cc_start: 0.7226 (m-40) cc_final: 0.6881 (m-40) REVERT: F 146 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: F 200 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F 225 GLN cc_start: 0.7274 (mt0) cc_final: 0.6785 (tt0) REVERT: F 237 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7784 (mmm) REVERT: F 421 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6762 (mmm) REVERT: D 84 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.5152 (tt) REVERT: I 115 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: J 78 LEU cc_start: 0.3513 (OUTLIER) cc_final: 0.2911 (tt) REVERT: C 43 LYS cc_start: 0.8073 (tppt) cc_final: 0.7859 (tppp) REVERT: B 82 ASP cc_start: 0.6660 (m-30) cc_final: 0.6223 (t70) REVERT: B 90 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8229 (pp30) REVERT: G 25 SER cc_start: 0.8502 (t) cc_final: 0.7967 (m) REVERT: G 56 GLU cc_start: 0.2564 (OUTLIER) cc_final: 0.1846 (pt0) REVERT: G 80 ASP cc_start: 0.7865 (p0) cc_final: 0.7471 (p0) REVERT: G 107 MET cc_start: 0.5426 (tmm) cc_final: 0.3573 (mmt) outliers start: 107 outliers final: 79 residues processed: 246 average time/residue: 0.1055 time to fit residues: 38.5726 Evaluate side-chains 250 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 158 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 44 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN B 90 GLN ** H 89 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 = 0.4138 r_free = 0.4138 target = 0.186239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143551 restraints weight = 15817.899| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.01 r_work: 0.3584 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14157 Z= 0.134 Angle : 0.630 8.409 19290 Z= 0.326 Chirality : 0.046 0.252 2176 Planarity : 0.006 0.122 2451 Dihedral : 6.738 59.754 2071 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.35 % Favored : 90.19 % Rotamer: Outliers : 5.49 % Allowed : 26.23 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1764 helix: 0.44 (0.94), residues: 32 sheet: -0.50 (0.21), residues: 682 loop : -1.75 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.036 0.002 TYR D 109 PHE 0.011 0.001 PHE H 71 TRP 0.024 0.001 TRP G 110 HIS 0.005 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (14130) covalent geometry : angle 0.62651 / 0.33 (19234) SS BOND : bond 0.00285 / 0.20 ( 22) SS BOND : angle 0.86396 / 0.66 ( 44) hydrogen bonds : bond 0.03272 / 2.13 ( 405) hydrogen bonds : angle 5.80844 / 3.98 ( 1080) Misc. bond : bond 0.00152 / 0.08 ( 1) link_BETA1-4 : bond 0.00361 / 0.19 ( 1) link_BETA1-4 : angle 0.78412 / 0.42 ( 3) link_BETA1-6 : bond 0.00291 / 0.14 ( 2) link_BETA1-6 : angle 1.60662 / 1.05 ( 6) link_NAG-ASN : bond 0.00300 / 0.16 ( 1) link_NAG-ASN : angle 4.25815 / 2.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 155 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7914 (mm) cc_final: 0.7658 (mt) REVERT: A 41 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6839 (mmp) REVERT: A 81 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: A 128 ASN cc_start: 0.7335 (m-40) cc_final: 0.7122 (m-40) REVERT: A 231 GLN cc_start: 0.7134 (mt0) cc_final: 0.6736 (tt0) REVERT: A 419 LYS cc_start: 0.7620 (tttt) cc_final: 0.7013 (tppt) REVERT: A 427 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6760 (mmm) REVERT: F 35 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6786 (mmp) REVERT: F 72 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7650 (mtt90) REVERT: F 122 ASN cc_start: 0.7123 (m-40) cc_final: 0.6842 (m-40) REVERT: F 133 LYS cc_start: 0.7499 (mttt) cc_final: 0.7066 (mmtt) REVERT: F 137 ARG cc_start: 0.6220 (mmm-85) cc_final: 0.5983 (mtt180) REVERT: F 200 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7933 (tt) REVERT: F 225 GLN cc_start: 0.7116 (mt0) cc_final: 0.6630 (tt0) REVERT: F 237 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7728 (mmm) REVERT: F 421 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6715 (mmm) REVERT: D 84 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5050 (tt) REVERT: I 115 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: J 78 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2752 (tt) REVERT: C 43 LYS cc_start: 0.7893 (tppt) cc_final: 0.7687 (tppp) REVERT: C 67 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6038 (ptm-80) REVERT: B 82 ASP cc_start: 0.6576 (m-30) cc_final: 0.6180 (t70) REVERT: B 90 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8126 (pp30) REVERT: G 25 SER cc_start: 0.8258 (t) cc_final: 0.7749 (m) REVERT: G 56 GLU cc_start: 0.2392 (OUTLIER) cc_final: 0.1725 (pt0) REVERT: G 80 ASP cc_start: 0.7669 (p0) cc_final: 0.7255 (p0) REVERT: G 87 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7481 (ttp-110) REVERT: G 107 MET cc_start: 0.5336 (tmm) cc_final: 0.3383 (mmt) outliers start: 85 outliers final: 69 residues processed: 220 average time/residue: 0.1058 time to fit residues: 35.0320 Evaluate side-chains 236 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 154 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 138 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** H 89 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 = 0.4139 r_free = 0.4139 target = 0.186344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144657 restraints weight = 16048.127| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.83 r_work: 0.3553 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 14157 Z= 0.174 Angle : 0.657 9.136 19290 Z= 0.340 Chirality : 0.047 0.256 2176 Planarity : 0.006 0.121 2451 Dihedral : 6.764 59.279 2071 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.43 % Favored : 89.06 % Rotamer: Outliers : 5.56 % Allowed : 26.36 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.20), residues: 1764 helix: 0.51 (0.96), residues: 32 sheet: -0.50 (0.21), residues: 691 loop : -1.80 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.033 0.002 TYR G 32 PHE 0.012 0.002 PHE D 80 TRP 0.023 0.002 TRP G 110 HIS 0.006 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (14130) covalent geometry : angle 0.65436 / 0.34 (19234) SS BOND : bond 0.00299 / 0.20 ( 22) SS BOND : angle 0.88098 / 0.67 ( 44) hydrogen bonds : bond 0.03427 / 2.25 ( 405) hydrogen bonds : angle 5.83504 / 4.00 ( 1080) Misc. bond : bond 0.00183 / 0.10 ( 1) link_BETA1-4 : bond 0.00433 / 0.23 ( 1) link_BETA1-4 : angle 0.81056 / 0.43 ( 3) link_BETA1-6 : bond 0.00361 / 0.18 ( 2) link_BETA1-6 : angle 1.57708 / 0.99 ( 6) link_NAG-ASN : bond 0.00429 / 0.23 ( 1) link_NAG-ASN : angle 4.12626 / 2.12 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 156 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7951 (mm) cc_final: 0.7689 (mt) REVERT: A 41 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.6908 (mmp) REVERT: A 81 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: A 231 GLN cc_start: 0.7222 (mt0) cc_final: 0.6775 (tt0) REVERT: A 419 LYS cc_start: 0.7650 (tttt) cc_final: 0.7070 (tppt) REVERT: A 427 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6863 (mmm) REVERT: F 35 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6851 (mmp) REVERT: F 122 ASN cc_start: 0.7187 (m-40) cc_final: 0.6901 (m-40) REVERT: F 200 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8011 (tt) REVERT: F 225 GLN cc_start: 0.7204 (mt0) cc_final: 0.6788 (tt0) REVERT: F 237 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7743 (mmm) REVERT: F 421 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6814 (mmm) REVERT: D 84 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.5107 (tt) REVERT: I 115 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: J 78 LEU cc_start: 0.3426 (OUTLIER) cc_final: 0.2808 (tt) REVERT: C 43 LYS cc_start: 0.7960 (tppt) cc_final: 0.7757 (tppp) REVERT: B 82 ASP cc_start: 0.6641 (m-30) cc_final: 0.6209 (t70) REVERT: B 89 GLN cc_start: 0.7873 (tm-30) cc_final: 0.6964 (tt0) REVERT: B 90 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: G 25 SER cc_start: 0.8322 (t) cc_final: 0.7814 (m) REVERT: G 56 GLU cc_start: 0.2492 (OUTLIER) cc_final: 0.1812 (pt0) REVERT: G 80 ASP cc_start: 0.7886 (p0) cc_final: 0.7428 (p0) REVERT: G 107 MET cc_start: 0.5528 (tmm) cc_final: 0.3792 (mmt) REVERT: G 112 GLN cc_start: 0.7757 (mp10) cc_final: 0.7165 (pt0) REVERT: H 49 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6612 (t80) outliers start: 86 outliers final: 70 residues processed: 221 average time/residue: 0.1098 time to fit residues: 36.5565 Evaluate side-chains 237 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 154 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** H 89 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 = 0.4145 r_free = 0.4145 target = 0.186918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145472 restraints weight = 15907.125| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.87 r_work: 0.3581 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14157 Z= 0.127 Angle : 0.618 9.135 19290 Z= 0.319 Chirality : 0.046 0.244 2176 Planarity : 0.006 0.120 2451 Dihedral : 6.512 59.932 2068 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.24 % Favored : 90.31 % Rotamer: Outliers : 5.49 % Allowed : 26.49 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.32 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1764 helix: 0.61 (0.96), residues: 32 sheet: -0.45 (0.21), residues: 676 loop : -1.71 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.033 0.002 TYR D 109 PHE 0.009 0.001 PHE D 80 TRP 0.034 0.001 TRP G 110 HIS 0.006 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14130) covalent geometry : angle 0.61470 / 0.32 (19234) SS BOND : bond 0.00263 / 0.18 ( 22) SS BOND : angle 0.80780 / 0.62 ( 44) hydrogen bonds : bond 0.03114 / 2.04 ( 405) hydrogen bonds : angle 5.66073 / 3.88 ( 1080) Misc. bond : bond 0.00148 / 0.08 ( 1) link_BETA1-4 : bond 0.00435 / 0.23 ( 1) link_BETA1-4 : angle 0.76504 / 0.41 ( 3) link_BETA1-6 : bond 0.00348 / 0.17 ( 2) link_BETA1-6 : angle 1.59509 / 1.05 ( 6) link_NAG-ASN : bond 0.00231 / 0.12 ( 1) link_NAG-ASN : angle 4.24471 / 2.19 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.22 seconds wall clock time: 53 minutes 12.79 seconds (3192.79 seconds total)