Starting phenix.real_space_refine on Sun Aug 24 12:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_17960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_17960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_17960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_17960.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_17960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvb_17960/08_2025/8pvb_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 2.66, per 1000 atoms: 0.14 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: 1.33 Conformation dependent library (CDL) restraints added in 767.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.83 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: 3.61 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3418 1.33 - 1.46: 5987 1.46 - 1.58: 10105 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 19680 Sorted by residual: bond pdb=" CG HIS A 119 " pdb=" CD2 HIS A 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" CG HIS Q 119 " pdb=" CD2 HIS Q 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.91e+01 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS L 119 " pdb=" CD2 HIS L 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS D 119 " pdb=" CD2 HIS D 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.88e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19557 1.82 - 3.65: 6094 3.65 - 5.47: 856 5.47 - 7.30: 113 7.30 - 9.12: 10 Bond angle restraints: 26630 Sorted by residual: angle pdb=" CA ASP A 101 " pdb=" CB ASP A 101 " pdb=" CG ASP A 101 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 angle pdb=" CA ASP Q 101 " pdb=" CB ASP Q 101 " pdb=" CG ASP Q 101 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA ASP D 101 " pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP L 101 " pdb=" CB ASP L 101 " pdb=" CG ASP L 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.39e+01 ... (remaining 26625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 11074 20.75 - 41.49: 646 41.49 - 62.24: 135 62.24 - 82.98: 70 82.98 - 103.73: 25 Dihedral angle restraints: 11950 sinusoidal: 5300 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 11947 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: 0.06 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: 1.960 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 16.050 Find NCS groups from input model: 0.170 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.065 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 : 16.051 103.727 7705 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 5.22 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01049 (19680) covalent geometry : angle 1.70069 (26630) SS BOND : bond 0.01005 ( 5) SS BOND : angle 2.35004 ( 10) hydrogen bonds : bond 0.18631 ( 925) hydrogen bonds : angle 7.25285 ( 2760) link_ALPHA1-3 : bond 0.03524 ( 5) link_ALPHA1-3 : angle 7.42163 ( 15) link_ALPHA1-6 : bond 0.02872 ( 5) link_ALPHA1-6 : angle 7.04574 ( 15) link_BETA1-4 : bond 0.04636 ( 15) link_BETA1-4 : angle 7.94350 ( 45) link_NAG-ASN : bond 0.04757 ( 10) link_NAG-ASN : angle 8.23235 ( 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 : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8142 (t) cc_final: 0.7938 (m) REVERT: A 51 SER cc_start: 0.7489 (t) cc_final: 0.6681 (p) REVERT: A 99 LEU cc_start: 0.8533 (tt) cc_final: 0.8292 (tt) REVERT: A 139 ASP cc_start: 0.7484 (t0) cc_final: 0.7039 (p0) REVERT: A 148 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7377 (mm110) REVERT: A 163 ASP cc_start: 0.7616 (m-30) cc_final: 0.7041 (m-30) REVERT: A 190 GLU cc_start: 0.7612 (tt0) cc_final: 0.7297 (tt0) REVERT: A 213 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6652 (tpp80) REVERT: A 283 MET cc_start: 0.8211 (mmm) cc_final: 0.7866 (mmt) REVERT: D 12 VAL cc_start: 0.8217 (t) cc_final: 0.7890 (m) REVERT: D 41 ASN cc_start: 0.8235 (m110) cc_final: 0.7951 (m-40) REVERT: D 51 SER cc_start: 0.7687 (t) cc_final: 0.6826 (p) REVERT: D 139 ASP cc_start: 0.7445 (t0) cc_final: 0.7034 (p0) REVERT: D 148 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7284 (mm-40) REVERT: D 155 GLU cc_start: 0.8540 (tt0) cc_final: 0.8275 (tt0) REVERT: D 163 ASP cc_start: 0.7610 (m-30) cc_final: 0.7123 (m-30) REVERT: D 190 GLU cc_start: 0.7467 (tt0) cc_final: 0.7162 (tt0) REVERT: D 213 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6620 (tpp80) REVERT: D 301 PHE cc_start: 0.7842 (t80) cc_final: 0.7630 (t80) REVERT: D 425 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7072 (ttp-110) REVERT: H 16 VAL cc_start: 0.8085 (t) cc_final: 0.7859 (m) REVERT: H 51 SER cc_start: 0.7679 (t) cc_final: 0.6669 (p) REVERT: H 139 ASP cc_start: 0.7462 (t0) cc_final: 0.6918 (p0) REVERT: H 147 GLU cc_start: 0.6541 (tt0) cc_final: 0.6235 (mm-30) REVERT: H 148 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7348 (mm-40) REVERT: H 155 GLU cc_start: 0.8581 (tt0) cc_final: 0.8250 (tt0) REVERT: H 163 ASP cc_start: 0.7605 (m-30) cc_final: 0.7296 (m-30) REVERT: H 190 GLU cc_start: 0.7607 (tt0) cc_final: 0.7280 (tt0) REVERT: H 213 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6408 (tpp80) REVERT: H 283 MET cc_start: 0.8229 (mmm) cc_final: 0.7989 (mmt) REVERT: H 301 PHE cc_start: 0.7944 (t80) cc_final: 0.7730 (t80) REVERT: L 16 VAL cc_start: 0.8175 (t) cc_final: 0.7932 (m) REVERT: L 41 ASN cc_start: 0.8240 (m110) cc_final: 0.7785 (m110) REVERT: L 51 SER cc_start: 0.7615 (t) cc_final: 0.6633 (p) REVERT: L 61 MET cc_start: 0.9039 (ptt) cc_final: 0.8805 (ptt) REVERT: L 139 ASP cc_start: 0.7590 (t0) cc_final: 0.7130 (p0) REVERT: L 144 PRO cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (Cg_endo) REVERT: L 148 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7393 (mm-40) REVERT: L 153 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8037 (mm-30) REVERT: L 155 GLU cc_start: 0.8538 (tt0) cc_final: 0.8090 (tt0) REVERT: L 163 ASP cc_start: 0.7732 (m-30) cc_final: 0.7408 (m-30) REVERT: L 190 GLU cc_start: 0.7622 (tt0) cc_final: 0.7259 (tt0) REVERT: L 213 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6694 (tpp80) REVERT: L 303 ASN cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: L 425 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7174 (ttp-170) REVERT: Q 41 ASN cc_start: 0.8261 (m110) cc_final: 0.7911 (m-40) REVERT: Q 43 ASP cc_start: 0.8304 (t70) cc_final: 0.8068 (t70) REVERT: Q 51 SER cc_start: 0.7523 (t) cc_final: 0.6585 (p) REVERT: Q 139 ASP cc_start: 0.7474 (t0) cc_final: 0.7097 (p0) REVERT: Q 153 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8120 (mm-30) REVERT: Q 163 ASP cc_start: 0.7598 (m-30) cc_final: 0.7157 (m-30) REVERT: Q 180 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6673 (mtt180) REVERT: Q 190 GLU cc_start: 0.7631 (tt0) cc_final: 0.7322 (tt0) REVERT: Q 224 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: Q 227 MET cc_start: 0.7599 (ttm) cc_final: 0.7325 (ttp) REVERT: Q 425 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7081 (ttp-170) outliers start: 25 outliers final: 16 residues processed: 426 average time/residue: 0.1734 time to fit residues: 107.7962 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 : 0.752 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 185 GLN D 185 GLN H 41 ASN H 185 GLN L 185 GLN L 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111445 restraints weight = 23481.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109621 restraints weight = 46273.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.106281 restraints weight = 40098.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.102115 restraints weight = 23828.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.102392 restraints weight = 24988.061| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1861 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= 0.155 Angle : 0.642 6.811 26745 Z= 0.336 Chirality : 0.047 0.182 2995 Planarity : 0.004 0.041 3260 Dihedral : 11.375 77.020 3589 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.92 % Allowed : 7.14 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2245 helix: 1.42 (0.20), residues: 615 sheet: 0.66 (0.19), residues: 670 loop : 0.33 (0.20), residues: 960 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 0.018 0.002 PHE L 306 TRP 0.008 0.001 TRP R 440 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00335 (19680) covalent geometry : angle 0.62200 (26630) SS BOND : bond 0.00382 ( 5) SS BOND : angle 0.77014 ( 10) hydrogen bonds : bond 0.05593 ( 925) hydrogen bonds : angle 5.03502 ( 2760) link_ALPHA1-3 : bond 0.00907 ( 5) link_ALPHA1-3 : angle 2.15436 ( 15) link_ALPHA1-6 : bond 0.00366 ( 5) link_ALPHA1-6 : angle 1.42638 ( 15) link_BETA1-4 : bond 0.00335 ( 15) link_BETA1-4 : angle 2.53154 ( 45) link_NAG-ASN : bond 0.00426 ( 10) link_NAG-ASN : angle 3.28113 ( 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 331 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8262 (t) cc_final: 0.7867 (p) REVERT: A 55 MET cc_start: 0.7645 (mtp) cc_final: 0.7426 (mtt) REVERT: A 298 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7753 (tm-30) REVERT: D 41 ASN cc_start: 0.8360 (m110) cc_final: 0.8113 (m110) REVERT: D 51 SER cc_start: 0.8320 (t) cc_final: 0.7948 (p) REVERT: D 99 LEU cc_start: 0.8883 (tt) cc_final: 0.8639 (tt) REVERT: H 51 SER cc_start: 0.8375 (t) cc_final: 0.7859 (p) REVERT: H 155 GLU cc_start: 0.7957 (tt0) cc_final: 0.7756 (tt0) REVERT: H 190 GLU cc_start: 0.7603 (tt0) cc_final: 0.7396 (tt0) REVERT: H 283 MET cc_start: 0.7988 (mmm) cc_final: 0.7496 (mmt) REVERT: L 51 SER cc_start: 0.8280 (t) cc_final: 0.7760 (p) REVERT: L 303 ASN cc_start: 0.8909 (t0) cc_final: 0.8696 (t0) REVERT: Q 51 SER cc_start: 0.8239 (t) cc_final: 0.7724 (p) REVERT: Q 224 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: R 424 PHE cc_start: 0.5986 (m-80) cc_final: 0.5773 (m-80) outliers start: 38 outliers final: 24 residues processed: 320 average time/residue: 0.1662 time to fit residues: 78.5286 Evaluate side-chains 290 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 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 M residue 459 ARG Chi-restraints excluded: chain Q residue 162 ASP 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: 0.9980 chunk 128 optimal weight: 9.9990 chunk 164 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 64 GLN D 185 GLN H 41 ASN 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 = 0.3547 r_free = 0.3547 target = 0.146311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.105148 restraints weight = 23560.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.099901 restraints weight = 24165.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.099787 restraints weight = 26792.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.101184 restraints weight = 22770.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.101238 restraints weight = 18080.054| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- 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 = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19720 Z= 0.178 Angle : 0.608 7.029 26745 Z= 0.318 Chirality : 0.047 0.235 2995 Planarity : 0.004 0.040 3260 Dihedral : 10.571 72.551 3573 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.87 % Allowed : 9.87 % Favored : 88.25 % 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 aren not related in a simple way. whole: 1.04 (0.17), residues: 2245 helix: 1.70 (0.20), residues: 615 sheet: 0.56 (0.19), residues: 680 loop : 0.25 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 213 TYR 0.028 0.002 TYR D 299 PHE 0.014 0.002 PHE D 98 TRP 0.008 0.001 TRP H 443 HIS 0.003 0.001 HIS H 267 Details of bonding type rmsd covalent geometry : bond 0.00410 (19680) covalent geometry : angle 0.59173 (26630) SS BOND : bond 0.00422 ( 5) SS BOND : angle 0.50495 ( 10) hydrogen bonds : bond 0.05057 ( 925) hydrogen bonds : angle 4.57771 ( 2760) link_ALPHA1-3 : bond 0.01058 ( 5) link_ALPHA1-3 : angle 1.42009 ( 15) link_ALPHA1-6 : bond 0.00543 ( 5) link_ALPHA1-6 : angle 1.64242 ( 15) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 2.32602 ( 45) link_NAG-ASN : bond 0.00153 ( 10) link_NAG-ASN : angle 2.90765 ( 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 308 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.756 Fit side-chains REVERT: A 51 SER cc_start: 0.8265 (t) cc_final: 0.7940 (p) REVERT: A 180 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7752 (mtm180) REVERT: O 421 MET cc_start: 0.7152 (mmm) cc_final: 0.6304 (mmm) REVERT: O 470 MET cc_start: 0.3552 (mpp) cc_final: 0.3082 (mtm) REVERT: D 51 SER cc_start: 0.8226 (t) cc_final: 0.7966 (p) REVERT: E 421 MET cc_start: 0.7143 (mmm) cc_final: 0.6391 (mmm) REVERT: E 470 MET cc_start: 0.3651 (mpp) cc_final: 0.3298 (mtm) REVERT: H 40 MET cc_start: 0.8564 (mtt) cc_final: 0.8148 (mtt) REVERT: H 51 SER cc_start: 0.8393 (t) cc_final: 0.8002 (p) REVERT: H 147 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6556 (mm-30) REVERT: H 425 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7712 (mtm-85) REVERT: I 470 MET cc_start: 0.3681 (mpp) cc_final: 0.3197 (mtm) REVERT: L 51 SER cc_start: 0.8257 (t) cc_final: 0.7998 (p) REVERT: L 298 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8184 (tm-30) REVERT: Q 51 SER cc_start: 0.8253 (t) cc_final: 0.7896 (p) REVERT: Q 224 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: R 421 MET cc_start: 0.7052 (mmm) cc_final: 0.6249 (mmm) outliers start: 37 outliers final: 21 residues processed: 296 average time/residue: 0.1692 time to fit residues: 73.9537 Evaluate side-chains 269 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 223 LEU 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 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: 0.9980 chunk 30 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 64 GLN D 185 GLN 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 = 0.3547 r_free = 0.3547 target = 0.146128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.105444 restraints weight = 23562.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.100353 restraints weight = 23733.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.100242 restraints weight = 24813.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.101020 restraints weight = 22281.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.101014 restraints weight = 21931.114| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19720 Z= 0.165 Angle : 0.573 6.643 26745 Z= 0.298 Chirality : 0.046 0.187 2995 Planarity : 0.004 0.040 3260 Dihedral : 9.936 67.045 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.23 % Allowed : 10.23 % Favored : 87.54 % 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 aren not related in a simple way. whole: 1.07 (0.18), residues: 2245 helix: 1.86 (0.20), residues: 615 sheet: 0.51 (0.19), residues: 690 loop : 0.22 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 213 TYR 0.028 0.002 TYR D 299 PHE 0.016 0.002 PHE R 424 TRP 0.007 0.001 TRP A 67 HIS 0.004 0.001 HIS L 267 Details of bonding type rmsd covalent geometry : bond 0.00379 (19680) covalent geometry : angle 0.55754 (26630) SS BOND : bond 0.00500 ( 5) SS BOND : angle 0.45436 ( 10) hydrogen bonds : bond 0.04710 ( 925) hydrogen bonds : angle 4.42781 ( 2760) link_ALPHA1-3 : bond 0.00908 ( 5) link_ALPHA1-3 : angle 1.84203 ( 15) link_ALPHA1-6 : bond 0.00741 ( 5) link_ALPHA1-6 : angle 1.58313 ( 15) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 2.06789 ( 45) link_NAG-ASN : bond 0.00220 ( 10) link_NAG-ASN : angle 2.64935 ( 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 315 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.827 Fit side-chains REVERT: A 40 MET cc_start: 0.8739 (mtt) cc_final: 0.8317 (mtt) REVERT: A 51 SER cc_start: 0.8175 (t) cc_final: 0.7846 (p) REVERT: A 298 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8117 (tm-30) REVERT: O 470 MET cc_start: 0.3981 (mpp) cc_final: 0.3502 (mtm) REVERT: D 51 SER cc_start: 0.8198 (t) cc_final: 0.7892 (p) REVERT: H 40 MET cc_start: 0.8631 (mtt) cc_final: 0.8234 (mtt) REVERT: H 51 SER cc_start: 0.8368 (t) cc_final: 0.8001 (p) REVERT: L 51 SER cc_start: 0.8322 (t) cc_final: 0.7973 (p) REVERT: M 421 MET cc_start: 0.7241 (mmm) cc_final: 0.6193 (mmm) REVERT: Q 20 LEU cc_start: 0.7915 (mt) cc_final: 0.7706 (mt) REVERT: Q 51 SER cc_start: 0.8291 (t) cc_final: 0.7929 (p) REVERT: Q 224 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.6903 (mp10) outliers start: 44 outliers final: 35 residues processed: 305 average time/residue: 0.1512 time to fit residues: 70.0763 Evaluate side-chains 282 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 255 ILE 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 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 423 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN L 64 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.106662 restraints weight = 23398.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.102012 restraints weight = 22303.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.101545 restraints weight = 24539.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.102395 restraints weight = 21963.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.102646 restraints weight = 17710.759| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 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 = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19720 Z= 0.135 Angle : 0.546 7.851 26745 Z= 0.281 Chirality : 0.045 0.214 2995 Planarity : 0.004 0.038 3260 Dihedral : 9.429 62.427 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.13 % Allowed : 11.54 % Favored : 86.33 % 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 aren not related in a simple way. whole: 1.01 (0.18), residues: 2245 helix: 1.73 (0.20), residues: 645 sheet: 0.63 (0.19), residues: 680 loop : 0.05 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 213 TYR 0.029 0.002 TYR L 299 PHE 0.011 0.001 PHE A 98 TRP 0.008 0.001 TRP L 67 HIS 0.003 0.001 HIS H 267 Details of bonding type rmsd covalent geometry : bond 0.00306 (19680) covalent geometry : angle 0.53330 (26630) SS BOND : bond 0.00477 ( 5) SS BOND : angle 0.37192 ( 10) hydrogen bonds : bond 0.04352 ( 925) hydrogen bonds : angle 4.30946 ( 2760) link_ALPHA1-3 : bond 0.00988 ( 5) link_ALPHA1-3 : angle 1.68854 ( 15) link_ALPHA1-6 : bond 0.00894 ( 5) link_ALPHA1-6 : angle 1.53717 ( 15) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.87094 ( 45) link_NAG-ASN : bond 0.00170 ( 10) link_NAG-ASN : angle 2.39962 ( 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 303 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8194 (t) cc_final: 0.7883 (p) REVERT: O 470 MET cc_start: 0.3989 (mpp) cc_final: 0.3607 (mtm) REVERT: D 51 SER cc_start: 0.8129 (t) cc_final: 0.7851 (p) REVERT: E 421 MET cc_start: 0.7132 (mmm) cc_final: 0.6203 (mmm) REVERT: H 40 MET cc_start: 0.8650 (mtt) cc_final: 0.8242 (mtt) REVERT: H 51 SER cc_start: 0.8324 (t) cc_final: 0.7845 (p) REVERT: L 51 SER cc_start: 0.8267 (t) cc_final: 0.7925 (p) REVERT: Q 51 SER cc_start: 0.8303 (t) cc_final: 0.7957 (p) REVERT: Q 224 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: R 421 MET cc_start: 0.7187 (mmm) cc_final: 0.6375 (mmm) outliers start: 42 outliers final: 33 residues processed: 293 average time/residue: 0.1638 time to fit residues: 72.1075 Evaluate side-chains 279 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain D residue 164 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 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 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 Chi-restraints excluded: chain R residue 459 ARG 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: 1.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 309 GLN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.145359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.103881 restraints weight = 23365.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.101931 restraints weight = 40256.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103748 restraints weight = 33852.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.103315 restraints weight = 21840.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.103939 restraints weight = 22629.507| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19720 Z= 0.200 Angle : 0.594 7.518 26745 Z= 0.306 Chirality : 0.046 0.219 2995 Planarity : 0.004 0.037 3260 Dihedral : 9.745 60.718 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.63 % Allowed : 12.20 % Favored : 85.16 % 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 aren not related in a simple way. whole: 0.80 (0.18), residues: 2245 helix: 1.61 (0.20), residues: 645 sheet: 0.31 (0.19), residues: 710 loop : 0.05 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 180 TYR 0.028 0.002 TYR D 299 PHE 0.014 0.002 PHE A 98 TRP 0.006 0.001 TRP I 440 HIS 0.004 0.001 HIS L 267 Details of bonding type rmsd covalent geometry : bond 0.00473 (19680) covalent geometry : angle 0.57899 (26630) SS BOND : bond 0.00504 ( 5) SS BOND : angle 0.42964 ( 10) hydrogen bonds : bond 0.04798 ( 925) hydrogen bonds : angle 4.36516 ( 2760) link_ALPHA1-3 : bond 0.00931 ( 5) link_ALPHA1-3 : angle 1.77876 ( 15) link_ALPHA1-6 : bond 0.00887 ( 5) link_ALPHA1-6 : angle 1.54857 ( 15) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 2.08501 ( 45) link_NAG-ASN : bond 0.00129 ( 10) link_NAG-ASN : angle 2.73221 ( 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 311 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8235 (t) cc_final: 0.7898 (p) REVERT: O 470 MET cc_start: 0.4134 (mpp) cc_final: 0.3602 (mtm) REVERT: D 51 SER cc_start: 0.8132 (t) cc_final: 0.7858 (p) REVERT: H 40 MET cc_start: 0.8653 (mtt) cc_final: 0.8233 (mtt) REVERT: H 51 SER cc_start: 0.8283 (t) cc_final: 0.7918 (p) REVERT: I 470 MET cc_start: 0.3970 (mpp) cc_final: 0.3560 (mpp) REVERT: L 40 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7410 (mmt) REVERT: L 51 SER cc_start: 0.8298 (t) cc_final: 0.7936 (p) REVERT: L 298 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8128 (tm-30) REVERT: Q 51 SER cc_start: 0.8332 (t) cc_final: 0.7995 (p) REVERT: Q 224 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: Q 298 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8101 (tm-30) outliers start: 52 outliers final: 39 residues processed: 295 average time/residue: 0.1704 time to fit residues: 74.6519 Evaluate side-chains 282 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 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 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 I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 130 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 119 optimal weight: 0.0270 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 461 ASN D 185 GLN E 461 ASN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.147926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.111787 restraints weight = 23366.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109394 restraints weight = 52206.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110337 restraints weight = 41977.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109101 restraints weight = 26864.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109811 restraints weight = 24055.798| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 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 = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19720 Z= 0.109 Angle : 0.530 7.561 26745 Z= 0.272 Chirality : 0.044 0.242 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.858 59.511 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.42 % Allowed : 14.53 % Favored : 84.05 % 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 aren not related in a simple way. whole: 1.03 (0.18), residues: 2245 helix: 1.81 (0.20), residues: 645 sheet: 0.38 (0.19), residues: 705 loop : 0.25 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.028 0.001 TYR Q 299 PHE 0.014 0.001 PHE L 11 TRP 0.007 0.001 TRP L 67 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd covalent geometry : bond 0.00233 (19680) covalent geometry : angle 0.52063 (26630) SS BOND : bond 0.00550 ( 5) SS BOND : angle 0.36701 ( 10) hydrogen bonds : bond 0.04003 ( 925) hydrogen bonds : angle 4.21702 ( 2760) link_ALPHA1-3 : bond 0.01033 ( 5) link_ALPHA1-3 : angle 1.60519 ( 15) link_ALPHA1-6 : bond 0.01139 ( 5) link_ALPHA1-6 : angle 1.46386 ( 15) link_BETA1-4 : bond 0.00339 ( 15) link_BETA1-4 : angle 1.56879 ( 45) link_NAG-ASN : bond 0.00208 ( 10) link_NAG-ASN : angle 2.01147 ( 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 289 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.8220 (t) cc_final: 0.7889 (p) REVERT: O 470 MET cc_start: 0.4054 (mpp) cc_final: 0.3465 (mtm) REVERT: D 51 SER cc_start: 0.8150 (t) cc_final: 0.7909 (p) REVERT: E 421 MET cc_start: 0.6989 (mmm) cc_final: 0.6454 (mmm) REVERT: H 40 MET cc_start: 0.8597 (mtt) cc_final: 0.8206 (mtt) REVERT: H 51 SER cc_start: 0.8338 (t) cc_final: 0.7973 (p) REVERT: H 235 LEU cc_start: 0.9283 (tp) cc_final: 0.8994 (tt) REVERT: I 470 MET cc_start: 0.3929 (mpp) cc_final: 0.3482 (mpp) REVERT: L 40 MET cc_start: 0.8429 (mmt) cc_final: 0.8221 (mtt) REVERT: L 51 SER cc_start: 0.8194 (t) cc_final: 0.7841 (p) REVERT: Q 51 SER cc_start: 0.8286 (t) cc_final: 0.7959 (p) REVERT: Q 224 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6656 (mp10) REVERT: Q 298 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 28 outliers final: 23 residues processed: 283 average time/residue: 0.1632 time to fit residues: 69.5385 Evaluate side-chains 272 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE 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 M residue 459 ARG 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: 9.9990 chunk 60 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.0570 chunk 161 optimal weight: 4.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 185 GLN 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 = 0.3547 r_free = 0.3547 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107712 restraints weight = 23434.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.106085 restraints weight = 39801.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.105871 restraints weight = 34366.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102446 restraints weight = 19116.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102667 restraints weight = 18798.861| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19720 Z= 0.151 Angle : 0.557 7.549 26745 Z= 0.285 Chirality : 0.045 0.245 2995 Planarity : 0.004 0.036 3260 Dihedral : 8.676 57.703 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.82 % Allowed : 15.65 % Favored : 82.53 % 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 aren not related in a simple way. whole: 0.95 (0.18), residues: 2245 helix: 1.73 (0.20), residues: 645 sheet: 0.37 (0.19), residues: 705 loop : 0.18 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.028 0.002 TYR H 299 PHE 0.013 0.001 PHE Q 31 TRP 0.010 0.001 TRP R 440 HIS 0.002 0.001 HIS Q 191 Details of bonding type rmsd covalent geometry : bond 0.00349 (19680) covalent geometry : angle 0.54507 (26630) SS BOND : bond 0.00563 ( 5) SS BOND : angle 0.21720 ( 10) hydrogen bonds : bond 0.04298 ( 925) hydrogen bonds : angle 4.21074 ( 2760) link_ALPHA1-3 : bond 0.01004 ( 5) link_ALPHA1-3 : angle 1.57238 ( 15) link_ALPHA1-6 : bond 0.01099 ( 5) link_ALPHA1-6 : angle 1.42651 ( 15) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 1.80796 ( 45) link_NAG-ASN : bond 0.00157 ( 10) link_NAG-ASN : angle 2.28216 ( 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 288 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.8244 (t) cc_final: 0.7890 (p) REVERT: O 421 MET cc_start: 0.7225 (mmm) cc_final: 0.6779 (mmm) REVERT: O 470 MET cc_start: 0.3967 (mpp) cc_final: 0.3666 (mtm) REVERT: D 51 SER cc_start: 0.8159 (t) cc_final: 0.7871 (p) REVERT: E 421 MET cc_start: 0.7134 (mmm) cc_final: 0.6862 (mmm) REVERT: H 40 MET cc_start: 0.8613 (mtt) cc_final: 0.8208 (mtt) REVERT: H 51 SER cc_start: 0.8372 (t) cc_final: 0.7969 (p) REVERT: I 470 MET cc_start: 0.3765 (mpp) cc_final: 0.3092 (mpp) REVERT: L 51 SER cc_start: 0.8277 (t) cc_final: 0.7894 (p) REVERT: L 61 MET cc_start: 0.8752 (ptt) cc_final: 0.8519 (ptt) REVERT: L 298 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8238 (tm-30) REVERT: Q 51 SER cc_start: 0.8328 (t) cc_final: 0.7982 (p) REVERT: Q 224 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: Q 298 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8151 (tm-30) REVERT: R 421 MET cc_start: 0.7355 (mmm) cc_final: 0.6727 (mmm) outliers start: 36 outliers final: 31 residues processed: 277 average time/residue: 0.1658 time to fit residues: 68.7402 Evaluate side-chains 273 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 223 LEU 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 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 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: 3.9990 chunk 100 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN H 41 ASN H 64 GLN M 461 ASN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109092 restraints weight = 23251.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107766 restraints weight = 40896.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108260 restraints weight = 38341.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108174 restraints weight = 22927.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108522 restraints weight = 20442.828| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3539 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 : 0.534 7.932 26745 Z= 0.272 Chirality : 0.044 0.248 2995 Planarity : 0.004 0.036 3260 Dihedral : 8.188 59.517 3553 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.37 % Allowed : 15.95 % Favored : 82.68 % 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 aren not related in a simple way. whole: 1.00 (0.18), residues: 2245 helix: 1.81 (0.20), residues: 645 sheet: 0.40 (0.19), residues: 710 loop : 0.16 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.028 0.001 TYR D 299 PHE 0.011 0.001 PHE L 11 TRP 0.007 0.001 TRP H 168 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd covalent geometry : bond 0.00273 (19680) covalent geometry : angle 0.52486 (26630) SS BOND : bond 0.00544 ( 5) SS BOND : angle 0.23791 ( 10) hydrogen bonds : bond 0.04013 ( 925) hydrogen bonds : angle 4.15704 ( 2760) link_ALPHA1-3 : bond 0.01028 ( 5) link_ALPHA1-3 : angle 1.51432 ( 15) link_ALPHA1-6 : bond 0.01188 ( 5) link_ALPHA1-6 : angle 1.40192 ( 15) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.55815 ( 45) link_NAG-ASN : bond 0.00179 ( 10) link_NAG-ASN : angle 1.99478 ( 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 275 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.881 Fit side-chains REVERT: A 51 SER cc_start: 0.8232 (t) cc_final: 0.7894 (p) REVERT: O 421 MET cc_start: 0.7179 (mmm) cc_final: 0.6702 (mmm) REVERT: O 470 MET cc_start: 0.3963 (mpp) cc_final: 0.3515 (mtm) REVERT: D 51 SER cc_start: 0.8132 (t) cc_final: 0.7867 (p) REVERT: H 40 MET cc_start: 0.8606 (mtt) cc_final: 0.8204 (mtt) REVERT: H 51 SER cc_start: 0.8335 (t) cc_final: 0.7984 (p) REVERT: H 235 LEU cc_start: 0.9270 (tp) cc_final: 0.8992 (tt) REVERT: I 470 MET cc_start: 0.3937 (mpp) cc_final: 0.3254 (mpp) REVERT: L 51 SER cc_start: 0.8245 (t) cc_final: 0.7895 (p) REVERT: Q 51 SER cc_start: 0.8298 (t) cc_final: 0.7971 (p) REVERT: Q 224 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: Q 298 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8217 (tm-30) REVERT: R 421 MET cc_start: 0.7306 (mmm) cc_final: 0.6683 (mmm) outliers start: 27 outliers final: 23 residues processed: 269 average time/residue: 0.1602 time to fit residues: 65.4684 Evaluate side-chains 268 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 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: 0.9980 chunk 218 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109538 restraints weight = 23448.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107811 restraints weight = 42241.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.108171 restraints weight = 37658.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.107030 restraints weight = 24847.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107693 restraints weight = 21718.976| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3658 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= 0.114 Angle : 0.528 8.041 26745 Z= 0.268 Chirality : 0.044 0.246 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.677 57.600 3552 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 : 1.06 % Allowed : 16.61 % 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 aren not related in a simple way. whole: 1.05 (0.18), residues: 2245 helix: 1.87 (0.20), residues: 645 sheet: 0.59 (0.19), residues: 690 loop : 0.04 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.029 0.001 TYR Q 299 PHE 0.011 0.001 PHE L 11 TRP 0.009 0.001 TRP E 440 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd covalent geometry : bond 0.00250 (19680) covalent geometry : angle 0.51897 (26630) SS BOND : bond 0.00619 ( 5) SS BOND : angle 0.20260 ( 10) hydrogen bonds : bond 0.03875 ( 925) hydrogen bonds : angle 4.10477 ( 2760) link_ALPHA1-3 : bond 0.01046 ( 5) link_ALPHA1-3 : angle 1.44411 ( 15) link_ALPHA1-6 : bond 0.01228 ( 5) link_ALPHA1-6 : angle 1.37471 ( 15) link_BETA1-4 : bond 0.00317 ( 15) link_BETA1-4 : angle 1.54412 ( 45) link_NAG-ASN : bond 0.00172 ( 10) link_NAG-ASN : angle 1.88129 ( 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 270 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.772 Fit side-chains REVERT: A 51 SER cc_start: 0.8237 (t) cc_final: 0.7922 (p) REVERT: O 421 MET cc_start: 0.7207 (mmm) cc_final: 0.6668 (mmm) REVERT: O 470 MET cc_start: 0.3899 (mpp) cc_final: 0.3527 (mtm) REVERT: D 51 SER cc_start: 0.8171 (t) cc_final: 0.7920 (p) REVERT: D 261 MET cc_start: 0.8900 (mmm) cc_final: 0.8513 (mmm) REVERT: E 421 MET cc_start: 0.7201 (mmm) cc_final: 0.6717 (mmm) REVERT: E 470 MET cc_start: 0.4209 (mpp) cc_final: 0.3662 (mtm) REVERT: H 40 MET cc_start: 0.8631 (mtt) cc_final: 0.8215 (mtt) REVERT: H 51 SER cc_start: 0.8313 (t) cc_final: 0.7992 (p) REVERT: H 235 LEU cc_start: 0.9242 (tp) cc_final: 0.9003 (tt) REVERT: L 51 SER cc_start: 0.8252 (t) cc_final: 0.7911 (p) REVERT: L 68 ARG cc_start: 0.7307 (ttm170) cc_final: 0.7003 (ttm170) REVERT: Q 41 ASN cc_start: 0.8115 (m110) cc_final: 0.7763 (m-40) REVERT: Q 51 SER cc_start: 0.8306 (t) cc_final: 0.7989 (p) REVERT: Q 224 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: Q 298 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8254 (tm-30) REVERT: R 421 MET cc_start: 0.7173 (mmm) cc_final: 0.6602 (mmm) outliers start: 21 outliers final: 20 residues processed: 268 average time/residue: 0.1594 time to fit residues: 65.0630 Evaluate side-chains 262 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 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 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: 0.9990 chunk 124 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.147373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.105867 restraints weight = 23420.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.100462 restraints weight = 21939.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.100815 restraints weight = 22854.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.101399 restraints weight = 21059.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.101602 restraints weight = 17527.185| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3704 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= 0.126 Angle : 0.535 7.817 26745 Z= 0.273 Chirality : 0.044 0.247 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.499 57.624 3549 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.11 % Allowed : 16.46 % Favored : 82.43 % 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 aren not related in a simple way. whole: 1.04 (0.18), residues: 2245 helix: 1.84 (0.20), residues: 645 sheet: 0.48 (0.19), residues: 710 loop : 0.13 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.031 0.002 TYR H 66 PHE 0.020 0.001 PHE Q 301 TRP 0.006 0.001 TRP A 168 HIS 0.003 0.001 HIS Q 191 Details of bonding type rmsd covalent geometry : bond 0.00282 (19680) covalent geometry : angle 0.52642 (26630) SS BOND : bond 0.00551 ( 5) SS BOND : angle 0.08932 ( 10) hydrogen bonds : bond 0.03975 ( 925) hydrogen bonds : angle 4.11111 ( 2760) link_ALPHA1-3 : bond 0.01073 ( 5) link_ALPHA1-3 : angle 1.41252 ( 15) link_ALPHA1-6 : bond 0.01245 ( 5) link_ALPHA1-6 : angle 1.33369 ( 15) link_BETA1-4 : bond 0.00294 ( 15) link_BETA1-4 : angle 1.55801 ( 45) link_NAG-ASN : bond 0.00157 ( 10) link_NAG-ASN : angle 1.96650 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3457.34 seconds wall clock time: 60 minutes 41.33 seconds (3641.33 seconds total)