Starting phenix.real_space_refine on Tue May 20 10:24:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvb_17960/05_2025/8pvb_17960.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 Cl 10 4.86 5 C 12530 2.51 5 N 3080 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Restraints were copied for chains: D, H, L, Q, I, M, O, R, F, J, N, S, G, K, P, T Residues with excluded nonbonded symmetry interactions: 5 residue: pdb="CL CL A5407 " occ=0.20 residue: pdb="CL CL D5407 " occ=0.20 residue: pdb="CL CL H5407 " occ=0.20 residue: pdb="CL CL L5407 " occ=0.20 residue: pdb="CL CL Q5407 " occ=0.20 Time building chain proxies: 8.46, per 1000 atoms: 0.44 Number of scatterers: 19225 At special positions: 0 Unit cell: (142.416, 141.588, 125.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 100 16.00 O 3505 8.00 N 3080 7.00 C 12530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG B 1 " - " ASN A 80 " " NAG C 1 " - " ASN A 149 " " NAG F 1 " - " ASN D 80 " " NAG G 1 " - " ASN D 149 " " NAG J 1 " - " ASN H 80 " " NAG K 1 " - " ASN H 149 " " NAG N 1 " - " ASN L 80 " " NAG P 1 " - " ASN L 149 " " NAG S 1 " - " ASN Q 80 " " NAG T 1 " - " ASN Q 149 " Time building additional restraints: 5.97 Conformation dependent library (CDL) restraints added in 2.4 seconds 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 33.6% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'O' and resid 449 through 452 Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 246 through 270 removed outlier: 3.809A pdb=" N THR D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 449 through 452 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'H' and resid 8 through 21 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 84 through 91 Processing helix chain 'H' and resid 170 through 173 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP H 237 " --> pdb=" O THR H 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER H 239 " --> pdb=" O LEU H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 242 No H-bonds generated for 'chain 'H' and resid 240 through 242' Processing helix chain 'H' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 306 Processing helix chain 'H' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Proline residue: H 432 - end of helix Processing helix chain 'I' and resid 449 through 452 Processing helix chain 'I' and resid 495 through 497 No H-bonds generated for 'chain 'I' and resid 495 through 497' Processing helix chain 'L' and resid 8 through 21 Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 84 through 91 Processing helix chain 'L' and resid 170 through 173 Processing helix chain 'L' and resid 177 through 181 Processing helix chain 'L' and resid 218 through 225 Processing helix chain 'L' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER L 239 " --> pdb=" O LEU L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 242 No H-bonds generated for 'chain 'L' and resid 240 through 242' Processing helix chain 'L' and resid 246 through 270 removed outlier: 3.809A pdb=" N THR L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 263 " --> pdb=" O LEU L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 306 Processing helix chain 'L' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Proline residue: L 432 - end of helix Processing helix chain 'M' and resid 449 through 452 Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing helix chain 'Q' and resid 8 through 21 Processing helix chain 'Q' and resid 70 through 73 Processing helix chain 'Q' and resid 84 through 91 Processing helix chain 'Q' and resid 170 through 173 Processing helix chain 'Q' and resid 177 through 181 Processing helix chain 'Q' and resid 218 through 225 Processing helix chain 'Q' and resid 225 through 239 removed outlier: 3.691A pdb=" N TRP Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL Q 238 " --> pdb=" O ILE Q 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER Q 239 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 242 No H-bonds generated for 'chain 'Q' and resid 240 through 242' Processing helix chain 'Q' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR Q 262 " --> pdb=" O VAL Q 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Q 263 " --> pdb=" O LEU Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 306 Processing helix chain 'Q' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE Q 429 " --> pdb=" O ARG Q 425 " (cutoff:3.500A) Proline residue: Q 432 - end of helix Processing helix chain 'R' and resid 449 through 452 Processing helix chain 'R' and resid 495 through 497 No H-bonds generated for 'chain 'R' and resid 495 through 497' Processing sheet with id=1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A 66 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A 66 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=5, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS O 483 " --> pdb=" O TRP O 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP O 502 " --> pdb=" O CYS O 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA O 485 " --> pdb=" O ASP O 500 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR D 66 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN D 41 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.809A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR D 66 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN D 41 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=11, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 420 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG E 425 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE E 434 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS E 483 " --> pdb=" O TRP E 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP E 502 " --> pdb=" O CYS E 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA E 485 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 81 through 83 removed outlier: 4.341A pdb=" N ILE H 116 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR H 66 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN H 41 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR H 133 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER H 104 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR H 131 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL H 106 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG H 129 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR H 66 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN H 41 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER H 156 " --> pdb=" O PRO H 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 190 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS H 215 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE H 188 " --> pdb=" O LYS H 215 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=17, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE I 420 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG I 425 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE I 434 " --> pdb=" O ARG I 425 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS I 483 " --> pdb=" O TRP I 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP I 502 " --> pdb=" O CYS I 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA I 485 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'L' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE L 116 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR L 66 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN L 41 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR L 133 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER L 104 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR L 131 " --> pdb=" O SER L 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL L 106 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG L 129 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR L 66 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN L 41 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.631A pdb=" N SER L 156 " --> pdb=" O PRO L 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU L 190 " --> pdb=" O ARG L 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS L 215 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE L 188 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=23, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS M 483 " --> pdb=" O TRP M 502 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 502 " --> pdb=" O CYS M 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA M 485 " --> pdb=" O ASP M 500 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE Q 116 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR Q 66 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN Q 41 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR Q 133 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER Q 104 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR Q 131 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL Q 106 " --> pdb=" O ARG Q 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG Q 129 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR Q 66 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN Q 41 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER Q 156 " --> pdb=" O PRO Q 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Q 190 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS Q 215 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE Q 188 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'R' and resid 2 through 7 Processing sheet with id=29, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE R 420 " --> pdb=" O LYS R 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG R 425 " --> pdb=" O PHE R 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE R 434 " --> pdb=" O ARG R 425 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS R 483 " --> pdb=" O TRP R 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP R 502 " --> pdb=" O CYS R 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA R 485 " --> pdb=" O ASP R 500 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2760 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: 6.89 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3418 1.33 - 1.46: 5987 1.46 - 1.58: 10105 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 19680 Sorted by residual: bond pdb=" CG HIS A 119 " pdb=" CD2 HIS A 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" CG HIS Q 119 " pdb=" CD2 HIS Q 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.91e+01 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS L 119 " pdb=" CD2 HIS L 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS D 119 " pdb=" CD2 HIS D 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.88e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19557 1.82 - 3.65: 6094 3.65 - 5.47: 856 5.47 - 7.30: 113 7.30 - 9.12: 10 Bond angle restraints: 26630 Sorted by residual: angle pdb=" CA ASP A 101 " pdb=" CB ASP A 101 " pdb=" CG ASP A 101 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 angle pdb=" CA ASP Q 101 " pdb=" CB ASP Q 101 " pdb=" CG ASP Q 101 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA ASP D 101 " pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP L 101 " pdb=" CB ASP L 101 " pdb=" CG ASP L 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.39e+01 ... (remaining 26625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 11059 20.75 - 41.49: 646 41.49 - 62.24: 135 62.24 - 82.98: 70 82.98 - 103.73: 25 Dihedral angle restraints: 11935 sinusoidal: 5285 harmonic: 6650 Sorted by residual: dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER H 46 " pdb=" C SER H 46 " pdb=" N ILE H 47 " pdb=" CA ILE H 47 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1405 0.055 - 0.110: 955 0.110 - 0.165: 483 0.165 - 0.219: 134 0.219 - 0.274: 18 Chirality restraints: 2995 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.74e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.68e+01 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.62e+01 ... (remaining 2992 not shown) Planarity restraints: 3270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG F 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.057 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" C7 NAG N 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.056 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" C7 NAG J 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.009 2.00e-02 2.50e+03 ... (remaining 3267 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 0 1.96 - 2.94: 7546 2.94 - 3.92: 50552 3.92 - 4.90: 101745 Warning: very small nonbonded interaction distances. Nonbonded interactions: 159853 Sorted by model distance: nonbonded pdb="CL CL A5407 " pdb="CL CL D5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL L5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL Q5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 ... (remaining 159848 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'T' } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 42.790 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.011 0.065 19715 Z= 0.675 Angle : 1.767 14.784 26735 Z= 1.138 Chirality : 0.086 0.274 2995 Planarity : 0.012 0.135 3260 Dihedral : 16.051 103.727 7705 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 5.22 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2245 helix: -0.65 (0.18), residues: 615 sheet: 0.50 (0.20), residues: 645 loop : 0.07 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP L 237 HIS 0.009 0.002 HIS A 119 PHE 0.040 0.008 PHE H 221 TYR 0.043 0.007 TYR L 299 ARG 0.056 0.005 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.04757 ( 10) link_NAG-ASN : angle 8.23235 ( 30) link_ALPHA1-6 : bond 0.02872 ( 5) link_ALPHA1-6 : angle 7.04574 ( 15) link_BETA1-4 : bond 0.04636 ( 15) link_BETA1-4 : angle 7.94350 ( 45) link_ALPHA1-3 : bond 0.03524 ( 5) link_ALPHA1-3 : angle 7.42163 ( 15) hydrogen bonds : bond 0.18631 ( 925) hydrogen bonds : angle 7.25285 ( 2760) covalent geometry : bond 0.01049 (19680) covalent geometry : angle 1.70069 (26630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 406 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8142 (t) cc_final: 0.7938 (m) REVERT: A 51 SER cc_start: 0.7489 (t) cc_final: 0.6681 (p) REVERT: A 99 LEU cc_start: 0.8533 (tt) cc_final: 0.8292 (tt) REVERT: A 139 ASP cc_start: 0.7484 (t0) cc_final: 0.7039 (p0) REVERT: A 148 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7377 (mm110) REVERT: A 163 ASP cc_start: 0.7616 (m-30) cc_final: 0.7041 (m-30) REVERT: A 190 GLU cc_start: 0.7612 (tt0) cc_final: 0.7297 (tt0) REVERT: A 213 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6652 (tpp80) REVERT: A 283 MET cc_start: 0.8211 (mmm) cc_final: 0.7866 (mmt) REVERT: D 12 VAL cc_start: 0.8217 (t) cc_final: 0.7890 (m) REVERT: D 41 ASN cc_start: 0.8235 (m110) cc_final: 0.7951 (m-40) REVERT: D 51 SER cc_start: 0.7687 (t) cc_final: 0.6826 (p) REVERT: D 139 ASP cc_start: 0.7445 (t0) cc_final: 0.7034 (p0) REVERT: D 148 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7284 (mm-40) REVERT: D 155 GLU cc_start: 0.8540 (tt0) cc_final: 0.8275 (tt0) REVERT: D 163 ASP cc_start: 0.7610 (m-30) cc_final: 0.7123 (m-30) REVERT: D 190 GLU cc_start: 0.7467 (tt0) cc_final: 0.7162 (tt0) REVERT: D 213 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6620 (tpp80) REVERT: D 301 PHE cc_start: 0.7842 (t80) cc_final: 0.7630 (t80) REVERT: D 425 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7072 (ttp-110) REVERT: H 16 VAL cc_start: 0.8085 (t) cc_final: 0.7859 (m) REVERT: H 51 SER cc_start: 0.7679 (t) cc_final: 0.6669 (p) REVERT: H 139 ASP cc_start: 0.7462 (t0) cc_final: 0.6918 (p0) REVERT: H 147 GLU cc_start: 0.6541 (tt0) cc_final: 0.6235 (mm-30) REVERT: H 148 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7348 (mm-40) REVERT: H 155 GLU cc_start: 0.8581 (tt0) cc_final: 0.8250 (tt0) REVERT: H 163 ASP cc_start: 0.7605 (m-30) cc_final: 0.7296 (m-30) REVERT: H 190 GLU cc_start: 0.7607 (tt0) cc_final: 0.7280 (tt0) REVERT: H 213 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6408 (tpp80) REVERT: H 283 MET cc_start: 0.8229 (mmm) cc_final: 0.7989 (mmt) REVERT: H 301 PHE cc_start: 0.7944 (t80) cc_final: 0.7730 (t80) REVERT: L 16 VAL cc_start: 0.8175 (t) cc_final: 0.7932 (m) REVERT: L 41 ASN cc_start: 0.8240 (m110) cc_final: 0.7785 (m110) REVERT: L 51 SER cc_start: 0.7615 (t) cc_final: 0.6633 (p) REVERT: L 61 MET cc_start: 0.9039 (ptt) cc_final: 0.8805 (ptt) REVERT: L 139 ASP cc_start: 0.7590 (t0) cc_final: 0.7130 (p0) REVERT: L 144 PRO cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (Cg_endo) REVERT: L 148 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7393 (mm-40) REVERT: L 153 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8037 (mm-30) REVERT: L 155 GLU cc_start: 0.8538 (tt0) cc_final: 0.8090 (tt0) REVERT: L 163 ASP cc_start: 0.7732 (m-30) cc_final: 0.7408 (m-30) REVERT: L 190 GLU cc_start: 0.7622 (tt0) cc_final: 0.7259 (tt0) REVERT: L 213 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6694 (tpp80) REVERT: L 303 ASN cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: L 425 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7174 (ttp-170) REVERT: Q 41 ASN cc_start: 0.8261 (m110) cc_final: 0.7911 (m-40) REVERT: Q 43 ASP cc_start: 0.8304 (t70) cc_final: 0.8068 (t70) REVERT: Q 51 SER cc_start: 0.7523 (t) cc_final: 0.6585 (p) REVERT: Q 139 ASP cc_start: 0.7474 (t0) cc_final: 0.7097 (p0) REVERT: Q 153 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8120 (mm-30) REVERT: Q 163 ASP cc_start: 0.7598 (m-30) cc_final: 0.7157 (m-30) REVERT: Q 180 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6673 (mtt180) REVERT: Q 190 GLU cc_start: 0.7631 (tt0) cc_final: 0.7322 (tt0) REVERT: Q 224 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: Q 227 MET cc_start: 0.7599 (ttm) cc_final: 0.7325 (ttp) REVERT: Q 425 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7081 (ttp-170) outliers start: 25 outliers final: 16 residues processed: 426 average time/residue: 0.3564 time to fit residues: 220.8325 Evaluate side-chains 319 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 144 PRO Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 144 PRO Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 176 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 131 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 185 GLN D 185 GLN H 41 ASN H 185 GLN L 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.110954 restraints weight = 23669.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.108705 restraints weight = 56576.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.110269 restraints weight = 42840.773| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19715 Z= 0.135 Angle : 0.630 6.769 26735 Z= 0.330 Chirality : 0.046 0.163 2995 Planarity : 0.004 0.038 3260 Dihedral : 11.383 77.364 3589 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.82 % Allowed : 6.99 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2245 helix: 1.48 (0.20), residues: 615 sheet: 0.61 (0.19), residues: 675 loop : 0.40 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 440 HIS 0.002 0.001 HIS D 267 PHE 0.017 0.002 PHE L 306 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.001 ARG H 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 10) link_NAG-ASN : angle 3.30821 ( 30) link_ALPHA1-6 : bond 0.00340 ( 5) link_ALPHA1-6 : angle 1.47679 ( 15) link_BETA1-4 : bond 0.00420 ( 15) link_BETA1-4 : angle 2.49581 ( 45) link_ALPHA1-3 : bond 0.00895 ( 5) link_ALPHA1-3 : angle 1.89581 ( 15) hydrogen bonds : bond 0.05497 ( 925) hydrogen bonds : angle 5.06963 ( 2760) covalent geometry : bond 0.00270 (19680) covalent geometry : angle 0.60974 (26630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8219 (t) cc_final: 0.7773 (p) REVERT: A 55 MET cc_start: 0.7599 (mtp) cc_final: 0.7346 (mtt) REVERT: A 235 LEU cc_start: 0.9182 (tp) cc_final: 0.8871 (tt) REVERT: A 298 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 51 SER cc_start: 0.8307 (t) cc_final: 0.7886 (p) REVERT: D 163 ASP cc_start: 0.7522 (m-30) cc_final: 0.7316 (m-30) REVERT: H 51 SER cc_start: 0.8377 (t) cc_final: 0.7818 (p) REVERT: H 155 GLU cc_start: 0.7915 (tt0) cc_final: 0.7692 (tt0) REVERT: L 11 PHE cc_start: 0.6982 (t80) cc_final: 0.6720 (t80) REVERT: L 41 ASN cc_start: 0.8326 (m110) cc_final: 0.8066 (m110) REVERT: L 51 SER cc_start: 0.8267 (t) cc_final: 0.7695 (p) REVERT: Q 51 SER cc_start: 0.8211 (t) cc_final: 0.7717 (p) outliers start: 36 outliers final: 21 residues processed: 331 average time/residue: 0.3449 time to fit residues: 167.1825 Evaluate side-chains 301 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 162 ASP Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 148 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 190 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 41 ASN D 64 GLN H 41 ASN H 64 GLN H 185 GLN L 64 GLN Q 41 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3022 r_free = 0.3022 target = 0.106778 restraints weight = 23533.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.101964 restraints weight = 21785.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.102141 restraints weight = 27133.692| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19715 Z= 0.115 Angle : 0.562 7.446 26735 Z= 0.293 Chirality : 0.045 0.196 2995 Planarity : 0.004 0.037 3260 Dihedral : 9.959 70.447 3570 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.32 % Allowed : 9.37 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2245 helix: 1.88 (0.19), residues: 615 sheet: 0.69 (0.19), residues: 680 loop : 0.47 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 168 HIS 0.005 0.001 HIS H 267 PHE 0.013 0.001 PHE D 221 TYR 0.028 0.001 TYR L 299 ARG 0.004 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 10) link_NAG-ASN : angle 2.51536 ( 30) link_ALPHA1-6 : bond 0.00772 ( 5) link_ALPHA1-6 : angle 1.39210 ( 15) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 2.08959 ( 45) link_ALPHA1-3 : bond 0.01108 ( 5) link_ALPHA1-3 : angle 1.42416 ( 15) hydrogen bonds : bond 0.04582 ( 925) hydrogen bonds : angle 4.53504 ( 2760) covalent geometry : bond 0.00238 (19680) covalent geometry : angle 0.54839 (26630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 1.986 Fit side-chains REVERT: A 51 SER cc_start: 0.8180 (t) cc_final: 0.7821 (p) REVERT: A 55 MET cc_start: 0.7713 (mtp) cc_final: 0.7460 (mtt) REVERT: A 137 MET cc_start: 0.7378 (tpp) cc_final: 0.7135 (tpp) REVERT: A 180 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7753 (mtm180) REVERT: O 470 MET cc_start: 0.3317 (mpp) cc_final: 0.3052 (mtm) REVERT: D 51 SER cc_start: 0.8284 (t) cc_final: 0.7983 (p) REVERT: D 223 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8842 (tm) REVERT: E 421 MET cc_start: 0.6898 (mmm) cc_final: 0.5972 (mmm) REVERT: H 51 SER cc_start: 0.8375 (t) cc_final: 0.7935 (p) REVERT: H 425 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7856 (mtm-85) REVERT: L 51 SER cc_start: 0.8256 (t) cc_final: 0.7907 (p) REVERT: M 470 MET cc_start: 0.3351 (mpp) cc_final: 0.3110 (mtm) REVERT: Q 51 SER cc_start: 0.8314 (t) cc_final: 0.7885 (p) outliers start: 26 outliers final: 16 residues processed: 295 average time/residue: 0.3413 time to fit residues: 148.8463 Evaluate side-chains 274 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 14 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 64 GLN D 185 GLN H 41 ASN L 64 GLN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.104046 restraints weight = 23668.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.099948 restraints weight = 22934.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.099674 restraints weight = 22852.676| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19715 Z= 0.162 Angle : 0.572 6.468 26735 Z= 0.297 Chirality : 0.046 0.186 2995 Planarity : 0.004 0.039 3260 Dihedral : 9.498 65.846 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.57 % Allowed : 10.73 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2245 helix: 1.95 (0.20), residues: 615 sheet: 0.62 (0.19), residues: 715 loop : 0.39 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 443 HIS 0.005 0.001 HIS L 267 PHE 0.013 0.002 PHE D 98 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 10) link_NAG-ASN : angle 2.67541 ( 30) link_ALPHA1-6 : bond 0.00726 ( 5) link_ALPHA1-6 : angle 1.57307 ( 15) link_BETA1-4 : bond 0.00297 ( 15) link_BETA1-4 : angle 2.15933 ( 45) link_ALPHA1-3 : bond 0.00937 ( 5) link_ALPHA1-3 : angle 1.79514 ( 15) hydrogen bonds : bond 0.04667 ( 925) hydrogen bonds : angle 4.35259 ( 2760) covalent geometry : bond 0.00374 (19680) covalent geometry : angle 0.55640 (26630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 1.982 Fit side-chains REVERT: A 51 SER cc_start: 0.8225 (t) cc_final: 0.7939 (p) REVERT: O 470 MET cc_start: 0.3715 (mpp) cc_final: 0.3484 (mtm) REVERT: D 51 SER cc_start: 0.8241 (t) cc_final: 0.7998 (p) REVERT: H 40 MET cc_start: 0.8649 (mtt) cc_final: 0.8343 (mtt) REVERT: H 51 SER cc_start: 0.8415 (t) cc_final: 0.8029 (p) REVERT: L 40 MET cc_start: 0.8372 (mtt) cc_final: 0.7955 (mtt) REVERT: L 51 SER cc_start: 0.8265 (t) cc_final: 0.7968 (p) REVERT: L 232 ILE cc_start: 0.8770 (mm) cc_final: 0.8445 (mm) REVERT: Q 20 LEU cc_start: 0.7895 (mt) cc_final: 0.7680 (mt) REVERT: Q 51 SER cc_start: 0.8301 (t) cc_final: 0.7857 (p) outliers start: 31 outliers final: 23 residues processed: 291 average time/residue: 0.3268 time to fit residues: 141.8149 Evaluate side-chains 278 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 173 optimal weight: 0.0030 chunk 214 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN D 309 GLN L 64 GLN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.143385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.102676 restraints weight = 23863.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.097487 restraints weight = 22972.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.097331 restraints weight = 25258.464| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19715 Z= 0.261 Angle : 0.655 7.394 26735 Z= 0.338 Chirality : 0.049 0.183 2995 Planarity : 0.005 0.041 3260 Dihedral : 10.391 65.651 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.23 % Allowed : 10.84 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2245 helix: 1.31 (0.20), residues: 645 sheet: 0.51 (0.19), residues: 715 loop : -0.09 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 241 HIS 0.005 0.001 HIS H 267 PHE 0.018 0.002 PHE A 98 TYR 0.026 0.002 TYR L 299 ARG 0.004 0.001 ARG L 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 10) link_NAG-ASN : angle 3.29775 ( 30) link_ALPHA1-6 : bond 0.00729 ( 5) link_ALPHA1-6 : angle 1.68821 ( 15) link_BETA1-4 : bond 0.00330 ( 15) link_BETA1-4 : angle 2.39508 ( 45) link_ALPHA1-3 : bond 0.00959 ( 5) link_ALPHA1-3 : angle 1.95573 ( 15) hydrogen bonds : bond 0.05413 ( 925) hydrogen bonds : angle 4.56902 ( 2760) covalent geometry : bond 0.00618 (19680) covalent geometry : angle 0.63622 (26630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.989 Fit side-chains REVERT: A 51 SER cc_start: 0.8251 (t) cc_final: 0.7922 (p) REVERT: D 51 SER cc_start: 0.8140 (t) cc_final: 0.7918 (p) REVERT: D 298 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 421 MET cc_start: 0.6885 (mmm) cc_final: 0.6098 (mmm) REVERT: H 40 MET cc_start: 0.8673 (mtt) cc_final: 0.8401 (mtt) REVERT: H 51 SER cc_start: 0.8358 (t) cc_final: 0.7976 (p) REVERT: H 298 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8059 (tm-30) REVERT: L 51 SER cc_start: 0.8275 (t) cc_final: 0.7894 (p) REVERT: L 298 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8093 (tm-30) REVERT: Q 20 LEU cc_start: 0.7952 (mt) cc_final: 0.7749 (mt) REVERT: Q 51 SER cc_start: 0.8266 (t) cc_final: 0.7920 (p) REVERT: R 421 MET cc_start: 0.6972 (mmm) cc_final: 0.6234 (mmm) outliers start: 44 outliers final: 33 residues processed: 294 average time/residue: 0.3439 time to fit residues: 150.4407 Evaluate side-chains 280 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 153 optimal weight: 0.9990 chunk 211 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN L 64 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.146829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109083 restraints weight = 23654.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.107367 restraints weight = 42012.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107172 restraints weight = 36884.416| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19715 Z= 0.116 Angle : 0.539 7.481 26735 Z= 0.279 Chirality : 0.044 0.224 2995 Planarity : 0.004 0.038 3260 Dihedral : 9.356 59.408 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.67 % Allowed : 12.25 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2245 helix: 1.72 (0.20), residues: 645 sheet: 0.64 (0.19), residues: 680 loop : 0.00 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.002 0.001 HIS Q 191 PHE 0.011 0.001 PHE Q 221 TYR 0.029 0.001 TYR D 299 ARG 0.005 0.000 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 10) link_NAG-ASN : angle 2.31387 ( 30) link_ALPHA1-6 : bond 0.01037 ( 5) link_ALPHA1-6 : angle 1.47271 ( 15) link_BETA1-4 : bond 0.00302 ( 15) link_BETA1-4 : angle 1.70758 ( 45) link_ALPHA1-3 : bond 0.01001 ( 5) link_ALPHA1-3 : angle 1.69367 ( 15) hydrogen bonds : bond 0.04257 ( 925) hydrogen bonds : angle 4.32452 ( 2760) covalent geometry : bond 0.00248 (19680) covalent geometry : angle 0.52716 (26630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.063 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.8231 (t) cc_final: 0.7878 (p) REVERT: D 40 MET cc_start: 0.8593 (mtt) cc_final: 0.8259 (mtt) REVERT: D 51 SER cc_start: 0.8125 (t) cc_final: 0.7897 (p) REVERT: E 421 MET cc_start: 0.6711 (mmm) cc_final: 0.6301 (mmm) REVERT: H 40 MET cc_start: 0.8690 (mtt) cc_final: 0.8388 (mtt) REVERT: H 51 SER cc_start: 0.8357 (t) cc_final: 0.7956 (p) REVERT: L 51 SER cc_start: 0.8243 (t) cc_final: 0.7881 (p) REVERT: Q 51 SER cc_start: 0.8300 (t) cc_final: 0.7954 (p) outliers start: 33 outliers final: 24 residues processed: 292 average time/residue: 0.3257 time to fit residues: 143.4192 Evaluate side-chains 268 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 309 GLN H 64 GLN Q 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.146747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109226 restraints weight = 23539.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108006 restraints weight = 41865.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108174 restraints weight = 39282.091| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19715 Z= 0.126 Angle : 0.537 7.608 26735 Z= 0.276 Chirality : 0.044 0.235 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.946 59.448 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.97 % Allowed : 12.66 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2245 helix: 1.79 (0.20), residues: 645 sheet: 0.59 (0.19), residues: 685 loop : 0.12 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.002 0.001 HIS Q 191 PHE 0.011 0.001 PHE L 98 TYR 0.029 0.002 TYR D 299 ARG 0.008 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 10) link_NAG-ASN : angle 2.18027 ( 30) link_ALPHA1-6 : bond 0.01058 ( 5) link_ALPHA1-6 : angle 1.46998 ( 15) link_BETA1-4 : bond 0.00308 ( 15) link_BETA1-4 : angle 1.73801 ( 45) link_ALPHA1-3 : bond 0.01008 ( 5) link_ALPHA1-3 : angle 1.63689 ( 15) hydrogen bonds : bond 0.04164 ( 925) hydrogen bonds : angle 4.22499 ( 2760) covalent geometry : bond 0.00283 (19680) covalent geometry : angle 0.52525 (26630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8237 (t) cc_final: 0.7866 (p) REVERT: D 51 SER cc_start: 0.8165 (t) cc_final: 0.7929 (p) REVERT: H 40 MET cc_start: 0.8646 (mtt) cc_final: 0.8342 (mtt) REVERT: H 51 SER cc_start: 0.8385 (t) cc_final: 0.8026 (p) REVERT: L 51 SER cc_start: 0.8202 (t) cc_final: 0.7834 (p) REVERT: L 61 MET cc_start: 0.8724 (ptt) cc_final: 0.8472 (ptt) REVERT: Q 51 SER cc_start: 0.8302 (t) cc_final: 0.7956 (p) outliers start: 39 outliers final: 34 residues processed: 285 average time/residue: 0.3310 time to fit residues: 140.2357 Evaluate side-chains 279 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 197 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 143 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN D 309 GLN L 64 GLN L 185 GLN Q 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108162 restraints weight = 23583.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106698 restraints weight = 43659.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106422 restraints weight = 35770.333| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19715 Z= 0.144 Angle : 0.547 7.433 26735 Z= 0.281 Chirality : 0.045 0.244 2995 Planarity : 0.004 0.036 3260 Dihedral : 8.721 59.583 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.28 % Allowed : 13.27 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2245 helix: 1.74 (0.20), residues: 645 sheet: 0.55 (0.19), residues: 725 loop : 0.20 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 168 HIS 0.002 0.001 HIS Q 191 PHE 0.014 0.001 PHE Q 31 TYR 0.028 0.002 TYR H 299 ARG 0.008 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 10) link_NAG-ASN : angle 2.22911 ( 30) link_ALPHA1-6 : bond 0.01116 ( 5) link_ALPHA1-6 : angle 1.42822 ( 15) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 1.72040 ( 45) link_ALPHA1-3 : bond 0.01037 ( 5) link_ALPHA1-3 : angle 1.60014 ( 15) hydrogen bonds : bond 0.04250 ( 925) hydrogen bonds : angle 4.20497 ( 2760) covalent geometry : bond 0.00330 (19680) covalent geometry : angle 0.53567 (26630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8240 (t) cc_final: 0.7875 (p) REVERT: D 51 SER cc_start: 0.8153 (t) cc_final: 0.7886 (p) REVERT: E 421 MET cc_start: 0.6798 (mmm) cc_final: 0.6353 (mmm) REVERT: H 40 MET cc_start: 0.8679 (mtt) cc_final: 0.8359 (mtt) REVERT: H 51 SER cc_start: 0.8374 (t) cc_final: 0.8003 (p) REVERT: L 51 SER cc_start: 0.8253 (t) cc_final: 0.7875 (p) REVERT: Q 51 SER cc_start: 0.8312 (t) cc_final: 0.7978 (p) REVERT: Q 298 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8231 (tm-30) outliers start: 45 outliers final: 36 residues processed: 288 average time/residue: 0.3405 time to fit residues: 146.0517 Evaluate side-chains 282 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN D 309 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109720 restraints weight = 23506.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.108089 restraints weight = 44092.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.109145 restraints weight = 36611.076| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19715 Z= 0.109 Angle : 0.527 7.874 26735 Z= 0.269 Chirality : 0.044 0.245 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.191 59.265 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.37 % Allowed : 14.43 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2245 helix: 1.85 (0.20), residues: 645 sheet: 0.58 (0.19), residues: 705 loop : 0.22 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 168 HIS 0.002 0.001 HIS Q 191 PHE 0.010 0.001 PHE H 301 TYR 0.028 0.001 TYR Q 299 ARG 0.007 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 10) link_NAG-ASN : angle 1.90876 ( 30) link_ALPHA1-6 : bond 0.01192 ( 5) link_ALPHA1-6 : angle 1.42068 ( 15) link_BETA1-4 : bond 0.00350 ( 15) link_BETA1-4 : angle 1.51573 ( 45) link_ALPHA1-3 : bond 0.01046 ( 5) link_ALPHA1-3 : angle 1.51501 ( 15) hydrogen bonds : bond 0.03899 ( 925) hydrogen bonds : angle 4.12764 ( 2760) covalent geometry : bond 0.00236 (19680) covalent geometry : angle 0.51761 (26630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 1.958 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.8218 (t) cc_final: 0.7866 (p) REVERT: D 40 MET cc_start: 0.8555 (mtt) cc_final: 0.8199 (mtt) REVERT: D 261 MET cc_start: 0.8855 (mmm) cc_final: 0.8498 (mmm) REVERT: H 40 MET cc_start: 0.8635 (mtt) cc_final: 0.8319 (mtt) REVERT: H 51 SER cc_start: 0.8386 (t) cc_final: 0.8013 (p) REVERT: L 51 SER cc_start: 0.8206 (t) cc_final: 0.7851 (p) REVERT: Q 51 SER cc_start: 0.8296 (t) cc_final: 0.7969 (p) outliers start: 27 outliers final: 26 residues processed: 275 average time/residue: 0.3189 time to fit residues: 132.7625 Evaluate side-chains 266 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 96 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN L 41 ASN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.147706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110293 restraints weight = 23399.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.108959 restraints weight = 42717.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109462 restraints weight = 38813.493| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19715 Z= 0.113 Angle : 0.524 7.644 26735 Z= 0.268 Chirality : 0.044 0.245 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.804 58.836 3549 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.37 % Allowed : 15.04 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2245 helix: 1.85 (0.20), residues: 645 sheet: 0.60 (0.19), residues: 705 loop : 0.21 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 168 HIS 0.002 0.001 HIS Q 191 PHE 0.009 0.001 PHE D 221 TYR 0.029 0.001 TYR D 299 ARG 0.006 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 10) link_NAG-ASN : angle 1.90702 ( 30) link_ALPHA1-6 : bond 0.01204 ( 5) link_ALPHA1-6 : angle 1.36514 ( 15) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.54601 ( 45) link_ALPHA1-3 : bond 0.01101 ( 5) link_ALPHA1-3 : angle 1.48624 ( 15) hydrogen bonds : bond 0.03852 ( 925) hydrogen bonds : angle 4.07115 ( 2760) covalent geometry : bond 0.00249 (19680) covalent geometry : angle 0.51540 (26630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8219 (t) cc_final: 0.7841 (p) REVERT: D 261 MET cc_start: 0.8964 (mmm) cc_final: 0.8589 (mmm) REVERT: H 40 MET cc_start: 0.8655 (mtt) cc_final: 0.8337 (mtt) REVERT: H 51 SER cc_start: 0.8377 (t) cc_final: 0.7976 (p) REVERT: L 51 SER cc_start: 0.8217 (t) cc_final: 0.7819 (p) REVERT: Q 51 SER cc_start: 0.8319 (t) cc_final: 0.7950 (p) outliers start: 27 outliers final: 26 residues processed: 278 average time/residue: 0.3212 time to fit residues: 134.3237 Evaluate side-chains 272 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.0020 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 185 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.149534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110046 restraints weight = 23575.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107912 restraints weight = 47718.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109642 restraints weight = 37207.553| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19715 Z= 0.095 Angle : 0.504 7.575 26735 Z= 0.257 Chirality : 0.043 0.238 2995 Planarity : 0.004 0.037 3260 Dihedral : 7.182 58.785 3546 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.96 % Allowed : 15.44 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2245 helix: 1.96 (0.20), residues: 645 sheet: 0.69 (0.19), residues: 705 loop : 0.27 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 67 HIS 0.002 0.001 HIS Q 191 PHE 0.010 0.001 PHE H 301 TYR 0.026 0.001 TYR H 299 ARG 0.006 0.000 ARG D 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 10) link_NAG-ASN : angle 1.57702 ( 30) link_ALPHA1-6 : bond 0.01228 ( 5) link_ALPHA1-6 : angle 1.35718 ( 15) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 1.37786 ( 45) link_ALPHA1-3 : bond 0.01072 ( 5) link_ALPHA1-3 : angle 1.40842 ( 15) hydrogen bonds : bond 0.03539 ( 925) hydrogen bonds : angle 3.99368 ( 2760) covalent geometry : bond 0.00195 (19680) covalent geometry : angle 0.49679 (26630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6353.50 seconds wall clock time: 112 minutes 5.87 seconds (6725.87 seconds total)