Starting phenix.real_space_refine on Sat Sep 28 16:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_17960.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_17960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_17960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_17960.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/09_2024/8pvb_17960.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 Cl 10 4.86 5 C 12530 2.51 5 N 3080 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Restraints were copied for chains: D, H, L, Q, I, M, O, R, F, J, N, S, G, K, P, T Residues with excluded nonbonded symmetry interactions: 5 residue: pdb="CL CL A5407 " occ=0.20 residue: pdb="CL CL D5407 " occ=0.20 residue: pdb="CL CL H5407 " occ=0.20 residue: pdb="CL CL L5407 " occ=0.20 residue: pdb="CL CL Q5407 " occ=0.20 Time building chain proxies: 8.15, per 1000 atoms: 0.42 Number of scatterers: 19225 At special positions: 0 Unit cell: (142.416, 141.588, 125.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 100 16.00 O 3505 8.00 N 3080 7.00 C 12530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG B 1 " - " ASN A 80 " " NAG C 1 " - " ASN A 149 " " NAG F 1 " - " ASN D 80 " " NAG G 1 " - " ASN D 149 " " NAG J 1 " - " ASN H 80 " " NAG K 1 " - " ASN H 149 " " NAG N 1 " - " ASN L 80 " " NAG P 1 " - " ASN L 149 " " NAG S 1 " - " ASN Q 80 " " NAG T 1 " - " ASN Q 149 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 33.6% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'O' and resid 449 through 452 Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 246 through 270 removed outlier: 3.809A pdb=" N THR D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 449 through 452 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'H' and resid 8 through 21 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 84 through 91 Processing helix chain 'H' and resid 170 through 173 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP H 237 " --> pdb=" O THR H 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER H 239 " --> pdb=" O LEU H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 242 No H-bonds generated for 'chain 'H' and resid 240 through 242' Processing helix chain 'H' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 306 Processing helix chain 'H' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Proline residue: H 432 - end of helix Processing helix chain 'I' and resid 449 through 452 Processing helix chain 'I' and resid 495 through 497 No H-bonds generated for 'chain 'I' and resid 495 through 497' Processing helix chain 'L' and resid 8 through 21 Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 84 through 91 Processing helix chain 'L' and resid 170 through 173 Processing helix chain 'L' and resid 177 through 181 Processing helix chain 'L' and resid 218 through 225 Processing helix chain 'L' and resid 225 through 239 removed outlier: 3.690A pdb=" N TRP L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER L 239 " --> pdb=" O LEU L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 242 No H-bonds generated for 'chain 'L' and resid 240 through 242' Processing helix chain 'L' and resid 246 through 270 removed outlier: 3.809A pdb=" N THR L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 263 " --> pdb=" O LEU L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 306 Processing helix chain 'L' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Proline residue: L 432 - end of helix Processing helix chain 'M' and resid 449 through 452 Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing helix chain 'Q' and resid 8 through 21 Processing helix chain 'Q' and resid 70 through 73 Processing helix chain 'Q' and resid 84 through 91 Processing helix chain 'Q' and resid 170 through 173 Processing helix chain 'Q' and resid 177 through 181 Processing helix chain 'Q' and resid 218 through 225 Processing helix chain 'Q' and resid 225 through 239 removed outlier: 3.691A pdb=" N TRP Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL Q 238 " --> pdb=" O ILE Q 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER Q 239 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 242 No H-bonds generated for 'chain 'Q' and resid 240 through 242' Processing helix chain 'Q' and resid 246 through 270 removed outlier: 3.808A pdb=" N THR Q 262 " --> pdb=" O VAL Q 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Q 263 " --> pdb=" O LEU Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 306 Processing helix chain 'Q' and resid 309 through 447 removed outlier: 4.376A pdb=" N ILE Q 429 " --> pdb=" O ARG Q 425 " (cutoff:3.500A) Proline residue: Q 432 - end of helix Processing helix chain 'R' and resid 449 through 452 Processing helix chain 'R' and resid 495 through 497 No H-bonds generated for 'chain 'R' and resid 495 through 497' Processing sheet with id=1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A 66 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A 66 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 41 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=5, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS O 483 " --> pdb=" O TRP O 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP O 502 " --> pdb=" O CYS O 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA O 485 " --> pdb=" O ASP O 500 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR D 66 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN D 41 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.809A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR D 66 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN D 41 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=11, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 420 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG E 425 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE E 434 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS E 483 " --> pdb=" O TRP E 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP E 502 " --> pdb=" O CYS E 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA E 485 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 81 through 83 removed outlier: 4.341A pdb=" N ILE H 116 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR H 66 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN H 41 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR H 133 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER H 104 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR H 131 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL H 106 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG H 129 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR H 66 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN H 41 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER H 156 " --> pdb=" O PRO H 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 190 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS H 215 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE H 188 " --> pdb=" O LYS H 215 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=17, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE I 420 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG I 425 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE I 434 " --> pdb=" O ARG I 425 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS I 483 " --> pdb=" O TRP I 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP I 502 " --> pdb=" O CYS I 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA I 485 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'L' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE L 116 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR L 66 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN L 41 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR L 133 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER L 104 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR L 131 " --> pdb=" O SER L 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL L 106 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG L 129 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR L 66 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN L 41 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.631A pdb=" N SER L 156 " --> pdb=" O PRO L 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU L 190 " --> pdb=" O ARG L 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS L 215 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE L 188 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=23, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS M 483 " --> pdb=" O TRP M 502 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 502 " --> pdb=" O CYS M 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA M 485 " --> pdb=" O ASP M 500 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 81 through 83 removed outlier: 4.340A pdb=" N ILE Q 116 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR Q 66 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN Q 41 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR Q 133 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER Q 104 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR Q 131 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL Q 106 " --> pdb=" O ARG Q 129 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG Q 129 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR Q 66 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN Q 41 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER Q 156 " --> pdb=" O PRO Q 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Q 190 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS Q 215 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE Q 188 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'R' and resid 2 through 7 Processing sheet with id=29, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE R 420 " --> pdb=" O LYS R 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG R 425 " --> pdb=" O PHE R 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE R 434 " --> pdb=" O ARG R 425 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.052A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS R 483 " --> pdb=" O TRP R 502 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP R 502 " --> pdb=" O CYS R 483 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA R 485 " --> pdb=" O ASP R 500 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.77 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3418 1.33 - 1.46: 5987 1.46 - 1.58: 10105 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 19680 Sorted by residual: bond pdb=" CG HIS A 119 " pdb=" CD2 HIS A 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" CG HIS Q 119 " pdb=" CD2 HIS Q 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.91e+01 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS L 119 " pdb=" CD2 HIS L 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS D 119 " pdb=" CD2 HIS D 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.88e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19557 1.82 - 3.65: 6094 3.65 - 5.47: 856 5.47 - 7.30: 113 7.30 - 9.12: 10 Bond angle restraints: 26630 Sorted by residual: angle pdb=" CA ASP A 101 " pdb=" CB ASP A 101 " pdb=" CG ASP A 101 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 angle pdb=" CA ASP Q 101 " pdb=" CB ASP Q 101 " pdb=" CG ASP Q 101 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA ASP D 101 " pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP L 101 " pdb=" CB ASP L 101 " pdb=" CG ASP L 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.39e+01 ... (remaining 26625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 11059 20.75 - 41.49: 646 41.49 - 62.24: 135 62.24 - 82.98: 70 82.98 - 103.73: 25 Dihedral angle restraints: 11935 sinusoidal: 5285 harmonic: 6650 Sorted by residual: dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER H 46 " pdb=" C SER H 46 " pdb=" N ILE H 47 " pdb=" CA ILE H 47 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1405 0.055 - 0.110: 955 0.110 - 0.165: 483 0.165 - 0.219: 134 0.219 - 0.274: 18 Chirality restraints: 2995 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.74e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.68e+01 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.62e+01 ... (remaining 2992 not shown) Planarity restraints: 3270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG F 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.057 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" C7 NAG N 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.056 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" C7 NAG J 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.009 2.00e-02 2.50e+03 ... (remaining 3267 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 0 1.96 - 2.94: 7546 2.94 - 3.92: 50552 3.92 - 4.90: 101745 Warning: very small nonbonded interaction distances. Nonbonded interactions: 159853 Sorted by model distance: nonbonded pdb="CL CL A5407 " pdb="CL CL D5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL L5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL Q5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 ... (remaining 159848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } 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' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'R' } 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: 2.510 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 40.620 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- 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 : 0.010 0.065 19680 Z= 0.674 Angle : 1.701 9.123 26630 Z= 1.129 Chirality : 0.086 0.274 2995 Planarity : 0.012 0.135 3260 Dihedral : 16.051 103.727 7705 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 5.22 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2245 helix: -0.65 (0.18), residues: 615 sheet: 0.50 (0.20), residues: 645 loop : 0.07 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP L 237 HIS 0.009 0.002 HIS A 119 PHE 0.040 0.008 PHE H 221 TYR 0.043 0.007 TYR L 299 ARG 0.056 0.005 ARG A 269 *********************** 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 fitting. rotamer outliers: 25 poor density : 406 time to evaluate : 2.166 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: 0.3484 time to fit residues: 215.4861 Evaluate side-chains 319 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 301 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 144 PRO Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 144 PRO Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 176 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 131 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 185 GLN D 185 GLN H 41 ASN H 185 GLN L 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19680 Z= 0.173 Angle : 0.610 6.739 26630 Z= 0.326 Chirality : 0.046 0.163 2995 Planarity : 0.004 0.038 3260 Dihedral : 11.383 77.364 3589 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.82 % Allowed : 6.99 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2245 helix: 1.48 (0.20), residues: 615 sheet: 0.61 (0.19), residues: 675 loop : 0.40 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 440 HIS 0.002 0.001 HIS D 267 PHE 0.017 0.002 PHE L 306 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7714 (m110) cc_final: 0.7455 (m110) REVERT: A 51 SER cc_start: 0.7530 (t) cc_final: 0.6724 (p) REVERT: A 55 MET cc_start: 0.7537 (mtp) cc_final: 0.7049 (mtt) REVERT: A 64 GLN cc_start: 0.7566 (mp10) cc_final: 0.7028 (mt0) REVERT: A 139 ASP cc_start: 0.7331 (t0) cc_final: 0.6812 (p0) REVERT: A 163 ASP cc_start: 0.7618 (m-30) cc_final: 0.7160 (m-30) REVERT: A 190 GLU cc_start: 0.7741 (tt0) cc_final: 0.7345 (tt0) REVERT: A 213 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6681 (tpp80) REVERT: A 223 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7510 (tm) REVERT: A 235 LEU cc_start: 0.8438 (tp) cc_final: 0.8210 (tt) REVERT: A 298 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 425 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7330 (mtm-85) REVERT: D 51 SER cc_start: 0.7707 (t) cc_final: 0.6910 (p) REVERT: D 52 GLU cc_start: 0.8250 (mp0) cc_final: 0.7930 (mp0) REVERT: D 64 GLN cc_start: 0.7523 (mp10) cc_final: 0.7034 (mt0) REVERT: D 139 ASP cc_start: 0.7450 (t0) cc_final: 0.7056 (p0) REVERT: D 163 ASP cc_start: 0.7417 (m-30) cc_final: 0.6979 (m-30) REVERT: D 190 GLU cc_start: 0.7635 (tt0) cc_final: 0.7194 (tt0) REVERT: D 213 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6707 (tpp80) REVERT: D 223 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7637 (tm) REVERT: H 43 ASP cc_start: 0.8417 (t70) cc_final: 0.8190 (t0) REVERT: H 51 SER cc_start: 0.7644 (t) cc_final: 0.6731 (p) REVERT: H 64 GLN cc_start: 0.7497 (mp10) cc_final: 0.6994 (mt0) REVERT: H 139 ASP cc_start: 0.7414 (t0) cc_final: 0.6877 (p0) REVERT: H 148 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7512 (mm-40) REVERT: H 155 GLU cc_start: 0.8357 (tt0) cc_final: 0.8068 (tt0) REVERT: H 163 ASP cc_start: 0.7414 (m-30) cc_final: 0.7128 (m-30) REVERT: H 190 GLU cc_start: 0.7720 (tt0) cc_final: 0.7343 (tt0) REVERT: H 213 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6617 (tpp80) REVERT: H 223 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7426 (tm) REVERT: H 425 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7153 (mtp-110) REVERT: L 41 ASN cc_start: 0.8171 (m110) cc_final: 0.7794 (m110) REVERT: L 51 SER cc_start: 0.7570 (t) cc_final: 0.6619 (p) REVERT: L 52 GLU cc_start: 0.8245 (mp0) cc_final: 0.7969 (mp0) REVERT: L 64 GLN cc_start: 0.7452 (mp10) cc_final: 0.7057 (mt0) REVERT: L 139 ASP cc_start: 0.7406 (t0) cc_final: 0.6978 (p0) REVERT: L 190 GLU cc_start: 0.7790 (tt0) cc_final: 0.7434 (tt0) REVERT: L 213 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6709 (tpp80) REVERT: L 223 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7523 (tm) REVERT: Q 51 SER cc_start: 0.7446 (t) cc_final: 0.6564 (p) REVERT: Q 52 GLU cc_start: 0.8252 (mp0) cc_final: 0.7919 (mp0) REVERT: Q 64 GLN cc_start: 0.7539 (mp10) cc_final: 0.6985 (mt0) REVERT: Q 139 ASP cc_start: 0.7410 (t0) cc_final: 0.7061 (p0) REVERT: Q 163 ASP cc_start: 0.7369 (m-30) cc_final: 0.7026 (m-30) REVERT: Q 190 GLU cc_start: 0.7578 (tt0) cc_final: 0.7331 (tt0) REVERT: Q 223 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7689 (tm) outliers start: 36 outliers final: 21 residues processed: 331 average time/residue: 0.3569 time to fit residues: 173.0559 Evaluate side-chains 310 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 223 LEU 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 223 LEU 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 223 LEU 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 223 LEU 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 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 221 optimal weight: 0.0040 chunk 182 optimal weight: 0.0270 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 164 optimal weight: 0.0980 overall best weight: 0.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN H 41 ASN Q 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19680 Z= 0.129 Angle : 0.519 6.865 26630 Z= 0.276 Chirality : 0.045 0.239 2995 Planarity : 0.004 0.036 3260 Dihedral : 9.709 67.778 3580 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.16 % Allowed : 9.01 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2245 helix: 1.94 (0.19), residues: 615 sheet: 0.72 (0.19), residues: 680 loop : 0.50 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 67 HIS 0.004 0.001 HIS H 267 PHE 0.012 0.001 PHE H 221 TYR 0.028 0.001 TYR L 299 ARG 0.002 0.000 ARG Q 213 *********************** 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 315 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 2.007 Fit side-chains REVERT: A 51 SER cc_start: 0.7528 (t) cc_final: 0.6756 (p) REVERT: A 55 MET cc_start: 0.7542 (mtp) cc_final: 0.7189 (mtt) REVERT: A 64 GLN cc_start: 0.7351 (mp10) cc_final: 0.7113 (mt0) REVERT: A 139 ASP cc_start: 0.7394 (t0) cc_final: 0.6801 (p0) REVERT: A 163 ASP cc_start: 0.7482 (m-30) cc_final: 0.7011 (m-30) REVERT: A 180 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.7144 (mtm180) REVERT: A 190 GLU cc_start: 0.7782 (tt0) cc_final: 0.7430 (tt0) REVERT: A 213 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6797 (tpp80) REVERT: A 223 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7594 (tm) REVERT: A 425 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7302 (mtm-85) REVERT: D 51 SER cc_start: 0.7529 (t) cc_final: 0.6773 (p) REVERT: D 64 GLN cc_start: 0.7389 (mp10) cc_final: 0.7074 (mt0) REVERT: D 139 ASP cc_start: 0.7411 (t0) cc_final: 0.7087 (p0) REVERT: D 163 ASP cc_start: 0.7468 (m-30) cc_final: 0.7161 (m-30) REVERT: D 190 GLU cc_start: 0.7703 (tt0) cc_final: 0.7300 (tt0) REVERT: D 213 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6728 (tpp80) REVERT: D 223 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7795 (tm) REVERT: E 421 MET cc_start: 0.6938 (mmm) cc_final: 0.5953 (mmm) REVERT: H 51 SER cc_start: 0.7618 (t) cc_final: 0.6796 (p) REVERT: H 64 GLN cc_start: 0.7262 (mp10) cc_final: 0.7016 (mt0) REVERT: H 139 ASP cc_start: 0.7422 (t0) cc_final: 0.6812 (p0) REVERT: H 155 GLU cc_start: 0.8430 (tt0) cc_final: 0.8155 (tt0) REVERT: H 190 GLU cc_start: 0.7797 (tt0) cc_final: 0.7478 (tt0) REVERT: H 213 ARG cc_start: 0.6962 (ttp-110) cc_final: 0.6690 (tpp80) REVERT: H 223 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7754 (tm) REVERT: H 425 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7235 (mtm-85) REVERT: L 51 SER cc_start: 0.7651 (t) cc_final: 0.6914 (p) REVERT: L 64 GLN cc_start: 0.7375 (mp10) cc_final: 0.7092 (mt0) REVERT: L 139 ASP cc_start: 0.7301 (t0) cc_final: 0.6957 (p0) REVERT: L 155 GLU cc_start: 0.8412 (tt0) cc_final: 0.7934 (tt0) REVERT: L 190 GLU cc_start: 0.7808 (tt0) cc_final: 0.7459 (tt0) REVERT: L 213 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6773 (tpp80) REVERT: L 223 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (tm) REVERT: Q 51 SER cc_start: 0.7614 (t) cc_final: 0.6788 (p) REVERT: Q 64 GLN cc_start: 0.7392 (mp10) cc_final: 0.7023 (mt0) REVERT: Q 139 ASP cc_start: 0.7399 (t0) cc_final: 0.7098 (p0) REVERT: Q 163 ASP cc_start: 0.7425 (m-30) cc_final: 0.7084 (m-30) REVERT: Q 190 GLU cc_start: 0.7697 (tt0) cc_final: 0.7418 (tt0) REVERT: Q 223 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7913 (tm) outliers start: 23 outliers final: 13 residues processed: 304 average time/residue: 0.3268 time to fit residues: 148.1238 Evaluate side-chains 282 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 264 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN H 41 ASN L 41 ASN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19680 Z= 0.202 Angle : 0.524 6.402 26630 Z= 0.277 Chirality : 0.045 0.202 2995 Planarity : 0.004 0.038 3260 Dihedral : 9.169 63.048 3560 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.92 % Allowed : 10.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2245 helix: 2.09 (0.19), residues: 615 sheet: 0.83 (0.19), residues: 660 loop : 0.35 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 67 HIS 0.003 0.001 HIS H 267 PHE 0.011 0.001 PHE A 212 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.000 ARG Q 213 *********************** 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 320 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 1.973 Fit side-chains REVERT: A 51 SER cc_start: 0.7706 (t) cc_final: 0.6939 (p) REVERT: A 64 GLN cc_start: 0.7412 (mp10) cc_final: 0.7151 (mt0) REVERT: A 139 ASP cc_start: 0.7442 (t0) cc_final: 0.6865 (p0) REVERT: A 163 ASP cc_start: 0.7644 (m-30) cc_final: 0.7182 (m-30) REVERT: A 190 GLU cc_start: 0.7760 (tt0) cc_final: 0.7412 (tt0) REVERT: A 213 ARG cc_start: 0.6969 (ttp-110) cc_final: 0.6733 (tpp80) REVERT: A 223 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (tm) REVERT: A 425 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7286 (mtm-85) REVERT: D 51 SER cc_start: 0.7559 (t) cc_final: 0.6815 (p) REVERT: D 64 GLN cc_start: 0.7368 (mp10) cc_final: 0.7063 (mt0) REVERT: D 139 ASP cc_start: 0.7455 (t0) cc_final: 0.7014 (p0) REVERT: D 163 ASP cc_start: 0.7583 (m-30) cc_final: 0.7274 (m-30) REVERT: D 190 GLU cc_start: 0.7696 (tt0) cc_final: 0.7291 (tt0) REVERT: D 213 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6745 (tpp80) REVERT: D 223 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7721 (tm) REVERT: H 40 MET cc_start: 0.8891 (mtt) cc_final: 0.8465 (mtt) REVERT: H 51 SER cc_start: 0.7728 (t) cc_final: 0.6963 (p) REVERT: H 64 GLN cc_start: 0.7325 (mp10) cc_final: 0.7049 (mt0) REVERT: H 139 ASP cc_start: 0.7474 (t0) cc_final: 0.6848 (p0) REVERT: H 155 GLU cc_start: 0.8457 (tt0) cc_final: 0.8237 (tt0) REVERT: H 190 GLU cc_start: 0.7798 (tt0) cc_final: 0.7445 (tt0) REVERT: H 223 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (tm) REVERT: H 425 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.7240 (mtm-85) REVERT: L 51 SER cc_start: 0.7762 (t) cc_final: 0.6956 (p) REVERT: L 64 GLN cc_start: 0.7333 (mp10) cc_final: 0.7057 (mt0) REVERT: L 139 ASP cc_start: 0.7339 (t0) cc_final: 0.6866 (p0) REVERT: L 190 GLU cc_start: 0.7769 (tt0) cc_final: 0.7478 (tt0) REVERT: L 223 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7830 (tm) REVERT: L 232 ILE cc_start: 0.7274 (mm) cc_final: 0.6965 (mm) REVERT: Q 20 LEU cc_start: 0.7075 (mt) cc_final: 0.6840 (mt) REVERT: Q 51 SER cc_start: 0.7751 (t) cc_final: 0.6969 (p) REVERT: Q 64 GLN cc_start: 0.7501 (mp10) cc_final: 0.7120 (mt0) REVERT: Q 68 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7487 (ttm170) REVERT: Q 139 ASP cc_start: 0.7353 (t0) cc_final: 0.7014 (p0) REVERT: Q 163 ASP cc_start: 0.7589 (m-30) cc_final: 0.7346 (m-30) REVERT: Q 190 GLU cc_start: 0.7671 (tt0) cc_final: 0.7396 (tt0) REVERT: Q 223 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7965 (tm) outliers start: 38 outliers final: 26 residues processed: 310 average time/residue: 0.3236 time to fit residues: 150.3650 Evaluate side-chains 290 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 211 SER 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 162 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain H residue 223 LEU 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 211 SER Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 211 SER Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN H 41 ASN Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19680 Z= 0.315 Angle : 0.576 6.475 26630 Z= 0.304 Chirality : 0.047 0.205 2995 Planarity : 0.004 0.039 3260 Dihedral : 9.526 60.441 3560 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.92 % Allowed : 11.59 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2245 helix: 1.54 (0.20), residues: 645 sheet: 0.72 (0.19), residues: 660 loop : 0.01 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 67 HIS 0.005 0.001 HIS A 267 PHE 0.015 0.002 PHE H 98 TYR 0.028 0.002 TYR D 299 ARG 0.004 0.001 ARG Q 71 *********************** 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 319 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 2.246 Fit side-chains REVERT: A 40 MET cc_start: 0.9018 (mtt) cc_final: 0.8524 (mtt) REVERT: A 51 SER cc_start: 0.7636 (t) cc_final: 0.6890 (p) REVERT: A 64 GLN cc_start: 0.7613 (mp10) cc_final: 0.7208 (mt0) REVERT: A 139 ASP cc_start: 0.7515 (t0) cc_final: 0.6864 (p0) REVERT: A 142 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7661 (mmm160) REVERT: A 163 ASP cc_start: 0.7691 (m-30) cc_final: 0.7280 (m-30) REVERT: A 190 GLU cc_start: 0.7658 (tt0) cc_final: 0.7241 (tt0) REVERT: A 223 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7795 (tm) REVERT: A 425 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.7172 (mtm-85) REVERT: D 40 MET cc_start: 0.9009 (mtt) cc_final: 0.8556 (mtt) REVERT: D 51 SER cc_start: 0.7560 (t) cc_final: 0.6872 (p) REVERT: D 64 GLN cc_start: 0.7493 (mp10) cc_final: 0.7111 (mt0) REVERT: D 66 TYR cc_start: 0.7954 (m-80) cc_final: 0.7730 (m-80) REVERT: D 139 ASP cc_start: 0.7565 (t0) cc_final: 0.6958 (p0) REVERT: D 163 ASP cc_start: 0.7745 (m-30) cc_final: 0.7534 (m-30) REVERT: D 190 GLU cc_start: 0.7687 (tt0) cc_final: 0.7274 (tt0) REVERT: D 213 ARG cc_start: 0.6945 (ttp-110) cc_final: 0.6673 (tpp80) REVERT: D 223 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7753 (tm) REVERT: E 421 MET cc_start: 0.6967 (mmm) cc_final: 0.5887 (mmm) REVERT: H 40 MET cc_start: 0.9010 (mtt) cc_final: 0.8649 (mtt) REVERT: H 51 SER cc_start: 0.7696 (t) cc_final: 0.6937 (p) REVERT: H 64 GLN cc_start: 0.7535 (mp10) cc_final: 0.7143 (mt0) REVERT: H 139 ASP cc_start: 0.7565 (t0) cc_final: 0.6878 (p0) REVERT: H 190 GLU cc_start: 0.7688 (tt0) cc_final: 0.7426 (tt0) REVERT: H 223 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7795 (tm) REVERT: H 425 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7113 (mtm-85) REVERT: L 51 SER cc_start: 0.7772 (t) cc_final: 0.6994 (p) REVERT: L 64 GLN cc_start: 0.7506 (mp10) cc_final: 0.7022 (mt0) REVERT: L 139 ASP cc_start: 0.7405 (t0) cc_final: 0.6827 (p0) REVERT: L 190 GLU cc_start: 0.7710 (tt0) cc_final: 0.7471 (tt0) REVERT: L 223 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7767 (tm) REVERT: L 298 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7944 (tm-30) REVERT: Q 51 SER cc_start: 0.7850 (t) cc_final: 0.7104 (p) REVERT: Q 64 GLN cc_start: 0.7616 (mp10) cc_final: 0.7125 (mt0) REVERT: Q 139 ASP cc_start: 0.7447 (t0) cc_final: 0.6974 (p0) REVERT: Q 190 GLU cc_start: 0.7581 (tt0) cc_final: 0.7281 (tt0) REVERT: Q 223 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7830 (tm) REVERT: Q 301 PHE cc_start: 0.7532 (t80) cc_final: 0.7316 (t80) outliers start: 38 outliers final: 30 residues processed: 306 average time/residue: 0.3583 time to fit residues: 163.7002 Evaluate side-chains 295 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 211 SER 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 82 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 211 SER 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 82 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 211 SER Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 211 SER Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 217 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19680 Z= 0.155 Angle : 0.503 6.551 26630 Z= 0.264 Chirality : 0.044 0.233 2995 Planarity : 0.003 0.037 3260 Dihedral : 8.666 57.055 3560 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.82 % Allowed : 12.10 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2245 helix: 1.78 (0.20), residues: 645 sheet: 0.84 (0.19), residues: 655 loop : 0.06 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 67 HIS 0.002 0.001 HIS H 267 PHE 0.009 0.001 PHE R 424 TYR 0.029 0.001 TYR D 299 ARG 0.003 0.000 ARG A 213 *********************** 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 309 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 2.425 Fit side-chains REVERT: A 40 MET cc_start: 0.9047 (mtt) cc_final: 0.8569 (mtt) REVERT: A 41 ASN cc_start: 0.8068 (m110) cc_final: 0.7857 (m110) REVERT: A 51 SER cc_start: 0.7630 (t) cc_final: 0.6885 (p) REVERT: A 64 GLN cc_start: 0.7568 (mp10) cc_final: 0.7189 (mt0) REVERT: A 139 ASP cc_start: 0.7378 (t0) cc_final: 0.6769 (p0) REVERT: A 142 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7709 (mmm160) REVERT: A 163 ASP cc_start: 0.7638 (m-30) cc_final: 0.7182 (m-30) REVERT: A 190 GLU cc_start: 0.7655 (tt0) cc_final: 0.7361 (tt0) REVERT: A 223 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7771 (tm) REVERT: A 425 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7232 (mtm-85) REVERT: D 40 MET cc_start: 0.8945 (mtt) cc_final: 0.8480 (mtt) REVERT: D 51 SER cc_start: 0.7509 (t) cc_final: 0.6814 (p) REVERT: D 64 GLN cc_start: 0.7427 (mp10) cc_final: 0.7091 (mt0) REVERT: D 139 ASP cc_start: 0.7530 (t0) cc_final: 0.6987 (p0) REVERT: D 163 ASP cc_start: 0.7662 (m-30) cc_final: 0.7415 (m-30) REVERT: D 190 GLU cc_start: 0.7709 (tt0) cc_final: 0.7301 (tt0) REVERT: D 213 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6714 (tpp80) REVERT: D 223 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7811 (tm) REVERT: H 40 MET cc_start: 0.9000 (mtt) cc_final: 0.8595 (mtt) REVERT: H 51 SER cc_start: 0.7713 (t) cc_final: 0.6944 (p) REVERT: H 64 GLN cc_start: 0.7470 (mp10) cc_final: 0.7115 (mt0) REVERT: H 139 ASP cc_start: 0.7538 (t0) cc_final: 0.6892 (p0) REVERT: H 190 GLU cc_start: 0.7728 (tt0) cc_final: 0.7475 (tt0) REVERT: H 301 PHE cc_start: 0.7248 (t80) cc_final: 0.6954 (t80) REVERT: H 425 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7183 (mtm-85) REVERT: L 40 MET cc_start: 0.9029 (mtt) cc_final: 0.8701 (mtt) REVERT: L 51 SER cc_start: 0.7743 (t) cc_final: 0.6958 (p) REVERT: L 64 GLN cc_start: 0.7386 (mp10) cc_final: 0.7028 (mt0) REVERT: L 68 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7517 (ttm170) REVERT: L 139 ASP cc_start: 0.7369 (t0) cc_final: 0.6862 (p0) REVERT: L 190 GLU cc_start: 0.7651 (tt0) cc_final: 0.7382 (tt0) REVERT: Q 51 SER cc_start: 0.7848 (t) cc_final: 0.7032 (p) REVERT: Q 64 GLN cc_start: 0.7558 (mp10) cc_final: 0.7048 (mt0) REVERT: Q 68 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7548 (ttm170) REVERT: Q 139 ASP cc_start: 0.7416 (t0) cc_final: 0.6935 (p0) REVERT: Q 163 ASP cc_start: 0.7586 (m-30) cc_final: 0.7336 (m-30) REVERT: Q 190 GLU cc_start: 0.7719 (tt0) cc_final: 0.7456 (tt0) REVERT: Q 223 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7949 (tm) REVERT: Q 301 PHE cc_start: 0.7477 (t80) cc_final: 0.7262 (t80) outliers start: 36 outliers final: 27 residues processed: 299 average time/residue: 0.3478 time to fit residues: 156.3544 Evaluate side-chains 291 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 211 SER 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 162 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 211 SER 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 D residue 423 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 211 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 309 GLN Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 211 SER Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 0.0070 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Q 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19680 Z= 0.144 Angle : 0.499 6.850 26630 Z= 0.259 Chirality : 0.043 0.240 2995 Planarity : 0.003 0.036 3260 Dihedral : 7.887 56.843 3556 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.62 % Allowed : 12.81 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2245 helix: 2.24 (0.20), residues: 615 sheet: 0.81 (0.20), residues: 635 loop : 0.26 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 67 HIS 0.002 0.001 HIS H 191 PHE 0.013 0.001 PHE R 424 TYR 0.028 0.001 TYR D 299 ARG 0.005 0.000 ARG L 213 *********************** 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 310 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 2.176 Fit side-chains REVERT: A 41 ASN cc_start: 0.7998 (m110) cc_final: 0.7737 (m110) REVERT: A 51 SER cc_start: 0.7666 (t) cc_final: 0.6914 (p) REVERT: A 64 GLN cc_start: 0.7514 (mp10) cc_final: 0.7162 (mt0) REVERT: A 139 ASP cc_start: 0.7348 (t0) cc_final: 0.6761 (p0) REVERT: A 163 ASP cc_start: 0.7674 (m-30) cc_final: 0.7223 (m-30) REVERT: A 190 GLU cc_start: 0.7674 (tt0) cc_final: 0.7357 (tt0) REVERT: A 223 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7789 (tm) REVERT: A 425 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7222 (mtm-85) REVERT: D 40 MET cc_start: 0.8899 (mtt) cc_final: 0.8410 (mtt) REVERT: D 51 SER cc_start: 0.7559 (t) cc_final: 0.6854 (p) REVERT: D 64 GLN cc_start: 0.7397 (mp10) cc_final: 0.7084 (mt0) REVERT: D 139 ASP cc_start: 0.7516 (t0) cc_final: 0.6997 (p0) REVERT: D 155 GLU cc_start: 0.8477 (tt0) cc_final: 0.8199 (tt0) REVERT: D 163 ASP cc_start: 0.7630 (m-30) cc_final: 0.7366 (m-30) REVERT: D 190 GLU cc_start: 0.7787 (tt0) cc_final: 0.7419 (tt0) REVERT: D 213 ARG cc_start: 0.6982 (ttp-110) cc_final: 0.6647 (tpp80) REVERT: D 261 MET cc_start: 0.8551 (mmm) cc_final: 0.8140 (mmm) REVERT: H 40 MET cc_start: 0.8970 (mtt) cc_final: 0.8555 (mtt) REVERT: H 51 SER cc_start: 0.7734 (t) cc_final: 0.6983 (p) REVERT: H 64 GLN cc_start: 0.7430 (mp10) cc_final: 0.7097 (mt0) REVERT: H 139 ASP cc_start: 0.7527 (t0) cc_final: 0.6897 (p0) REVERT: H 190 GLU cc_start: 0.7750 (tt0) cc_final: 0.7498 (tt0) REVERT: H 425 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7158 (mtm-85) REVERT: L 40 MET cc_start: 0.8943 (mtt) cc_final: 0.8324 (mtt) REVERT: L 51 SER cc_start: 0.7714 (t) cc_final: 0.6947 (p) REVERT: L 64 GLN cc_start: 0.7363 (mp10) cc_final: 0.7051 (mt0) REVERT: L 68 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7390 (ttm170) REVERT: L 139 ASP cc_start: 0.7342 (t0) cc_final: 0.6896 (p0) REVERT: L 190 GLU cc_start: 0.7675 (tt0) cc_final: 0.7455 (tt0) REVERT: Q 17 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: Q 51 SER cc_start: 0.7827 (t) cc_final: 0.7066 (p) REVERT: Q 64 GLN cc_start: 0.7550 (mp10) cc_final: 0.7129 (mt0) REVERT: Q 139 ASP cc_start: 0.7387 (t0) cc_final: 0.6924 (p0) REVERT: Q 163 ASP cc_start: 0.7518 (m-30) cc_final: 0.7314 (m-30) REVERT: Q 190 GLU cc_start: 0.7735 (tt0) cc_final: 0.7478 (tt0) REVERT: Q 301 PHE cc_start: 0.7517 (t80) cc_final: 0.7298 (t80) outliers start: 32 outliers final: 26 residues processed: 302 average time/residue: 0.3197 time to fit residues: 145.3429 Evaluate side-chains 290 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 211 SER 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 211 SER Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 211 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 309 GLN Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 211 SER 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 134 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 137 optimal weight: 0.1980 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 L 185 GLN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19680 Z= 0.352 Angle : 0.603 6.986 26630 Z= 0.313 Chirality : 0.047 0.253 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.725 59.643 3551 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.18 % Allowed : 13.37 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2245 helix: 1.53 (0.20), residues: 645 sheet: 0.73 (0.20), residues: 635 loop : -0.06 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 241 HIS 0.003 0.001 HIS Q 267 PHE 0.017 0.002 PHE Q 31 TYR 0.027 0.002 TYR H 299 ARG 0.004 0.000 ARG L 213 *********************** 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 313 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 2.105 Fit side-chains REVERT: A 51 SER cc_start: 0.7722 (t) cc_final: 0.6983 (p) REVERT: A 64 GLN cc_start: 0.7632 (mp10) cc_final: 0.7179 (mt0) REVERT: A 139 ASP cc_start: 0.7422 (t0) cc_final: 0.6829 (p0) REVERT: A 142 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7632 (mmm160) REVERT: A 190 GLU cc_start: 0.7604 (tt0) cc_final: 0.7278 (tt0) REVERT: A 425 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7125 (mtm-85) REVERT: D 51 SER cc_start: 0.7609 (t) cc_final: 0.6910 (p) REVERT: D 64 GLN cc_start: 0.7538 (mp10) cc_final: 0.7091 (mt0) REVERT: D 66 TYR cc_start: 0.7951 (m-80) cc_final: 0.7742 (m-80) REVERT: D 139 ASP cc_start: 0.7517 (t0) cc_final: 0.6964 (p0) REVERT: D 190 GLU cc_start: 0.7670 (tt0) cc_final: 0.7263 (tt0) REVERT: D 213 ARG cc_start: 0.6897 (ttp-110) cc_final: 0.6646 (tpp80) REVERT: D 298 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 40 MET cc_start: 0.9018 (mtt) cc_final: 0.8627 (mtt) REVERT: H 51 SER cc_start: 0.7786 (t) cc_final: 0.7010 (p) REVERT: H 64 GLN cc_start: 0.7541 (mp10) cc_final: 0.7021 (mt0) REVERT: H 190 GLU cc_start: 0.7680 (tt0) cc_final: 0.7424 (tt0) REVERT: H 425 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.7106 (mtm-85) REVERT: L 40 MET cc_start: 0.8977 (mtt) cc_final: 0.8623 (mtt) REVERT: L 51 SER cc_start: 0.7781 (t) cc_final: 0.7009 (p) REVERT: L 61 MET cc_start: 0.9062 (ptt) cc_final: 0.8718 (ptt) REVERT: L 68 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7470 (ttm170) REVERT: L 139 ASP cc_start: 0.7443 (t0) cc_final: 0.6848 (p0) REVERT: L 190 GLU cc_start: 0.7705 (tt0) cc_final: 0.7465 (tt0) REVERT: L 298 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7975 (tm-30) REVERT: Q 51 SER cc_start: 0.7873 (t) cc_final: 0.7133 (p) REVERT: Q 64 GLN cc_start: 0.7690 (mp10) cc_final: 0.7175 (mt0) REVERT: Q 139 ASP cc_start: 0.7434 (t0) cc_final: 0.6935 (p0) REVERT: Q 190 GLU cc_start: 0.7591 (tt0) cc_final: 0.7255 (tt0) outliers start: 43 outliers final: 36 residues processed: 299 average time/residue: 0.3328 time to fit residues: 147.9824 Evaluate side-chains 297 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER 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 162 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 211 SER 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 211 SER Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 211 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 211 SER Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 182 optimal weight: 0.0470 chunk 191 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Q 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19680 Z= 0.142 Angle : 0.517 7.868 26630 Z= 0.266 Chirality : 0.043 0.244 2995 Planarity : 0.003 0.037 3260 Dihedral : 7.928 59.157 3551 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.37 % Allowed : 14.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2245 helix: 1.83 (0.20), residues: 645 sheet: 0.84 (0.19), residues: 660 loop : -0.01 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 67 HIS 0.002 0.001 HIS Q 191 PHE 0.015 0.001 PHE H 301 TYR 0.028 0.001 TYR H 299 ARG 0.004 0.000 ARG L 213 *********************** 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 289 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 2.054 Fit side-chains REVERT: A 41 ASN cc_start: 0.8054 (m110) cc_final: 0.7812 (m110) REVERT: A 51 SER cc_start: 0.7666 (t) cc_final: 0.6918 (p) REVERT: A 64 GLN cc_start: 0.7609 (mp10) cc_final: 0.7170 (mt0) REVERT: A 139 ASP cc_start: 0.7392 (t0) cc_final: 0.6806 (p0) REVERT: A 190 GLU cc_start: 0.7623 (tt0) cc_final: 0.7304 (tt0) REVERT: A 223 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7847 (tm) REVERT: A 425 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7166 (mtm-85) REVERT: D 40 MET cc_start: 0.8937 (mtt) cc_final: 0.8458 (mtt) REVERT: D 51 SER cc_start: 0.7590 (t) cc_final: 0.6877 (p) REVERT: D 64 GLN cc_start: 0.7410 (mp10) cc_final: 0.7073 (mt0) REVERT: D 139 ASP cc_start: 0.7474 (t0) cc_final: 0.6935 (p0) REVERT: D 155 GLU cc_start: 0.8518 (tt0) cc_final: 0.8258 (tt0) REVERT: D 190 GLU cc_start: 0.7779 (tt0) cc_final: 0.7410 (tt0) REVERT: D 213 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6701 (tpp80) REVERT: H 40 MET cc_start: 0.8994 (mtt) cc_final: 0.8572 (mtt) REVERT: H 51 SER cc_start: 0.7750 (t) cc_final: 0.6984 (p) REVERT: H 64 GLN cc_start: 0.7493 (mp10) cc_final: 0.7067 (mt0) REVERT: H 162 ASP cc_start: 0.7882 (m-30) cc_final: 0.7559 (p0) REVERT: H 190 GLU cc_start: 0.7742 (tt0) cc_final: 0.7483 (tt0) REVERT: H 425 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7140 (mtm-85) REVERT: L 40 MET cc_start: 0.8979 (mtt) cc_final: 0.8364 (mtt) REVERT: L 51 SER cc_start: 0.7688 (t) cc_final: 0.6900 (p) REVERT: L 68 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7335 (ttm170) REVERT: L 139 ASP cc_start: 0.7370 (t0) cc_final: 0.6875 (p0) REVERT: L 190 GLU cc_start: 0.7623 (tt0) cc_final: 0.7375 (tt0) REVERT: Q 51 SER cc_start: 0.7874 (t) cc_final: 0.7115 (p) REVERT: Q 64 GLN cc_start: 0.7619 (mp10) cc_final: 0.7107 (mt0) REVERT: Q 139 ASP cc_start: 0.7379 (t0) cc_final: 0.6962 (p0) REVERT: Q 190 GLU cc_start: 0.7675 (tt0) cc_final: 0.7421 (tt0) outliers start: 27 outliers final: 26 residues processed: 285 average time/residue: 0.3278 time to fit residues: 140.9534 Evaluate side-chains 281 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 211 SER 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 211 SER Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 211 SER 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 211 SER Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19680 Z= 0.162 Angle : 0.513 7.803 26630 Z= 0.264 Chirality : 0.044 0.242 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.620 59.430 3550 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.16 % Allowed : 15.19 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2245 helix: 2.17 (0.20), residues: 615 sheet: 0.84 (0.19), residues: 665 loop : 0.12 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.002 0.001 HIS H 191 PHE 0.009 0.001 PHE R 424 TYR 0.029 0.002 TYR H 299 ARG 0.004 0.000 ARG L 213 ********************** 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 284 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 2.004 Fit side-chains REVERT: A 41 ASN cc_start: 0.8057 (m110) cc_final: 0.7817 (m110) REVERT: A 51 SER cc_start: 0.7702 (t) cc_final: 0.6953 (p) REVERT: A 64 GLN cc_start: 0.7635 (mp10) cc_final: 0.7187 (mt0) REVERT: A 139 ASP cc_start: 0.7396 (t0) cc_final: 0.6841 (p0) REVERT: A 163 ASP cc_start: 0.7688 (m-30) cc_final: 0.7299 (m-30) REVERT: A 190 GLU cc_start: 0.7632 (tt0) cc_final: 0.7315 (tt0) REVERT: A 425 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7151 (mtm-85) REVERT: D 40 MET cc_start: 0.8935 (mtt) cc_final: 0.8440 (mtt) REVERT: D 51 SER cc_start: 0.7621 (t) cc_final: 0.6909 (p) REVERT: D 64 GLN cc_start: 0.7464 (mp10) cc_final: 0.7147 (mt0) REVERT: D 139 ASP cc_start: 0.7424 (t0) cc_final: 0.6964 (p0) REVERT: D 190 GLU cc_start: 0.7776 (tt0) cc_final: 0.7399 (tt0) REVERT: D 213 ARG cc_start: 0.6955 (ttp-110) cc_final: 0.6725 (tpp80) REVERT: D 261 MET cc_start: 0.8537 (mmm) cc_final: 0.8080 (mmm) REVERT: H 40 MET cc_start: 0.8982 (mtt) cc_final: 0.8568 (mtt) REVERT: H 51 SER cc_start: 0.7751 (t) cc_final: 0.6988 (p) REVERT: H 64 GLN cc_start: 0.7489 (mp10) cc_final: 0.7104 (mt0) REVERT: H 162 ASP cc_start: 0.7891 (m-30) cc_final: 0.7481 (p0) REVERT: H 190 GLU cc_start: 0.7742 (tt0) cc_final: 0.7490 (tt0) REVERT: H 425 ARG cc_start: 0.7406 (ttp-110) cc_final: 0.7131 (mtm-85) REVERT: L 40 MET cc_start: 0.8970 (mtt) cc_final: 0.8373 (mtt) REVERT: L 51 SER cc_start: 0.7712 (t) cc_final: 0.6926 (p) REVERT: L 68 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7381 (ttm170) REVERT: L 139 ASP cc_start: 0.7359 (t0) cc_final: 0.6893 (p0) REVERT: L 190 GLU cc_start: 0.7631 (tt0) cc_final: 0.7385 (tt0) REVERT: Q 51 SER cc_start: 0.7810 (t) cc_final: 0.7050 (p) REVERT: Q 64 GLN cc_start: 0.7608 (mp10) cc_final: 0.7103 (mt0) REVERT: Q 139 ASP cc_start: 0.7370 (t0) cc_final: 0.6975 (p0) REVERT: Q 190 GLU cc_start: 0.7703 (tt0) cc_final: 0.7435 (tt0) outliers start: 23 outliers final: 23 residues processed: 282 average time/residue: 0.3223 time to fit residues: 136.5035 Evaluate side-chains 273 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 211 SER 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 211 SER Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 211 SER 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 211 SER Chi-restraints excluded: chain Q residue 223 LEU 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 190 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Q 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108336 restraints weight = 23412.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106654 restraints weight = 39982.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108724 restraints weight = 34207.261| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19680 Z= 0.139 Angle : 0.504 7.751 26630 Z= 0.258 Chirality : 0.043 0.238 2995 Planarity : 0.003 0.036 3260 Dihedral : 7.244 58.964 3547 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.32 % Allowed : 15.09 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2245 helix: 1.90 (0.20), residues: 645 sheet: 0.90 (0.19), residues: 665 loop : 0.04 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 67 HIS 0.002 0.001 HIS H 191 PHE 0.009 0.001 PHE R 424 TYR 0.028 0.001 TYR D 299 ARG 0.004 0.000 ARG L 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.74 seconds wall clock time: 69 minutes 28.61 seconds (4168.61 seconds total)