Starting phenix.real_space_refine on Wed Mar 4 18:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uop_26652/03_2026/7uop_26652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uop_26652/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uop_26652/03_2026/7uop_26652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uop_26652/03_2026/7uop_26652.map" model { file = "/net/cci-nas-00/data/ceres_data/7uop_26652/03_2026/7uop_26652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uop_26652/03_2026/7uop_26652.cif" } 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-5986/lib/python3.9/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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.45, per 1000 atoms: 0.22 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: 1.28 Conformation dependent library (CDL) restraints added in 617.5 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: 0.75 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: 2.92 Time building geometry restraints manager: 1.72 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: 9144 17.33 - 34.65: 519 34.65 - 51.98: 109 51.98 - 69.30: 34 69.30 - 86.63: 19 Dihedral angle restraints: 9825 sinusoidal: 3972 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 9822 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: 3.310 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.530 Find NCS groups from input model: 0.280 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 12.278 86.626 5997 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 covalent geometry : bond 0.00357 (15993) covalent geometry : angle 0.58686 (21714) SS BOND : bond 0.00891 ( 24) SS BOND : angle 1.15855 ( 48) hydrogen bonds : bond 0.24202 ( 627) hydrogen bonds : angle 7.47413 ( 1698) link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.24961 ( 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 : 0.585 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: 0.7545 time to fit residues: 163.8681 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 : 0.600 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.092462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073141 restraints weight = 27729.463| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.67 r_work: 0.2835 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1373 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= 0.121 Angle : 0.533 8.360 21798 Z= 0.288 Chirality : 0.046 0.166 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.406 53.414 2400 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.31 % Allowed : 8.08 % Favored : 90.61 % 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: 1.98 (0.27), residues: 444 sheet: 0.31 (0.21), residues: 654 loop : -0.74 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 30 TYR 0.021 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 covalent geometry : bond 0.00267 (15993) covalent geometry : angle 0.52869 (21714) SS BOND : bond 0.00439 ( 24) SS BOND : angle 1.24195 ( 48) hydrogen bonds : bond 0.04774 ( 627) hydrogen bonds : angle 5.19196 ( 1698) link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 1.24677 ( 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 170 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.557 Fit side-chains REVERT: A 411 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8124 (tmm) REVERT: D 76 MET cc_start: 0.8749 (mmm) cc_final: 0.8379 (mmm) REVERT: G 411 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (tmm) REVERT: H 16 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 16 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 23 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7170 (tttp) REVERT: B 82 ASN cc_start: 0.7011 (OUTLIER) cc_final: 0.6797 (m110) REVERT: C 46 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8318 (mtmt) outliers start: 23 outliers final: 10 residues processed: 157 average time/residue: 0.7400 time to fit residues: 125.7650 Evaluate side-chains 149 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 3.9990 chunk 154 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 197 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.072365 restraints weight = 27948.385| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.64 r_work: 0.2816 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16029 Z= 0.112 Angle : 0.504 8.993 21798 Z= 0.269 Chirality : 0.045 0.159 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.250 54.466 2399 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 9.16 % Favored : 88.96 % 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: 0.34 (0.19), residues: 1986 helix: 2.11 (0.27), residues: 444 sheet: 0.33 (0.21), residues: 651 loop : -0.81 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.012 0.001 TYR E 87 PHE 0.011 0.001 PHE C 91 TRP 0.008 0.001 TRP D 308 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00251 (15993) covalent geometry : angle 0.49864 (21714) SS BOND : bond 0.00401 ( 24) SS BOND : angle 1.23217 ( 48) hydrogen bonds : bond 0.04328 ( 627) hydrogen bonds : angle 4.82966 ( 1698) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.33572 ( 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 171 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.596 Fit side-chains REVERT: A 411 MET cc_start: 0.8503 (tmm) cc_final: 0.8266 (tmm) REVERT: D 76 MET cc_start: 0.8750 (mmm) cc_final: 0.8402 (mmm) REVERT: G 322 LEU cc_start: 0.8098 (mm) cc_final: 0.7665 (mt) REVERT: H 16 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7918 (mt-10) REVERT: H 72 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: B 16 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 46 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8353 (mtmt) outliers start: 33 outliers final: 21 residues processed: 158 average time/residue: 0.7363 time to fit residues: 126.4972 Evaluate side-chains 154 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 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: 0.0770 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.0040 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 0.0070 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074966 restraints weight = 28002.470| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.65 r_work: 0.2870 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1773 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= 0.086 Angle : 0.462 8.758 21798 Z= 0.244 Chirality : 0.044 0.155 2571 Planarity : 0.004 0.034 2730 Dihedral : 4.923 52.553 2399 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 9.78 % Favored : 88.51 % 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: 0.50 (0.20), residues: 1986 helix: 2.23 (0.27), residues: 444 sheet: 0.32 (0.20), residues: 693 loop : -0.63 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 65 TYR 0.007 0.001 TYR G 292 PHE 0.008 0.001 PHE G 376 TRP 0.007 0.001 TRP D 308 HIS 0.001 0.000 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00180 (15993) covalent geometry : angle 0.45612 (21714) SS BOND : bond 0.00366 ( 24) SS BOND : angle 1.19572 ( 48) hydrogen bonds : bond 0.03255 ( 627) hydrogen bonds : angle 4.46239 ( 1698) link_NAG-ASN : bond 0.00225 ( 12) link_NAG-ASN : angle 1.28408 ( 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 165 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.498 Fit side-chains REVERT: A 411 MET cc_start: 0.8507 (tmm) cc_final: 0.8199 (tmm) REVERT: D 76 MET cc_start: 0.8693 (mmm) cc_final: 0.8387 (mmm) REVERT: D 138 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8044 (tpp) REVERT: D 250 THR cc_start: 0.7204 (t) cc_final: 0.6769 (t) REVERT: G 322 LEU cc_start: 0.8040 (mm) cc_final: 0.7596 (mt) REVERT: H 16 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7911 (mt-10) REVERT: H 72 GLU cc_start: 0.7888 (tt0) cc_final: 0.6685 (tm-30) REVERT: L 11 MET cc_start: 0.8797 (ttp) cc_final: 0.8395 (ptp) REVERT: B 16 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 12 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7534 (mptp) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 0.7128 time to fit residues: 118.4058 Evaluate side-chains 151 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 335 LYS 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 138 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 302 ASN 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 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 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: 4.9990 chunk 17 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 HIS C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068233 restraints weight = 27680.823| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.61 r_work: 0.2765 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16029 Z= 0.211 Angle : 0.646 8.790 21798 Z= 0.344 Chirality : 0.049 0.188 2571 Planarity : 0.005 0.051 2730 Dihedral : 5.955 59.115 2399 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.28 % Allowed : 10.07 % 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: 0.12 (0.19), residues: 1986 helix: 1.76 (0.26), residues: 462 sheet: 0.30 (0.21), residues: 681 loop : -1.05 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 65 TYR 0.023 0.002 TYR F 94 PHE 0.015 0.002 PHE B 91 TRP 0.009 0.002 TRP A 308 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00519 (15993) covalent geometry : angle 0.63613 (21714) SS BOND : bond 0.00716 ( 24) SS BOND : angle 2.00691 ( 48) hydrogen bonds : bond 0.05913 ( 627) hydrogen bonds : angle 4.85084 ( 1698) link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 1.74920 ( 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 176 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.525 Fit side-chains REVERT: A 411 MET cc_start: 0.8627 (tmm) cc_final: 0.8374 (tmm) REVERT: D 76 MET cc_start: 0.8701 (mmm) cc_final: 0.8353 (mmm) REVERT: H 16 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7770 (mt-10) REVERT: H 72 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: B 16 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 23 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7683 (tttp) REVERT: C 13 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8565 (ttmt) outliers start: 40 outliers final: 20 residues processed: 160 average time/residue: 0.7223 time to fit residues: 125.4886 Evaluate side-chains 152 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain D residue 421 VAL 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 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 22 THR 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: 7.9990 chunk 141 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.068681 restraints weight = 27612.362| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.62 r_work: 0.2777 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16029 Z= 0.169 Angle : 0.586 9.529 21798 Z= 0.312 Chirality : 0.047 0.169 2571 Planarity : 0.005 0.039 2730 Dihedral : 5.773 57.195 2399 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 11.26 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1986 helix: 2.02 (0.27), residues: 441 sheet: 0.28 (0.21), residues: 666 loop : -1.16 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 65 TYR 0.017 0.002 TYR F 94 PHE 0.012 0.001 PHE C 91 TRP 0.008 0.001 TRP G 308 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00413 (15993) covalent geometry : angle 0.57919 (21714) SS BOND : bond 0.00587 ( 24) SS BOND : angle 1.51340 ( 48) hydrogen bonds : bond 0.05096 ( 627) hydrogen bonds : angle 4.70152 ( 1698) link_NAG-ASN : bond 0.00255 ( 12) link_NAG-ASN : angle 1.67089 ( 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 167 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.608 Fit side-chains REVERT: A 411 MET cc_start: 0.8645 (tmm) cc_final: 0.8392 (tmm) REVERT: D 76 MET cc_start: 0.8624 (mmm) cc_final: 0.8327 (mmm) REVERT: H 16 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7761 (mt-10) REVERT: H 72 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: L 81 GLU cc_start: 0.8069 (pm20) cc_final: 0.7600 (pm20) REVERT: B 16 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 13 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8580 (ttmt) REVERT: C 43 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8616 (mmmm) REVERT: F 79 GLU cc_start: 0.8056 (mp0) cc_final: 0.7531 (mp0) outliers start: 35 outliers final: 23 residues processed: 156 average time/residue: 0.6985 time to fit residues: 118.6740 Evaluate side-chains 155 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 187 ILE 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 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 72 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER 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: 0.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 196 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.069852 restraints weight = 27284.003| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.61 r_work: 0.2799 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16029 Z= 0.130 Angle : 0.544 9.681 21798 Z= 0.288 Chirality : 0.046 0.168 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.512 55.248 2399 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.93 % Allowed : 11.77 % Favored : 86.29 % 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: 0.23 (0.20), residues: 1986 helix: 2.08 (0.27), residues: 444 sheet: 0.36 (0.21), residues: 696 loop : -1.07 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.011 0.001 TYR F 94 PHE 0.009 0.001 PHE C 91 TRP 0.008 0.001 TRP D 308 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00308 (15993) covalent geometry : angle 0.53836 (21714) SS BOND : bond 0.00481 ( 24) SS BOND : angle 1.19914 ( 48) hydrogen bonds : bond 0.04378 ( 627) hydrogen bonds : angle 4.53943 ( 1698) link_NAG-ASN : bond 0.00214 ( 12) link_NAG-ASN : angle 1.53774 ( 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 166 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.588 Fit side-chains REVERT: A 411 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (tmm) REVERT: D 76 MET cc_start: 0.8621 (mmm) cc_final: 0.8363 (mmm) REVERT: H 16 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7774 (mt-10) REVERT: H 30 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8413 (mmt180) REVERT: H 72 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: L 11 MET cc_start: 0.8783 (ttp) cc_final: 0.8441 (ptp) REVERT: L 81 GLU cc_start: 0.8074 (pm20) cc_final: 0.7589 (pm20) REVERT: B 16 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 13 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8621 (ttmt) REVERT: C 43 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8628 (mmmm) REVERT: F 79 GLU cc_start: 0.8060 (mp0) cc_final: 0.7361 (mp0) REVERT: F 81 GLU cc_start: 0.7918 (pm20) cc_final: 0.7702 (pm20) outliers start: 34 outliers final: 21 residues processed: 152 average time/residue: 0.6980 time to fit residues: 115.5076 Evaluate side-chains 153 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 335 LYS 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 421 VAL 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 11 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.069986 restraints weight = 27637.291| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.62 r_work: 0.2801 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16029 Z= 0.126 Angle : 0.542 9.801 21798 Z= 0.286 Chirality : 0.046 0.163 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.445 55.568 2399 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.93 % Allowed : 12.00 % Favored : 86.06 % 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: 0.19 (0.20), residues: 1986 helix: 2.13 (0.27), residues: 444 sheet: 0.35 (0.21), residues: 663 loop : -1.10 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 50 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00298 (15993) covalent geometry : angle 0.53627 (21714) SS BOND : bond 0.00479 ( 24) SS BOND : angle 1.16704 ( 48) hydrogen bonds : bond 0.04259 ( 627) hydrogen bonds : angle 4.46376 ( 1698) link_NAG-ASN : bond 0.00219 ( 12) link_NAG-ASN : angle 1.51074 ( 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 169 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.613 Fit side-chains REVERT: A 411 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: D 76 MET cc_start: 0.8625 (mmm) cc_final: 0.8375 (mmm) REVERT: D 327 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: G 335 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8644 (tptm) REVERT: H 16 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7756 (mt-10) REVERT: H 30 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8432 (mmt180) REVERT: H 72 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: L 11 MET cc_start: 0.8791 (ttp) cc_final: 0.8408 (ptp) REVERT: L 81 GLU cc_start: 0.8096 (pm20) cc_final: 0.7597 (pm20) REVERT: B 16 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 13 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8677 (ttmt) REVERT: C 43 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8635 (mmmm) REVERT: F 79 GLU cc_start: 0.8014 (mp0) cc_final: 0.7548 (mp0) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 0.7397 time to fit residues: 122.8330 Evaluate side-chains 157 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 421 VAL 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 74 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain E residue 11 MET 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: 5.9990 chunk 134 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 290 GLN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070496 restraints weight = 27519.649| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.62 r_work: 0.2812 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16029 Z= 0.117 Angle : 0.529 9.840 21798 Z= 0.279 Chirality : 0.045 0.163 2571 Planarity : 0.004 0.038 2730 Dihedral : 5.341 54.830 2399 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.65 % Allowed : 12.34 % Favored : 86.01 % 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: 0.31 (0.20), residues: 1986 helix: 2.16 (0.27), residues: 444 sheet: 0.42 (0.21), residues: 693 loop : -1.04 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.014 0.001 TYR G 248 PHE 0.009 0.001 PHE G 301 TRP 0.007 0.001 TRP C 50 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00275 (15993) covalent geometry : angle 0.52462 (21714) SS BOND : bond 0.00445 ( 24) SS BOND : angle 1.06234 ( 48) hydrogen bonds : bond 0.04002 ( 627) hydrogen bonds : angle 4.39338 ( 1698) link_NAG-ASN : bond 0.00218 ( 12) link_NAG-ASN : angle 1.45897 ( 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 160 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.591 Fit side-chains REVERT: A 411 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8372 (tmm) REVERT: D 76 MET cc_start: 0.8650 (mmm) cc_final: 0.8415 (mmm) REVERT: H 16 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7747 (mt-10) REVERT: H 30 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8420 (mmt180) REVERT: H 72 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: L 81 GLU cc_start: 0.8103 (pm20) cc_final: 0.7596 (pm20) REVERT: B 16 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 13 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8667 (ttmt) REVERT: F 81 GLU cc_start: 0.8130 (pm20) cc_final: 0.7901 (pm20) outliers start: 29 outliers final: 21 residues processed: 148 average time/residue: 0.7149 time to fit residues: 115.0870 Evaluate side-chains 152 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 335 LYS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 74 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 290 GLN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.069946 restraints weight = 27544.905| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.62 r_work: 0.2798 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16029 Z= 0.132 Angle : 0.557 9.904 21798 Z= 0.293 Chirality : 0.046 0.164 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.433 55.767 2399 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.59 % Allowed : 12.57 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1986 helix: 2.13 (0.27), residues: 444 sheet: 0.37 (0.21), residues: 663 loop : -1.10 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.011 0.001 TYR G 275 PHE 0.009 0.001 PHE C 91 TRP 0.007 0.001 TRP C 50 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00317 (15993) covalent geometry : angle 0.55192 (21714) SS BOND : bond 0.00497 ( 24) SS BOND : angle 1.20421 ( 48) hydrogen bonds : bond 0.04295 ( 627) hydrogen bonds : angle 4.42378 ( 1698) link_NAG-ASN : bond 0.00214 ( 12) link_NAG-ASN : angle 1.51444 ( 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 158 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.442 Fit side-chains REVERT: A 411 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: D 76 MET cc_start: 0.8651 (mmm) cc_final: 0.8408 (mmm) REVERT: H 16 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7764 (mt-10) REVERT: H 30 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8424 (mmt180) REVERT: H 72 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: L 81 GLU cc_start: 0.8123 (pm20) cc_final: 0.7610 (pm20) REVERT: B 16 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7777 (mt-10) REVERT: C 13 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8671 (ttmt) REVERT: F 79 GLU cc_start: 0.8059 (mp0) cc_final: 0.7458 (mp0) outliers start: 28 outliers final: 22 residues processed: 147 average time/residue: 0.7385 time to fit residues: 117.8892 Evaluate side-chains 153 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 335 LYS 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 406 GLU Chi-restraints excluded: chain D residue 421 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 167 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 189 optimal weight: 0.0010 chunk 164 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071555 restraints weight = 27589.721| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.63 r_work: 0.2831 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16029 Z= 0.105 Angle : 0.514 10.138 21798 Z= 0.269 Chirality : 0.045 0.159 2571 Planarity : 0.004 0.038 2730 Dihedral : 5.191 53.894 2399 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.37 % Allowed : 12.57 % Favored : 86.06 % 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: 0.36 (0.20), residues: 1986 helix: 2.18 (0.27), residues: 444 sheet: 0.45 (0.21), residues: 693 loop : -1.01 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.014 0.001 TYR G 248 PHE 0.009 0.001 PHE G 376 TRP 0.007 0.001 TRP D 308 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00241 (15993) covalent geometry : angle 0.50999 (21714) SS BOND : bond 0.00390 ( 24) SS BOND : angle 0.90153 ( 48) hydrogen bonds : bond 0.03628 ( 627) hydrogen bonds : angle 4.30311 ( 1698) link_NAG-ASN : bond 0.00202 ( 12) link_NAG-ASN : angle 1.39377 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.05 seconds wall clock time: 87 minutes 24.01 seconds (5244.01 seconds total)