Starting phenix.real_space_refine on Sat Jul 4 09:02:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pvb_17960/07_2026/8pvb_17960.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: "O" 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 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: 6 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} Restraints were copied for chains: D, H, L, Q, E, I, M, 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: 3.56, per 1000 atoms: 0.19 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=5, symmetry=0 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.04 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 483 " distance=2.04 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 483 " distance=2.04 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.04 Simple disulfide: pdb=" SG CYS R 409 " - pdb=" SG CYS R 483 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 1.99 Conformation dependent library (CDL) restraints added in 820.0 milliseconds 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: 0.67 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: 3.59 Time building geometry restraints manager: 2.52 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 - 17.97: 10525 17.97 - 35.95: 890 35.95 - 53.92: 150 53.92 - 71.90: 75 71.90 - 89.87: 25 Dihedral angle restraints: 11665 sinusoidal: 5015 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 11662 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: 7541 2.94 - 3.92: 50542 3.92 - 4.90: 101745 Warning: very small nonbonded interaction distances. Nonbonded interactions: 159838 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 159833 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'E' selection = chain 'I' selection = chain 'M' 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: 3.250 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 19720 Z= 0.675 Angle : 1.767 14.784 26745 Z= 1.138 Chirality : 0.086 0.274 2995 Planarity : 0.012 0.135 3260 Dihedral : 14.665 89.871 7420 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (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 ARG 0.056 0.005 ARG A 269 TYR 0.043 0.007 TYR L 299 PHE 0.040 0.008 PHE H 221 TRP 0.031 0.005 TRP L 237 HIS 0.009 0.002 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.01049 / 0.67 (19680) covalent geometry : angle 1.70069 / 1.13 (26630) SS BOND : bond 0.01005 / 0.65 ( 5) SS BOND : angle 2.35004 / 1.60 ( 10) hydrogen bonds : bond 0.18631 / 12.50 ( 925) hydrogen bonds : angle 7.25285 / 5.04 ( 2760) link_ALPHA1-3 : bond 0.03524 / 2.30 ( 5) link_ALPHA1-3 : angle 7.42163 / 4.44 ( 15) link_ALPHA1-6 : bond 0.02872 / 1.86 ( 5) link_ALPHA1-6 : angle 7.04574 / 4.31 ( 15) link_BETA1-4 : bond 0.04636 / 3.14 ( 15) link_BETA1-4 : angle 7.94350 / 5.56 ( 45) link_NAG-ASN : bond 0.04757 / 3.31 ( 10) link_NAG-ASN : angle 8.23235 / 5.57 ( 30) *********************** 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 : 0.867 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: 0.8218 (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: 0.6827 (p) REVERT: D 139 ASP cc_start: 0.7444 (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: 0.7841 (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: 0.7604 (m-30) cc_final: 0.7296 (m-30) REVERT: H 190 GLU cc_start: 0.7608 (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: 0.8305 (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: 0.1678 time to fit residues: 105.0458 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 : 0.709 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3559 r_free = 0.3559 target = 0.147447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110551 restraints weight = 23508.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.108558 restraints weight = 48839.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.106406 restraints weight = 40461.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.102476 restraints weight = 21744.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.102825 restraints weight = 21641.733| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19720 Z= 0.152 Angle : 0.630 6.781 26745 Z= 0.333 Chirality : 0.046 0.182 2995 Planarity : 0.004 0.041 3260 Dihedral : 8.700 55.396 3304 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.87 % Allowed : 7.34 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2245 helix: 1.42 (0.20), residues: 615 sheet: 0.61 (0.19), residues: 680 loop : 0.35 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 213 TYR 0.028 0.002 TYR L 299 PHE 0.017 0.002 PHE L 306 TRP 0.007 0.001 TRP R 440 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (19680) covalent geometry : angle 0.61312 / 0.33 (26630) SS BOND : bond 0.00369 / 0.24 ( 5) SS BOND : angle 0.80194 / 0.54 ( 10) hydrogen bonds : bond 0.05617 / 3.76 ( 925) hydrogen bonds : angle 5.01825 / 3.47 ( 2760) link_ALPHA1-3 : bond 0.00357 / 0.24 ( 5) link_ALPHA1-3 : angle 1.40614 / 1.02 ( 15) link_ALPHA1-6 : bond 0.00173 / 0.09 ( 5) link_ALPHA1-6 : angle 1.49380 / 1.10 ( 15) link_BETA1-4 : bond 0.00300 / 0.20 ( 15) link_BETA1-4 : angle 2.36222 / 1.67 ( 45) link_NAG-ASN : bond 0.00469 / 0.33 ( 10) link_NAG-ASN : angle 3.14604 / 2.13 ( 30) *********************** 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 332 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8260 (t) cc_final: 0.7866 (p) REVERT: A 55 MET cc_start: 0.7642 (mtp) cc_final: 0.7428 (mtt) REVERT: A 298 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7794 (tm-30) REVERT: D 41 ASN cc_start: 0.8344 (m110) cc_final: 0.8107 (m110) REVERT: D 51 SER cc_start: 0.8277 (t) cc_final: 0.7886 (p) REVERT: D 99 LEU cc_start: 0.8880 (tt) cc_final: 0.8635 (tt) REVERT: H 51 SER cc_start: 0.8374 (t) cc_final: 0.7857 (p) REVERT: H 190 GLU cc_start: 0.7589 (tt0) cc_final: 0.7387 (tt0) REVERT: L 51 SER cc_start: 0.8291 (t) cc_final: 0.7761 (p) REVERT: L 303 ASN cc_start: 0.8914 (t0) cc_final: 0.8703 (t0) REVERT: Q 51 SER cc_start: 0.8236 (t) cc_final: 0.7720 (p) REVERT: Q 224 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: R 424 PHE cc_start: 0.6008 (m-80) cc_final: 0.5790 (m-80) outliers start: 37 outliers final: 21 residues processed: 321 average time/residue: 0.1660 time to fit residues: 78.9936 Evaluate side-chains 287 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 176 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 I residue 459 ARG Chi-restraints excluded: chain L residue 132 THR 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 M residue 459 ARG Chi-restraints excluded: chain Q residue 224 GLN 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 125 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN D 64 GLN D 185 GLN H 41 ASN H 64 GLN Q 41 ASN Q 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109192 restraints weight = 23589.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.105317 restraints weight = 52591.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.101423 restraints weight = 33493.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.100504 restraints weight = 28600.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.101278 restraints weight = 28158.053| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19720 Z= 0.181 Angle : 0.607 7.769 26745 Z= 0.318 Chirality : 0.046 0.184 2995 Planarity : 0.004 0.041 3260 Dihedral : 8.087 58.403 3288 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.82 % Allowed : 9.67 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2245 helix: 1.66 (0.19), residues: 615 sheet: 0.53 (0.19), residues: 685 loop : 0.28 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 213 TYR 0.028 0.002 TYR L 299 PHE 0.014 0.002 PHE D 98 TRP 0.008 0.001 TRP H 443 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (19680) covalent geometry : angle 0.59081 / 0.32 (26630) SS BOND : bond 0.00401 / 0.26 ( 5) SS BOND : angle 0.63467 / 0.43 ( 10) hydrogen bonds : bond 0.05105 / 3.44 ( 925) hydrogen bonds : angle 4.60085 / 3.18 ( 2760) link_ALPHA1-3 : bond 0.00428 / 0.28 ( 5) link_ALPHA1-3 : angle 1.38650 / 1.01 ( 15) link_ALPHA1-6 : bond 0.00106 / 0.06 ( 5) link_ALPHA1-6 : angle 1.90900 / 1.39 ( 15) link_BETA1-4 : bond 0.00298 / 0.20 ( 15) link_BETA1-4 : angle 2.30683 / 1.65 ( 45) link_NAG-ASN : bond 0.00134 / 0.10 ( 10) link_NAG-ASN : angle 2.85296 / 1.94 ( 30) *********************** 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 303 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.688 Fit side-chains REVERT: A 51 SER cc_start: 0.8279 (t) cc_final: 0.7956 (p) REVERT: A 180 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7767 (mtm180) REVERT: O 470 MET cc_start: 0.3737 (mpp) cc_final: 0.3120 (mtm) REVERT: D 51 SER cc_start: 0.8221 (t) cc_final: 0.7970 (p) REVERT: E 421 MET cc_start: 0.7129 (mmm) cc_final: 0.6422 (mmm) REVERT: E 470 MET cc_start: 0.3710 (mpp) cc_final: 0.3278 (mtm) REVERT: H 40 MET cc_start: 0.8521 (mtt) cc_final: 0.8096 (mtt) REVERT: H 51 SER cc_start: 0.8394 (t) cc_final: 0.7997 (p) REVERT: H 147 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6614 (mm-30) REVERT: H 425 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7809 (mtm-85) REVERT: I 470 MET cc_start: 0.3612 (mpp) cc_final: 0.3160 (mtm) REVERT: L 51 SER cc_start: 0.8247 (t) cc_final: 0.7990 (p) REVERT: L 298 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8204 (tm-30) REVERT: Q 51 SER cc_start: 0.8254 (t) cc_final: 0.7888 (p) REVERT: Q 224 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: R 421 MET cc_start: 0.7057 (mmm) cc_final: 0.6298 (mmm) outliers start: 36 outliers final: 21 residues processed: 291 average time/residue: 0.1659 time to fit residues: 71.6977 Evaluate side-chains 268 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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 164 ILE 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 223 LEU Chi-restraints excluded: chain Q residue 224 GLN 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 159 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN D 64 GLN D 185 GLN L 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 = 0.3527 r_free = 0.3527 target = 0.144334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.102776 restraints weight = 23656.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.098353 restraints weight = 22743.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.097912 restraints weight = 24166.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.098822 restraints weight = 21944.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.098765 restraints weight = 19897.995| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19720 Z= 0.233 Angle : 0.633 7.729 26745 Z= 0.330 Chirality : 0.047 0.188 2995 Planarity : 0.005 0.041 3260 Dihedral : 8.535 59.958 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.04 % Allowed : 10.08 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2245 helix: 1.33 (0.20), residues: 645 sheet: 0.42 (0.19), residues: 690 loop : -0.07 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 213 TYR 0.027 0.002 TYR L 299 PHE 0.016 0.002 PHE R 424 TRP 0.008 0.001 TRP H 443 HIS 0.006 0.001 HIS L 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (19680) covalent geometry : angle 0.61512 / 0.33 (26630) SS BOND : bond 0.00507 / 0.33 ( 5) SS BOND : angle 0.65090 / 0.44 ( 10) hydrogen bonds : bond 0.05268 / 3.53 ( 925) hydrogen bonds : angle 4.55477 / 3.14 ( 2760) link_ALPHA1-3 : bond 0.00538 / 0.37 ( 5) link_ALPHA1-3 : angle 1.46893 / 1.08 ( 15) link_ALPHA1-6 : bond 0.00068 / 0.04 ( 5) link_ALPHA1-6 : angle 2.19480 / 1.59 ( 15) link_BETA1-4 : bond 0.00358 / 0.23 ( 15) link_BETA1-4 : angle 2.31401 / 1.65 ( 45) link_NAG-ASN : bond 0.00123 / 0.09 ( 10) link_NAG-ASN : angle 3.08526 / 2.11 ( 30) *********************** 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 329 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8732 (mtt) cc_final: 0.8306 (mtt) REVERT: A 51 SER cc_start: 0.8264 (t) cc_final: 0.7946 (p) REVERT: O 470 MET cc_start: 0.3924 (mpp) cc_final: 0.3673 (mtm) REVERT: D 41 ASN cc_start: 0.8556 (m110) cc_final: 0.8257 (m-40) REVERT: D 51 SER cc_start: 0.8157 (t) cc_final: 0.7922 (p) REVERT: D 61 MET cc_start: 0.8986 (ptt) cc_final: 0.8761 (ptt) REVERT: D 298 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H 40 MET cc_start: 0.8663 (mtt) cc_final: 0.8315 (mtt) REVERT: H 51 SER cc_start: 0.8354 (t) cc_final: 0.7978 (p) REVERT: H 147 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6387 (mm-30) REVERT: H 232 ILE cc_start: 0.8687 (mm) cc_final: 0.8310 (mm) REVERT: H 298 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8086 (tm-30) REVERT: L 51 SER cc_start: 0.8290 (t) cc_final: 0.7911 (p) REVERT: L 298 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8083 (tm-30) REVERT: M 421 MET cc_start: 0.7221 (mmm) cc_final: 0.6172 (mmm) REVERT: Q 51 SER cc_start: 0.8271 (t) cc_final: 0.7922 (p) REVERT: Q 224 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.6980 (mp10) outliers start: 60 outliers final: 47 residues processed: 314 average time/residue: 0.1640 time to fit residues: 76.8469 Evaluate side-chains 291 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 109 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 223 LEU Chi-restraints excluded: chain D residue 231 LEU 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 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 H residue 309 GLN Chi-restraints excluded: chain H residue 423 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 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 231 LEU 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 M residue 459 ARG Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 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 224 GLN Chi-restraints excluded: chain Q residue 231 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 185 GLN O 461 ASN D 185 GLN E 461 ASN L 64 GLN L 185 GLN Q 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.103445 restraints weight = 23500.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.098528 restraints weight = 22833.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.098344 restraints weight = 22835.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.099115 restraints weight = 21360.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.099107 restraints weight = 20166.537| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19720 Z= 0.182 Angle : 0.574 8.223 26745 Z= 0.299 Chirality : 0.045 0.174 2995 Planarity : 0.004 0.040 3260 Dihedral : 8.300 59.923 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.48 % Allowed : 12.20 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2245 helix: 1.51 (0.20), residues: 645 sheet: 0.43 (0.19), residues: 680 loop : -0.13 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.028 0.002 TYR D 299 PHE 0.013 0.002 PHE A 98 TRP 0.006 0.001 TRP D 168 HIS 0.003 0.001 HIS H 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (19680) covalent geometry : angle 0.55945 / 0.30 (26630) SS BOND : bond 0.00500 / 0.32 ( 5) SS BOND : angle 0.53195 / 0.37 ( 10) hydrogen bonds : bond 0.04751 / 3.20 ( 925) hydrogen bonds : angle 4.42479 / 3.05 ( 2760) link_ALPHA1-3 : bond 0.00308 / 0.20 ( 5) link_ALPHA1-3 : angle 1.42380 / 1.05 ( 15) link_ALPHA1-6 : bond 0.00141 / 0.09 ( 5) link_ALPHA1-6 : angle 1.84237 / 1.35 ( 15) link_BETA1-4 : bond 0.00300 / 0.20 ( 15) link_BETA1-4 : angle 2.05669 / 1.44 ( 45) link_NAG-ASN : bond 0.00112 / 0.08 ( 10) link_NAG-ASN : angle 2.58900 / 1.76 ( 30) *********************** 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 317 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 0.622 Fit side-chains REVERT: A 40 MET cc_start: 0.8688 (mtt) cc_final: 0.8291 (mtt) REVERT: A 51 SER cc_start: 0.8251 (t) cc_final: 0.7919 (p) REVERT: A 298 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8176 (tm-30) REVERT: D 41 ASN cc_start: 0.8513 (m110) cc_final: 0.8222 (m110) REVERT: D 51 SER cc_start: 0.8137 (t) cc_final: 0.7880 (p) REVERT: E 421 MET cc_start: 0.7250 (mmm) cc_final: 0.6385 (mmm) REVERT: H 40 MET cc_start: 0.8648 (mtt) cc_final: 0.8269 (mtt) REVERT: H 51 SER cc_start: 0.8330 (t) cc_final: 0.7964 (p) REVERT: I 470 MET cc_start: 0.3696 (mpp) cc_final: 0.3209 (mpp) REVERT: L 40 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: L 51 SER cc_start: 0.8255 (t) cc_final: 0.7950 (p) REVERT: L 298 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8107 (tm-30) REVERT: M 421 MET cc_start: 0.7312 (mmm) cc_final: 0.6317 (mmm) REVERT: Q 51 SER cc_start: 0.8317 (t) cc_final: 0.7990 (p) REVERT: Q 224 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: R 421 MET cc_start: 0.7323 (mmm) cc_final: 0.6444 (mmm) outliers start: 49 outliers final: 37 residues processed: 299 average time/residue: 0.1537 time to fit residues: 69.9408 Evaluate side-chains 290 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 176 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 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 H residue 444 LEU Chi-restraints excluded: chain L residue 40 MET 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 109 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 224 GLN 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 96 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3557 r_free = 0.3557 target = 0.147082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.106185 restraints weight = 23307.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.103373 restraints weight = 49515.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.105357 restraints weight = 37252.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.105222 restraints weight = 26003.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105574 restraints weight = 21093.002| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19720 Z= 0.118 Angle : 0.524 8.018 26745 Z= 0.273 Chirality : 0.043 0.174 2995 Planarity : 0.004 0.039 3260 Dihedral : 7.696 59.302 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.87 % Allowed : 13.77 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2245 helix: 1.76 (0.20), residues: 645 sheet: 0.41 (0.19), residues: 690 loop : 0.02 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.029 0.001 TYR D 299 PHE 0.010 0.001 PHE Q 221 TRP 0.006 0.001 TRP D 67 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (19680) covalent geometry : angle 0.51228 / 0.27 (26630) SS BOND : bond 0.00571 / 0.37 ( 5) SS BOND : angle 0.30924 / 0.21 ( 10) hydrogen bonds : bond 0.04172 / 2.82 ( 925) hydrogen bonds : angle 4.25672 / 2.94 ( 2760) link_ALPHA1-3 : bond 0.00338 / 0.22 ( 5) link_ALPHA1-3 : angle 1.43975 / 1.06 ( 15) link_ALPHA1-6 : bond 0.00310 / 0.20 ( 5) link_ALPHA1-6 : angle 1.60485 / 1.18 ( 15) link_BETA1-4 : bond 0.00277 / 0.18 ( 15) link_BETA1-4 : angle 1.82032 / 1.26 ( 45) link_NAG-ASN : bond 0.00154 / 0.11 ( 10) link_NAG-ASN : angle 2.12250 / 1.45 ( 30) *********************** 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 313 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.732 Fit side-chains REVERT: A 40 MET cc_start: 0.8717 (mtt) cc_final: 0.8331 (mtt) REVERT: A 51 SER cc_start: 0.8257 (t) cc_final: 0.7930 (p) REVERT: D 41 ASN cc_start: 0.8373 (m110) cc_final: 0.8086 (m110) REVERT: D 51 SER cc_start: 0.8108 (t) cc_final: 0.7880 (p) REVERT: H 40 MET cc_start: 0.8630 (mtt) cc_final: 0.8238 (mtt) REVERT: H 51 SER cc_start: 0.8360 (t) cc_final: 0.8000 (p) REVERT: I 470 MET cc_start: 0.3882 (mpp) cc_final: 0.3386 (mpp) REVERT: L 51 SER cc_start: 0.8291 (t) cc_final: 0.7946 (p) REVERT: L 68 ARG cc_start: 0.7474 (ttm170) cc_final: 0.7261 (ttm170) REVERT: Q 51 SER cc_start: 0.8316 (t) cc_final: 0.8004 (p) REVERT: Q 224 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6802 (mp10) outliers start: 37 outliers final: 31 residues processed: 301 average time/residue: 0.1518 time to fit residues: 69.5494 Evaluate side-chains 280 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR 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 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 309 GLN 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 224 GLN 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 130 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN D 185 GLN H 41 ASN 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 = 0.3562 r_free = 0.3562 target = 0.147556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.106713 restraints weight = 23363.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.100284 restraints weight = 26187.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.101798 restraints weight = 26416.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102256 restraints weight = 21358.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.102187 restraints weight = 18570.798| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19720 Z= 0.114 Angle : 0.517 7.266 26745 Z= 0.269 Chirality : 0.042 0.169 2995 Planarity : 0.004 0.037 3260 Dihedral : 7.341 59.220 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.08 % Allowed : 14.53 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2245 helix: 1.83 (0.20), residues: 645 sheet: 0.47 (0.19), residues: 690 loop : 0.05 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 213 TYR 0.028 0.001 TYR D 299 PHE 0.009 0.001 PHE A 221 TRP 0.007 0.001 TRP Q 168 HIS 0.002 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (19680) covalent geometry : angle 0.50612 / 0.27 (26630) SS BOND : bond 0.00573 / 0.37 ( 5) SS BOND : angle 0.20887 / 0.14 ( 10) hydrogen bonds : bond 0.04033 / 2.73 ( 925) hydrogen bonds : angle 4.18574 / 2.89 ( 2760) link_ALPHA1-3 : bond 0.00357 / 0.23 ( 5) link_ALPHA1-3 : angle 1.39642 / 1.02 ( 15) link_ALPHA1-6 : bond 0.00341 / 0.22 ( 5) link_ALPHA1-6 : angle 1.57832 / 1.16 ( 15) link_BETA1-4 : bond 0.00298 / 0.19 ( 15) link_BETA1-4 : angle 1.76196 / 1.22 ( 45) link_NAG-ASN : bond 0.00172 / 0.12 ( 10) link_NAG-ASN : angle 2.01322 / 1.37 ( 30) *********************** 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 299 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.742 Fit side-chains REVERT: A 40 MET cc_start: 0.8714 (mtt) cc_final: 0.8325 (mtt) REVERT: A 51 SER cc_start: 0.8269 (t) cc_final: 0.7903 (p) REVERT: O 421 MET cc_start: 0.7298 (mmm) cc_final: 0.6780 (mmm) REVERT: D 51 SER cc_start: 0.8147 (t) cc_final: 0.7888 (p) REVERT: E 421 MET cc_start: 0.7217 (mmm) cc_final: 0.6462 (mmm) REVERT: H 40 MET cc_start: 0.8619 (mtt) cc_final: 0.8229 (mtt) REVERT: H 51 SER cc_start: 0.8362 (t) cc_final: 0.7993 (p) REVERT: I 470 MET cc_start: 0.3731 (mpp) cc_final: 0.3207 (mpp) REVERT: L 51 SER cc_start: 0.8235 (t) cc_final: 0.7877 (p) REVERT: Q 51 SER cc_start: 0.8311 (t) cc_final: 0.7982 (p) REVERT: Q 224 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.6693 (mp10) REVERT: Q 298 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8257 (tm-30) outliers start: 41 outliers final: 35 residues processed: 286 average time/residue: 0.1551 time to fit residues: 67.1328 Evaluate side-chains 285 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 115 MET 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 109 VAL Chi-restraints excluded: chain H residue 132 THR 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 309 GLN Chi-restraints excluded: chain H residue 444 LEU 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 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 309 GLN 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 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 128 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 82 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 185 GLN H 41 ASN L 185 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 = 0.3533 r_free = 0.3533 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.103978 restraints weight = 23418.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.096349 restraints weight = 24707.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.097217 restraints weight = 29248.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.098161 restraints weight = 25056.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.098328 restraints weight = 19503.777| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19720 Z= 0.197 Angle : 0.580 7.743 26745 Z= 0.300 Chirality : 0.045 0.206 2995 Planarity : 0.004 0.038 3260 Dihedral : 7.623 58.751 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.18 % Allowed : 14.94 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2245 helix: 1.64 (0.20), residues: 645 sheet: 0.43 (0.19), residues: 690 loop : -0.12 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.029 0.002 TYR Q 299 PHE 0.020 0.002 PHE Q 301 TRP 0.008 0.001 TRP R 440 HIS 0.003 0.001 HIS H 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (19680) covalent geometry : angle 0.56661 / 0.30 (26630) SS BOND : bond 0.00567 / 0.38 ( 5) SS BOND : angle 0.28221 / 0.18 ( 10) hydrogen bonds : bond 0.04668 / 3.15 ( 925) hydrogen bonds : angle 4.29352 / 2.97 ( 2760) link_ALPHA1-3 : bond 0.00382 / 0.25 ( 5) link_ALPHA1-3 : angle 1.31310 / 0.97 ( 15) link_ALPHA1-6 : bond 0.00208 / 0.14 ( 5) link_ALPHA1-6 : angle 1.87358 / 1.36 ( 15) link_BETA1-4 : bond 0.00313 / 0.21 ( 15) link_BETA1-4 : angle 2.04039 / 1.43 ( 45) link_NAG-ASN : bond 0.00141 / 0.10 ( 10) link_NAG-ASN : angle 2.46798 / 1.68 ( 30) *********************** 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 297 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8683 (mtt) cc_final: 0.8272 (mtt) REVERT: A 51 SER cc_start: 0.8264 (t) cc_final: 0.7897 (p) REVERT: O 421 MET cc_start: 0.7291 (mmm) cc_final: 0.6694 (mmm) REVERT: D 51 SER cc_start: 0.8110 (t) cc_final: 0.7860 (p) REVERT: H 40 MET cc_start: 0.8624 (mtt) cc_final: 0.8226 (mtt) REVERT: H 51 SER cc_start: 0.8372 (t) cc_final: 0.7958 (p) REVERT: L 40 MET cc_start: 0.8647 (mtt) cc_final: 0.8123 (mtt) REVERT: L 51 SER cc_start: 0.8283 (t) cc_final: 0.7904 (p) REVERT: L 298 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8192 (tm-30) REVERT: M 421 MET cc_start: 0.7296 (mmm) cc_final: 0.6584 (mmm) REVERT: Q 51 SER cc_start: 0.8321 (t) cc_final: 0.7991 (p) REVERT: Q 224 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: Q 298 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8207 (tm-30) REVERT: R 421 MET cc_start: 0.7468 (mmm) cc_final: 0.6817 (mmm) outliers start: 43 outliers final: 37 residues processed: 284 average time/residue: 0.1549 time to fit residues: 66.6393 Evaluate side-chains 280 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 109 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 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 H residue 309 GLN 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 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 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 69 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 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 = 0.3548 r_free = 0.3548 target = 0.146360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108362 restraints weight = 23259.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.106875 restraints weight = 39633.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.106263 restraints weight = 34403.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.102866 restraints weight = 20983.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.103433 restraints weight = 17464.952| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19720 Z= 0.146 Angle : 0.542 7.820 26745 Z= 0.281 Chirality : 0.043 0.198 2995 Planarity : 0.004 0.037 3260 Dihedral : 7.267 57.803 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.03 % Allowed : 15.65 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2245 helix: 1.68 (0.20), residues: 645 sheet: 0.34 (0.19), residues: 710 loop : 0.03 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.033 0.002 TYR H 66 PHE 0.013 0.001 PHE Q 301 TRP 0.007 0.001 TRP I 440 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19680) covalent geometry : angle 0.53073 / 0.28 (26630) SS BOND : bond 0.00564 / 0.37 ( 5) SS BOND : angle 0.21009 / 0.14 ( 10) hydrogen bonds : bond 0.04320 / 2.92 ( 925) hydrogen bonds : angle 4.22180 / 2.93 ( 2760) link_ALPHA1-3 : bond 0.00339 / 0.22 ( 5) link_ALPHA1-3 : angle 1.39258 / 1.02 ( 15) link_ALPHA1-6 : bond 0.00338 / 0.22 ( 5) link_ALPHA1-6 : angle 1.64561 / 1.21 ( 15) link_BETA1-4 : bond 0.00239 / 0.16 ( 15) link_BETA1-4 : angle 1.81840 / 1.26 ( 45) link_NAG-ASN : bond 0.00145 / 0.10 ( 10) link_NAG-ASN : angle 2.11132 / 1.44 ( 30) *********************** 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 294 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.747 Fit side-chains REVERT: A 40 MET cc_start: 0.8701 (mtt) cc_final: 0.8263 (mtt) REVERT: A 51 SER cc_start: 0.8209 (t) cc_final: 0.7863 (p) REVERT: O 421 MET cc_start: 0.7228 (mmm) cc_final: 0.6722 (mmm) REVERT: D 51 SER cc_start: 0.8105 (t) cc_final: 0.7847 (p) REVERT: D 261 MET cc_start: 0.8880 (mmm) cc_final: 0.8550 (mmm) REVERT: H 40 MET cc_start: 0.8651 (mtt) cc_final: 0.8247 (mtt) REVERT: H 51 SER cc_start: 0.8367 (t) cc_final: 0.7940 (p) REVERT: I 470 MET cc_start: 0.3605 (mpp) cc_final: 0.2811 (mpp) REVERT: L 51 SER cc_start: 0.8269 (t) cc_final: 0.7875 (p) REVERT: L 298 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8232 (tm-30) REVERT: M 421 MET cc_start: 0.7190 (mmm) cc_final: 0.6558 (mmm) REVERT: Q 51 SER cc_start: 0.8307 (t) cc_final: 0.7954 (p) REVERT: Q 224 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.6699 (mp10) REVERT: Q 298 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8249 (tm-30) REVERT: R 421 MET cc_start: 0.7400 (mmm) cc_final: 0.6730 (mmm) outliers start: 40 outliers final: 34 residues processed: 283 average time/residue: 0.1548 time to fit residues: 66.6762 Evaluate side-chains 278 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 131 THR 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 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 132 THR Chi-restraints excluded: chain D residue 176 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 109 VAL Chi-restraints excluded: chain H residue 132 THR 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 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 223 LEU Chi-restraints excluded: chain Q residue 224 GLN 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 147 optimal weight: 0.3980 chunk 218 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 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 = 0.3562 r_free = 0.3562 target = 0.147612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108629 restraints weight = 23422.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.106181 restraints weight = 47154.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107979 restraints weight = 38018.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107438 restraints weight = 23907.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107884 restraints weight = 22666.975| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19720 Z= 0.111 Angle : 0.517 7.907 26745 Z= 0.268 Chirality : 0.042 0.196 2995 Planarity : 0.004 0.037 3260 Dihedral : 6.753 58.957 3268 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2245 helix: 1.84 (0.20), residues: 645 sheet: 0.58 (0.19), residues: 690 loop : -0.05 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.028 0.001 TYR D 299 PHE 0.016 0.001 PHE Q 301 TRP 0.008 0.001 TRP A 67 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (19680) covalent geometry : angle 0.50816 / 0.27 (26630) SS BOND : bond 0.00596 / 0.39 ( 5) SS BOND : angle 0.24289 / 0.16 ( 10) hydrogen bonds : bond 0.03941 / 2.67 ( 925) hydrogen bonds : angle 4.12481 / 2.86 ( 2760) link_ALPHA1-3 : bond 0.00364 / 0.24 ( 5) link_ALPHA1-3 : angle 1.39204 / 1.02 ( 15) link_ALPHA1-6 : bond 0.00403 / 0.26 ( 5) link_ALPHA1-6 : angle 1.50947 / 1.11 ( 15) link_BETA1-4 : bond 0.00286 / 0.18 ( 15) link_BETA1-4 : angle 1.66918 / 1.15 ( 45) link_NAG-ASN : bond 0.00167 / 0.12 ( 10) link_NAG-ASN : angle 1.78820 / 1.23 ( 30) ********************** 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 289 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.774 Fit side-chains REVERT: A 40 MET cc_start: 0.8688 (mtt) cc_final: 0.8304 (mtt) REVERT: A 51 SER cc_start: 0.8166 (t) cc_final: 0.7823 (p) REVERT: O 421 MET cc_start: 0.7140 (mmm) cc_final: 0.6682 (mmm) REVERT: D 51 SER cc_start: 0.8088 (t) cc_final: 0.7820 (p) REVERT: D 261 MET cc_start: 0.8929 (mmm) cc_final: 0.8578 (mmm) REVERT: H 40 MET cc_start: 0.8632 (mtt) cc_final: 0.8242 (mtt) REVERT: H 51 SER cc_start: 0.8317 (t) cc_final: 0.7950 (p) REVERT: I 470 MET cc_start: 0.3781 (mpp) cc_final: 0.3050 (mpp) REVERT: L 51 SER cc_start: 0.8264 (t) cc_final: 0.7894 (p) REVERT: M 421 MET cc_start: 0.6930 (mmm) cc_final: 0.6500 (mmm) REVERT: Q 51 SER cc_start: 0.8311 (t) cc_final: 0.7960 (p) REVERT: Q 224 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: R 421 MET cc_start: 0.7085 (mmm) cc_final: 0.6638 (mmm) outliers start: 35 outliers final: 31 residues processed: 278 average time/residue: 0.1556 time to fit residues: 65.8127 Evaluate side-chains 281 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 132 THR Chi-restraints excluded: chain D residue 176 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 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 109 VAL Chi-restraints excluded: chain L residue 132 THR 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 223 LEU Chi-restraints excluded: chain Q residue 224 GLN 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 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 191 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 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 = 0.3554 r_free = 0.3554 target = 0.147011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109351 restraints weight = 23405.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.107428 restraints weight = 44762.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108752 restraints weight = 36034.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.108079 restraints weight = 22097.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108691 restraints weight = 20194.291| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19720 Z= 0.122 Angle : 0.527 7.740 26745 Z= 0.273 Chirality : 0.043 0.208 2995 Planarity : 0.004 0.036 3260 Dihedral : 6.610 57.607 3267 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.67 % Allowed : 16.30 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2245 helix: 1.83 (0.20), residues: 645 sheet: 0.63 (0.19), residues: 690 loop : -0.07 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.029 0.002 TYR D 299 PHE 0.016 0.001 PHE L 301 TRP 0.011 0.001 TRP I 440 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19680) covalent geometry : angle 0.51757 / 0.27 (26630) SS BOND : bond 0.00595 / 0.38 ( 5) SS BOND : angle 0.13791 / 0.09 ( 10) hydrogen bonds : bond 0.04019 / 2.72 ( 925) hydrogen bonds : angle 4.11323 / 2.86 ( 2760) link_ALPHA1-3 : bond 0.00355 / 0.23 ( 5) link_ALPHA1-3 : angle 1.32484 / 0.96 ( 15) link_ALPHA1-6 : bond 0.00394 / 0.26 ( 5) link_ALPHA1-6 : angle 1.54779 / 1.14 ( 15) link_BETA1-4 : bond 0.00270 / 0.17 ( 15) link_BETA1-4 : angle 1.69699 / 1.18 ( 45) link_NAG-ASN : bond 0.00168 / 0.12 ( 10) link_NAG-ASN : angle 1.85855 / 1.28 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.73 seconds wall clock time: 62 minutes 5.60 seconds (3725.60 seconds total)