Starting phenix.real_space_refine on Fri Jul 3 18:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uop_26652/07_2026/7uop_26652.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.142 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 90 5.16 5 C 9954 2.51 5 N 2562 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 15702 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "G" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.96, per 1000 atoms: 0.19 Number of scatterers: 15702 At special positions: 0 Unit cell: (125.4, 128.7, 141.9, 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 90 16.00 O 3096 8.00 N 2562 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.02 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 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=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 495.2 milliseconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 33 sheets defined 30.0% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.730A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.978A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.688A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.101A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.634A pdb=" N ALA A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.659A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.517A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.634A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.976A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.838A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.538A pdb=" N THR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.706A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.855A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.742A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.933A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.636A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 4.067A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.768A pdb=" N LYS D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.625A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.021A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.807A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.806A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 475 Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.698A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 3.936A pdb=" N SER G 69 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS G 71 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.576A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 4.100A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 136 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.572A pdb=" N ILE G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.698A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.746A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.694A pdb=" N LYS G 362 " --> pdb=" O SER G 359 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 359 through 363' Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.692A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 475 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.590A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.180A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.561A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.176A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.557A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 4.189A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 5.011A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.346A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.619A pdb=" N SER G 428 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.520A pdb=" N ARG A 399 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 5.003A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL D 338 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS D 45 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 340 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS D 47 " --> pdb=" O CYS D 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.328A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 315 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE D 326 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 400 removed outlier: 4.065A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 5.002A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL G 338 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 45 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS G 340 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS G 47 " --> pdb=" O CYS G 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.332A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.504A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.504A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.558A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS L 37 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.558A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.679A pdb=" N LEU B 80 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.924A pdb=" N VAL B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.878A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 101 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.516A pdb=" N MET E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS E 37 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.516A pdb=" N MET E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.515A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.907A pdb=" N VAL C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.457A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS F 37 " --> pdb=" O PRO F 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.457A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1698 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: 2.43 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4987 1.34 - 1.46: 3694 1.46 - 1.58: 7180 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 15993 Sorted by residual: bond pdb=" N CYS F 88 " pdb=" CA CYS F 88 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N CYS L 88 " pdb=" CA CYS L 88 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N TYR F 87 " pdb=" CA TYR F 87 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N TYR E 86 " pdb=" CA TYR E 86 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N GLN F 89 " pdb=" CA GLN F 89 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.27e-02 6.20e+03 9.80e+00 ... (remaining 15988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 20928 1.45 - 2.90: 672 2.90 - 4.34: 95 4.34 - 5.79: 17 5.79 - 7.24: 2 Bond angle restraints: 21714 Sorted by residual: angle pdb=" C CYS F 88 " pdb=" CA CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sigma weight residual 109.75 115.94 -6.19 1.65e+00 3.67e-01 1.41e+01 angle pdb=" CA ILE H 20 " pdb=" C ILE H 20 " pdb=" O ILE H 20 " ideal model delta sigma weight residual 121.93 117.85 4.08 1.12e+00 7.97e-01 1.33e+01 angle pdb=" CA SER B 25 " pdb=" C SER B 25 " pdb=" O SER B 25 " ideal model delta sigma weight residual 121.45 117.82 3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA ASN B 82B" pdb=" C ASN B 82B" pdb=" O ASN B 82B" ideal model delta sigma weight residual 122.03 118.08 3.95 1.17e+00 7.31e-01 1.14e+01 angle pdb=" CA SER E 24 " pdb=" C SER E 24 " pdb=" O SER E 24 " ideal model delta sigma weight residual 121.89 118.01 3.88 1.17e+00 7.31e-01 1.10e+01 ... (remaining 21709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 8923 17.33 - 34.65: 504 34.65 - 51.98: 98 51.98 - 69.30: 29 69.30 - 86.63: 19 Dihedral angle restraints: 9573 sinusoidal: 3720 harmonic: 5853 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -159.81 73.81 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -152.35 66.35 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -137.69 51.69 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 9570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2095 0.056 - 0.111: 376 0.111 - 0.167: 83 0.167 - 0.223: 11 0.223 - 0.278: 6 Chirality restraints: 2571 Sorted by residual: chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ARG B 94 " pdb=" N ARG B 94 " pdb=" C ARG B 94 " pdb=" CB ARG B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA CYS H 92 " pdb=" N CYS H 92 " pdb=" C CYS H 92 " pdb=" CB CYS H 92 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2568 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 86 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C TYR F 86 " 0.070 2.00e-02 2.50e+03 pdb=" O TYR F 86 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR F 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 86 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C TYR L 86 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR L 86 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR L 87 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 215 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO G 216 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 216 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 216 " 0.022 5.00e-02 4.00e+02 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 191 2.68 - 3.24: 13775 3.24 - 3.79: 21578 3.79 - 4.35: 29691 4.35 - 4.90: 51652 Nonbonded interactions: 116887 Sorted by model distance: nonbonded pdb=" OE2 GLU B 72 " pdb=" OG SER B 74 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR G 334 " pdb=" O SER G 337 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR D 334 " pdb=" O SER D 337 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASN C 35 " pdb=" OG1 THR C 95 " model vdw 2.260 3.040 ... (remaining 116882 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.004 0.045 16029 Z= 0.243 Angle : 0.590 7.239 21798 Z= 0.363 Chirality : 0.048 0.278 2571 Planarity : 0.004 0.040 2730 Dihedral : 12.261 86.626 5745 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.02 % Allowed : 0.80 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1986 helix: 2.30 (0.28), residues: 393 sheet: 0.39 (0.20), residues: 678 loop : -0.63 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.010 0.001 TYR G 473 PHE 0.009 0.001 PHE A 376 TRP 0.007 0.001 TRP H 103 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.24 (15993) covalent geometry : angle 0.58686 / 0.36 (21714) SS BOND : bond 0.00891 / 0.68 ( 24) SS BOND : angle 1.15855 / 0.85 ( 48) hydrogen bonds : bond 0.24202 / 16.23 ( 627) hydrogen bonds : angle 7.47413 / 5.28 ( 1698) link_NAG-ASN : bond 0.00296 / 0.19 ( 12) link_NAG-ASN : angle 1.24961 / 0.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.463 Fit side-chains REVERT: D 76 MET cc_start: 0.8096 (mmm) cc_final: 0.7763 (mmm) REVERT: C 74 SER cc_start: 0.8512 (p) cc_final: 0.6901 (p) outliers start: 18 outliers final: 2 residues processed: 201 average time/residue: 0.6780 time to fit residues: 147.4272 Evaluate side-chains 149 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain C residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN G 290 GLN B 6 GLN B 54 ASN B 82AASN C 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073163 restraints weight = 27747.546| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.66 r_work: 0.2836 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16029 Z= 0.123 Angle : 0.534 8.253 21798 Z= 0.288 Chirality : 0.046 0.169 2571 Planarity : 0.004 0.038 2730 Dihedral : 4.312 36.212 2148 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.31 % Allowed : 8.02 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1986 helix: 1.97 (0.27), residues: 444 sheet: 0.30 (0.21), residues: 654 loop : -0.74 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.022 0.001 TYR H 90 PHE 0.010 0.001 PHE C 91 TRP 0.009 0.001 TRP D 308 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15993) covalent geometry : angle 0.53019 / 0.29 (21714) SS BOND : bond 0.00435 / 0.34 ( 24) SS BOND : angle 1.24245 / 0.83 ( 48) hydrogen bonds : bond 0.04730 / 3.18 ( 627) hydrogen bonds : angle 5.15678 / 3.67 ( 1698) link_NAG-ASN : bond 0.00217 / 0.14 ( 12) link_NAG-ASN : angle 1.16960 / 0.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.653 Fit side-chains REVERT: A 411 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: D 76 MET cc_start: 0.8747 (mmm) cc_final: 0.8378 (mmm) REVERT: G 411 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8218 (tmm) REVERT: H 16 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 16 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 23 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7169 (tttp) REVERT: B 82 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6815 (m110) REVERT: C 46 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8346 (mtmt) outliers start: 23 outliers final: 10 residues processed: 158 average time/residue: 0.6155 time to fit residues: 105.8223 Evaluate side-chains 151 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 411 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.073249 restraints weight = 27985.260| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.67 r_work: 0.2840 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16029 Z= 0.099 Angle : 0.484 9.198 21798 Z= 0.258 Chirality : 0.044 0.162 2571 Planarity : 0.004 0.037 2730 Dihedral : 4.102 30.319 2147 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.88 % Allowed : 9.04 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1986 helix: 2.17 (0.27), residues: 444 sheet: 0.32 (0.21), residues: 651 loop : -0.76 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.010 0.001 TYR H 90 PHE 0.008 0.001 PHE B 91 TRP 0.007 0.001 TRP D 308 HIS 0.002 0.000 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (15993) covalent geometry : angle 0.48005 / 0.26 (21714) SS BOND : bond 0.00360 / 0.29 ( 24) SS BOND : angle 1.10380 / 0.72 ( 48) hydrogen bonds : bond 0.03979 / 2.65 ( 627) hydrogen bonds : angle 4.77876 / 3.43 ( 1698) link_NAG-ASN : bond 0.00204 / 0.13 ( 12) link_NAG-ASN : angle 1.17168 / 0.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.562 Fit side-chains REVERT: A 411 MET cc_start: 0.8472 (tmm) cc_final: 0.8230 (tmm) REVERT: D 76 MET cc_start: 0.8713 (mmm) cc_final: 0.8352 (mmm) REVERT: G 322 LEU cc_start: 0.8070 (mm) cc_final: 0.7638 (mt) REVERT: H 16 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7924 (mt-10) REVERT: H 72 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6415 (tm-30) REVERT: B 16 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 46 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8365 (mtmt) outliers start: 33 outliers final: 22 residues processed: 156 average time/residue: 0.6251 time to fit residues: 106.7148 Evaluate side-chains 154 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 177 optimal weight: 0.0570 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071034 restraints weight = 27992.026| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.66 r_work: 0.2793 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16029 Z= 0.123 Angle : 0.525 9.123 21798 Z= 0.279 Chirality : 0.045 0.169 2571 Planarity : 0.004 0.040 2730 Dihedral : 4.338 33.047 2147 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.22 % Allowed : 9.04 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1986 helix: 2.15 (0.27), residues: 444 sheet: 0.35 (0.21), residues: 651 loop : -0.87 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 65 TYR 0.015 0.001 TYR F 94 PHE 0.010 0.001 PHE B 91 TRP 0.008 0.001 TRP C 103 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (15993) covalent geometry : angle 0.51640 / 0.28 (21714) SS BOND : bond 0.00541 / 0.42 ( 24) SS BOND : angle 1.77567 / 1.11 ( 48) hydrogen bonds : bond 0.04317 / 2.87 ( 627) hydrogen bonds : angle 4.63113 / 3.31 ( 1698) link_NAG-ASN : bond 0.00222 / 0.15 ( 12) link_NAG-ASN : angle 1.27749 / 0.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.578 Fit side-chains REVERT: A 411 MET cc_start: 0.8528 (tmm) cc_final: 0.8280 (tmm) REVERT: D 76 MET cc_start: 0.8733 (mmm) cc_final: 0.8405 (mmm) REVERT: H 16 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7854 (mt-10) REVERT: H 72 GLU cc_start: 0.7888 (tt0) cc_final: 0.6624 (tm-30) REVERT: B 16 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 23 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7550 (tttp) outliers start: 39 outliers final: 25 residues processed: 154 average time/residue: 0.6578 time to fit residues: 110.1546 Evaluate side-chains 153 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 468 GLN B 82AASN C 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.072306 restraints weight = 27843.137| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.66 r_work: 0.2816 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16029 Z= 0.098 Angle : 0.485 8.998 21798 Z= 0.256 Chirality : 0.044 0.154 2571 Planarity : 0.004 0.036 2730 Dihedral : 4.170 32.928 2147 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.76 % Allowed : 10.47 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1986 helix: 2.25 (0.27), residues: 444 sheet: 0.35 (0.21), residues: 651 loop : -0.83 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.009 0.001 TYR E 87 PHE 0.008 0.001 PHE G 376 TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15993) covalent geometry : angle 0.48023 / 0.25 (21714) SS BOND : bond 0.00350 / 0.27 ( 24) SS BOND : angle 1.06813 / 0.69 ( 48) hydrogen bonds : bond 0.03649 / 2.43 ( 627) hydrogen bonds : angle 4.45696 / 3.21 ( 1698) link_NAG-ASN : bond 0.00189 / 0.12 ( 12) link_NAG-ASN : angle 1.23887 / 0.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.442 Fit side-chains REVERT: A 411 MET cc_start: 0.8519 (tmm) cc_final: 0.8250 (tmm) REVERT: D 76 MET cc_start: 0.8662 (mmm) cc_final: 0.8364 (mmm) REVERT: G 322 LEU cc_start: 0.7976 (mm) cc_final: 0.7494 (mt) REVERT: H 16 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7902 (mt-10) REVERT: H 72 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: B 16 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 12 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7551 (mptp) REVERT: C 13 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8526 (ttmt) outliers start: 31 outliers final: 22 residues processed: 155 average time/residue: 0.6924 time to fit residues: 117.0745 Evaluate side-chains 148 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 148 optimal weight: 0.0270 chunk 129 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.073021 restraints weight = 27834.278| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.64 r_work: 0.2832 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16029 Z= 0.092 Angle : 0.477 9.031 21798 Z= 0.250 Chirality : 0.044 0.153 2571 Planarity : 0.004 0.034 2730 Dihedral : 4.050 32.831 2147 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.10 % Allowed : 10.24 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1986 helix: 2.29 (0.27), residues: 444 sheet: 0.40 (0.21), residues: 684 loop : -0.78 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.009 0.001 TYR E 87 PHE 0.008 0.001 PHE G 376 TRP 0.006 0.001 TRP A 308 HIS 0.002 0.000 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (15993) covalent geometry : angle 0.47402 / 0.25 (21714) SS BOND : bond 0.00339 / 0.27 ( 24) SS BOND : angle 0.87190 / 0.55 ( 48) hydrogen bonds : bond 0.03367 / 2.24 ( 627) hydrogen bonds : angle 4.32391 / 3.11 ( 1698) link_NAG-ASN : bond 0.00196 / 0.13 ( 12) link_NAG-ASN : angle 1.19381 / 0.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.575 Fit side-chains REVERT: A 411 MET cc_start: 0.8594 (tmm) cc_final: 0.8309 (tmm) REVERT: D 76 MET cc_start: 0.8629 (mmm) cc_final: 0.8348 (mmm) REVERT: D 244 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7996 (ttp-110) REVERT: G 322 LEU cc_start: 0.7980 (mm) cc_final: 0.7509 (mt) REVERT: H 16 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 72 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: B 16 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7866 (mt-10) REVERT: C 12 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7531 (mptp) REVERT: C 13 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8507 (ttmt) outliers start: 37 outliers final: 22 residues processed: 152 average time/residue: 0.6412 time to fit residues: 106.7628 Evaluate side-chains 151 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072432 restraints weight = 27249.502| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.62 r_work: 0.2852 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16029 Z= 0.110 Angle : 0.503 8.701 21798 Z= 0.266 Chirality : 0.045 0.152 2571 Planarity : 0.004 0.037 2730 Dihedral : 4.183 33.659 2147 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 11.43 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1986 helix: 2.27 (0.27), residues: 444 sheet: 0.38 (0.21), residues: 651 loop : -0.85 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 65 TYR 0.011 0.001 TYR E 87 PHE 0.009 0.001 PHE B 91 TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15993) covalent geometry : angle 0.49914 / 0.26 (21714) SS BOND : bond 0.00427 / 0.34 ( 24) SS BOND : angle 1.07101 / 0.67 ( 48) hydrogen bonds : bond 0.03818 / 2.54 ( 627) hydrogen bonds : angle 4.37617 / 3.15 ( 1698) link_NAG-ASN : bond 0.00196 / 0.12 ( 12) link_NAG-ASN : angle 1.24812 / 0.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.544 Fit side-chains REVERT: A 411 MET cc_start: 0.8627 (tmm) cc_final: 0.8366 (tmm) REVERT: D 76 MET cc_start: 0.8651 (mmm) cc_final: 0.8390 (mmm) REVERT: G 322 LEU cc_start: 0.7983 (mm) cc_final: 0.7512 (mt) REVERT: H 16 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7692 (mt-10) REVERT: H 72 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: L 81 GLU cc_start: 0.7967 (pm20) cc_final: 0.7559 (pm20) REVERT: B 16 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7913 (mt-10) REVERT: C 13 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8547 (ttmt) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.7369 time to fit residues: 118.8625 Evaluate side-chains 153 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 161 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070381 restraints weight = 27643.990| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.63 r_work: 0.2812 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16029 Z= 0.142 Angle : 0.554 8.962 21798 Z= 0.293 Chirality : 0.046 0.160 2571 Planarity : 0.004 0.039 2730 Dihedral : 4.445 34.481 2147 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.71 % Allowed : 11.72 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1986 helix: 2.26 (0.27), residues: 444 sheet: 0.41 (0.21), residues: 666 loop : -0.92 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 65 TYR 0.014 0.001 TYR F 94 PHE 0.011 0.001 PHE B 91 TRP 0.008 0.001 TRP C 36 HIS 0.003 0.001 HIS F 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (15993) covalent geometry : angle 0.54838 / 0.29 (21714) SS BOND : bond 0.00540 / 0.42 ( 24) SS BOND : angle 1.36423 / 0.86 ( 48) hydrogen bonds : bond 0.04512 / 2.99 ( 627) hydrogen bonds : angle 4.53421 / 3.25 ( 1698) link_NAG-ASN : bond 0.00217 / 0.14 ( 12) link_NAG-ASN : angle 1.39056 / 0.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.667 Fit side-chains REVERT: A 411 MET cc_start: 0.8640 (tmm) cc_final: 0.8393 (tmm) REVERT: D 76 MET cc_start: 0.8660 (mmm) cc_final: 0.8386 (mmm) REVERT: G 322 LEU cc_start: 0.7981 (mm) cc_final: 0.7688 (mp) REVERT: H 16 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 72 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: L 81 GLU cc_start: 0.8023 (pm20) cc_final: 0.7571 (pm20) REVERT: B 16 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7736 (mt-10) REVERT: C 13 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8577 (ttmt) REVERT: F 79 GLU cc_start: 0.8251 (mp0) cc_final: 0.7606 (mp0) REVERT: F 81 GLU cc_start: 0.8152 (pm20) cc_final: 0.7695 (pm20) outliers start: 30 outliers final: 22 residues processed: 149 average time/residue: 0.7511 time to fit residues: 121.7441 Evaluate side-chains 148 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 49 HIS C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.069415 restraints weight = 27530.419| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.62 r_work: 0.2788 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16029 Z= 0.154 Angle : 0.573 9.186 21798 Z= 0.304 Chirality : 0.047 0.172 2571 Planarity : 0.004 0.038 2730 Dihedral : 4.616 34.396 2147 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.76 % Allowed : 11.89 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1986 helix: 2.17 (0.27), residues: 441 sheet: 0.43 (0.21), residues: 663 loop : -1.07 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 65 TYR 0.014 0.001 TYR G 275 PHE 0.010 0.001 PHE C 91 TRP 0.008 0.001 TRP C 103 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (15993) covalent geometry : angle 0.56692 / 0.30 (21714) SS BOND : bond 0.00569 / 0.44 ( 24) SS BOND : angle 1.41660 / 0.90 ( 48) hydrogen bonds : bond 0.04766 / 3.15 ( 627) hydrogen bonds : angle 4.59859 / 3.30 ( 1698) link_NAG-ASN : bond 0.00233 / 0.14 ( 12) link_NAG-ASN : angle 1.48380 / 0.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.572 Fit side-chains REVERT: A 411 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8393 (tmm) REVERT: D 76 MET cc_start: 0.8624 (mmm) cc_final: 0.8343 (mmm) REVERT: D 327 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: G 335 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8610 (tptm) REVERT: H 16 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7715 (mt-10) REVERT: H 72 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: L 81 GLU cc_start: 0.8073 (pm20) cc_final: 0.7601 (pm20) REVERT: B 16 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 13 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8622 (ttmt) REVERT: F 79 GLU cc_start: 0.8148 (mp0) cc_final: 0.7462 (mp0) REVERT: F 81 GLU cc_start: 0.8192 (pm20) cc_final: 0.7644 (pm20) outliers start: 31 outliers final: 23 residues processed: 151 average time/residue: 0.7005 time to fit residues: 115.2467 Evaluate side-chains 155 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 74 optimal weight: 0.8980 chunk 126 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070956 restraints weight = 27478.628| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.63 r_work: 0.2825 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16029 Z= 0.111 Angle : 0.531 9.355 21798 Z= 0.280 Chirality : 0.045 0.168 2571 Planarity : 0.004 0.036 2730 Dihedral : 4.422 33.606 2147 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.48 % Allowed : 12.34 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1986 helix: 2.19 (0.27), residues: 444 sheet: 0.44 (0.21), residues: 693 loop : -0.94 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 65 TYR 0.011 0.001 TYR A 248 PHE 0.008 0.001 PHE G 301 TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (15993) covalent geometry : angle 0.52672 / 0.28 (21714) SS BOND : bond 0.00431 / 0.34 ( 24) SS BOND : angle 1.03233 / 0.65 ( 48) hydrogen bonds : bond 0.03955 / 2.63 ( 627) hydrogen bonds : angle 4.51165 / 3.25 ( 1698) link_NAG-ASN : bond 0.00212 / 0.14 ( 12) link_NAG-ASN : angle 1.34161 / 0.83 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.524 Fit side-chains REVERT: A 411 MET cc_start: 0.8650 (tmm) cc_final: 0.8440 (tmm) REVERT: D 76 MET cc_start: 0.8647 (mmm) cc_final: 0.8395 (mmm) REVERT: D 327 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: H 16 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7761 (mt-10) REVERT: H 72 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: L 81 GLU cc_start: 0.8069 (pm20) cc_final: 0.7598 (pm20) REVERT: B 16 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 13 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8605 (ttmt) REVERT: F 79 GLU cc_start: 0.8153 (mp0) cc_final: 0.7445 (mp0) REVERT: F 81 GLU cc_start: 0.8137 (pm20) cc_final: 0.7669 (pm20) outliers start: 26 outliers final: 23 residues processed: 144 average time/residue: 0.6763 time to fit residues: 106.0878 Evaluate side-chains 152 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 193 optimal weight: 0.4980 chunk 189 optimal weight: 0.0670 chunk 164 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.071940 restraints weight = 27494.233| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.64 r_work: 0.2837 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16029 Z= 0.105 Angle : 0.511 9.421 21798 Z= 0.269 Chirality : 0.045 0.153 2571 Planarity : 0.004 0.036 2730 Dihedral : 4.257 33.516 2147 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.48 % Allowed : 12.40 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1986 helix: 2.22 (0.27), residues: 444 sheet: 0.46 (0.21), residues: 693 loop : -0.90 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.009 0.001 TYR E 87 PHE 0.008 0.001 PHE G 301 TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (15993) covalent geometry : angle 0.50790 / 0.27 (21714) SS BOND : bond 0.00401 / 0.31 ( 24) SS BOND : angle 0.96830 / 0.61 ( 48) hydrogen bonds : bond 0.03643 / 2.42 ( 627) hydrogen bonds : angle 4.37304 / 3.16 ( 1698) link_NAG-ASN : bond 0.00196 / 0.12 ( 12) link_NAG-ASN : angle 1.25107 / 0.78 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.58 seconds wall clock time: 84 minutes 52.66 seconds (5092.66 seconds total)