Starting phenix.real_space_refine on Fri Sep 27 11:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upd_26662/09_2024/7upd_26662.cif" } resolution = 2.4 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= -0.001 sd= 0.245 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10014 2.51 5 N 2574 2.21 5 O 3117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15801 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "D" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.33, per 1000 atoms: 0.65 Number of scatterers: 15801 At special positions: 0 Unit cell: (137.28, 132.66, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3117 8.00 N 2574 7.00 C 10014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.04 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 30 sheets defined 30.7% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.713A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.950A pdb=" N THR A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.681A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.514A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.641A pdb=" N THR B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 52A through 54 Processing helix chain 'B' and resid 83 through 87 removed outlier: 4.016A pdb=" N THR B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.642A pdb=" N THR C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 52A through 54 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.556A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.998A pdb=" N THR C 87 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 36 Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.690A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.716A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 137 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.653A pdb=" N LYS D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.962A pdb=" N THR D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.674A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.826A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.506A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 474 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.827A pdb=" N LEU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.854A pdb=" N LEU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.735A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 137 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.639A pdb=" N LYS G 146 " --> pdb=" O ASP G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.955A pdb=" N THR G 168 " --> pdb=" O ALA G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 182 through 187 removed outlier: 3.675A pdb=" N THR G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.830A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.514A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 474 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.621A pdb=" N THR H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.997A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.804A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.228A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY A 264 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 281 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE A 266 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 279 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 268 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.627A pdb=" N VAL G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.614A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY B 96 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY C 96 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.811A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.195A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.611A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.490A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.496A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.803A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL G 338 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS G 45 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N CYS G 340 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS G 47 " --> pdb=" O CYS G 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.232A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY G 264 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR G 281 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE G 266 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG G 279 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 268 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR G 275 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLY H 96 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.493A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1755 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: 5.91 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5020 1.34 - 1.46: 3684 1.46 - 1.58: 7238 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16086 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG G 503 " pdb=" O5 NAG G 503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 16081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20990 1.26 - 2.52: 666 2.52 - 3.79: 133 3.79 - 5.05: 28 5.05 - 6.31: 11 Bond angle restraints: 21828 Sorted by residual: angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.79 118.29 4.50 1.78e+00 3.16e-01 6.39e+00 angle pdb=" C PRO A 191 " pdb=" N CYS A 192 " pdb=" CA CYS A 192 " ideal model delta sigma weight residual 122.56 118.24 4.32 1.72e+00 3.38e-01 6.29e+00 angle pdb=" C ILE E 48 " pdb=" N TYR E 49 " pdb=" CA TYR E 49 " ideal model delta sigma weight residual 122.79 118.35 4.44 1.78e+00 3.16e-01 6.21e+00 angle pdb=" C PRO G 191 " pdb=" N CYS G 192 " pdb=" CA CYS G 192 " ideal model delta sigma weight residual 122.56 118.29 4.27 1.72e+00 3.38e-01 6.16e+00 angle pdb=" C ILE F 48 " pdb=" N TYR F 49 " pdb=" CA TYR F 49 " ideal model delta sigma weight residual 122.79 118.48 4.31 1.78e+00 3.16e-01 5.87e+00 ... (remaining 21823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8825 17.98 - 35.95: 763 35.95 - 53.93: 243 53.93 - 71.90: 59 71.90 - 89.88: 19 Dihedral angle restraints: 9909 sinusoidal: 4026 harmonic: 5883 Sorted by residual: dihedral pdb=" CB CYS G 104 " pdb=" SG CYS G 104 " pdb=" SG CYS G 114 " pdb=" CB CYS G 114 " ideal model delta sinusoidal sigma weight residual 93.00 5.80 87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 114 " pdb=" CB CYS A 114 " ideal model delta sinusoidal sigma weight residual -86.00 -0.92 -85.08 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS D 104 " pdb=" SG CYS D 104 " pdb=" SG CYS D 114 " pdb=" CB CYS D 114 " ideal model delta sinusoidal sigma weight residual -86.00 -6.37 -79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 9906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1507 0.032 - 0.065: 686 0.065 - 0.097: 217 0.097 - 0.130: 142 0.130 - 0.162: 22 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" C1 NAG G 502 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 502 " pdb=" O5 NAG G 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL G 312 " pdb=" N VAL G 312 " pdb=" C VAL G 312 " pdb=" CB VAL G 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2571 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 186 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C THR G 186 " 0.038 2.00e-02 2.50e+03 pdb=" O THR G 186 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE G 187 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 105 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" CD GLN B 105 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 105 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 105 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 31 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C THR B 31 " -0.028 2.00e-02 2.50e+03 pdb=" O THR B 31 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 32 " 0.010 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1735 2.76 - 3.29: 13976 3.29 - 3.83: 25669 3.83 - 4.36: 31371 4.36 - 4.90: 52973 Nonbonded interactions: 125724 Sorted by model distance: nonbonded pdb=" O TYR F 49 " pdb=" OH TYR F 91 " model vdw 2.222 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OH TYR L 91 " model vdw 2.227 3.040 nonbonded pdb=" O TYR E 49 " pdb=" OH TYR E 91 " model vdw 2.231 3.040 nonbonded pdb=" NH2 ARG E 54 " pdb=" OD1 ASP E 60 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS C 35 " pdb=" OE1 GLU C 95 " model vdw 2.401 3.120 ... (remaining 125719 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 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.650 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.740 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.003 0.031 16086 Z= 0.183 Angle : 0.569 6.310 21828 Z= 0.314 Chirality : 0.047 0.162 2574 Planarity : 0.004 0.038 2742 Dihedral : 15.736 89.880 6069 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 14.16 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.86 (0.19), residues: 1992 helix: 1.87 (0.25), residues: 435 sheet: 0.92 (0.20), residues: 642 loop : -0.28 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 50 HIS 0.006 0.001 HIS D 102 PHE 0.013 0.001 PHE G 301 TYR 0.019 0.001 TYR E 49 ARG 0.003 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 1.714 Fit side-chains REVERT: C 105 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8146 (mm110) outliers start: 21 outliers final: 18 residues processed: 268 average time/residue: 1.2229 time to fit residues: 362.6164 Evaluate side-chains 259 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 101 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.0060 chunk 115 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN G 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16086 Z= 0.176 Angle : 0.527 4.816 21828 Z= 0.292 Chirality : 0.046 0.182 2574 Planarity : 0.004 0.037 2742 Dihedral : 6.539 57.596 2444 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.78 % Allowed : 12.18 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 (0.19), residues: 1992 helix: 2.24 (0.26), residues: 441 sheet: 0.92 (0.21), residues: 600 loop : -0.15 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 50 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE D 301 TYR 0.020 0.001 TYR L 49 ARG 0.002 0.000 ARG G 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 251 time to evaluate : 1.791 Fit side-chains REVERT: A 240 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: A 410 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 3 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7972 (tp40) REVERT: C 3 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7937 (tp40) REVERT: D 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8046 (tp30) REVERT: F 103 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8132 (tmtp) REVERT: G 336 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7868 (mtp180) REVERT: H 3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (tp40) REVERT: H 82 MET cc_start: 0.8487 (mtm) cc_final: 0.8248 (mtm) outliers start: 67 outliers final: 26 residues processed: 291 average time/residue: 1.2199 time to fit residues: 394.5818 Evaluate side-chains 275 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 0.5980 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN D 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16086 Z= 0.121 Angle : 0.459 4.816 21828 Z= 0.254 Chirality : 0.044 0.174 2574 Planarity : 0.004 0.036 2742 Dihedral : 5.780 51.669 2436 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 13.14 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.16 (0.19), residues: 1992 helix: 2.49 (0.26), residues: 441 sheet: 0.89 (0.20), residues: 645 loop : -0.15 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 50 HIS 0.005 0.001 HIS D 102 PHE 0.010 0.001 PHE D 301 TYR 0.018 0.001 TYR L 49 ARG 0.002 0.000 ARG G 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 1.754 Fit side-chains REVERT: A 240 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: B 3 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7971 (tp40) REVERT: C 3 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: C 105 GLN cc_start: 0.8327 (mm110) cc_final: 0.8121 (mm110) REVERT: D 258 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: E 106 ILE cc_start: 0.8295 (mm) cc_final: 0.8072 (tp) REVERT: G 152 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: G 336 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7859 (mtp180) REVERT: H 3 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8004 (tp40) outliers start: 58 outliers final: 22 residues processed: 284 average time/residue: 1.2177 time to fit residues: 382.8498 Evaluate side-chains 273 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 465 GLN C 30 ASN D 102 HIS H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16086 Z= 0.292 Angle : 0.647 6.233 21828 Z= 0.358 Chirality : 0.051 0.213 2574 Planarity : 0.005 0.052 2742 Dihedral : 6.174 52.448 2433 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.72 % Allowed : 13.31 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.88 (0.19), residues: 1992 helix: 2.02 (0.25), residues: 459 sheet: 0.73 (0.21), residues: 591 loop : -0.18 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 50 HIS 0.005 0.001 HIS C 35 PHE 0.014 0.002 PHE A 301 TYR 0.027 0.002 TYR L 49 ARG 0.003 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 1.783 Fit side-chains REVERT: A 152 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: A 240 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: B 3 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7984 (tp40) REVERT: C 3 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: C 105 GLN cc_start: 0.8463 (mm110) cc_final: 0.8263 (mm110) REVERT: D 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: D 410 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8744 (mp) REVERT: G 152 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: G 336 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7909 (mtp180) REVERT: G 410 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9025 (mp) REVERT: G 468 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6275 (mp10) REVERT: H 3 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8036 (tp40) REVERT: L 55 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7381 (tp30) outliers start: 66 outliers final: 25 residues processed: 283 average time/residue: 1.1917 time to fit residues: 374.9282 Evaluate side-chains 270 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN G 102 HIS H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16086 Z= 0.343 Angle : 0.692 7.234 21828 Z= 0.383 Chirality : 0.053 0.221 2574 Planarity : 0.005 0.052 2742 Dihedral : 6.182 52.402 2429 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.61 % Allowed : 13.14 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.72 (0.18), residues: 1992 helix: 1.89 (0.25), residues: 456 sheet: 0.52 (0.20), residues: 621 loop : -0.21 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 50 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.002 PHE D 301 TYR 0.025 0.002 TYR L 49 ARG 0.004 0.001 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 239 time to evaluate : 1.963 Fit side-chains REVERT: A 152 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: A 240 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 350 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8233 (t0) REVERT: B 3 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7983 (tp40) REVERT: C 3 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: D 258 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: D 410 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8753 (mp) REVERT: F 103 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8142 (tttp) REVERT: G 139 LYS cc_start: 0.8445 (mptp) cc_final: 0.8241 (mmtm) REVERT: G 152 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: G 336 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7903 (mtp180) REVERT: G 468 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6308 (mp10) REVERT: H 3 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8032 (tp40) REVERT: L 55 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7425 (tp30) outliers start: 64 outliers final: 28 residues processed: 281 average time/residue: 1.2129 time to fit residues: 378.0034 Evaluate side-chains 278 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN D 465 GLN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16086 Z= 0.214 Angle : 0.580 6.331 21828 Z= 0.321 Chirality : 0.048 0.186 2574 Planarity : 0.004 0.040 2742 Dihedral : 5.834 51.483 2428 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.10 % Allowed : 13.87 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.78 (0.18), residues: 1992 helix: 2.26 (0.26), residues: 438 sheet: 0.55 (0.20), residues: 621 loop : -0.30 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 50 HIS 0.003 0.001 HIS G 102 PHE 0.013 0.001 PHE D 301 TYR 0.022 0.002 TYR L 49 ARG 0.002 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 1.871 Fit side-chains REVERT: A 152 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 240 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: B 3 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: C 3 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: D 258 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: F 103 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (tttp) REVERT: G 139 LYS cc_start: 0.8414 (mptp) cc_final: 0.8211 (mmtm) REVERT: G 152 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: H 3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (tp40) outliers start: 55 outliers final: 30 residues processed: 267 average time/residue: 1.2222 time to fit residues: 361.7168 Evaluate side-chains 271 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN C 105 GLN D 465 GLN G 102 HIS G 465 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16086 Z= 0.246 Angle : 0.613 6.248 21828 Z= 0.338 Chirality : 0.049 0.199 2574 Planarity : 0.004 0.042 2742 Dihedral : 5.871 51.762 2428 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.33 % Allowed : 13.76 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.75 (0.18), residues: 1992 helix: 2.23 (0.26), residues: 438 sheet: 0.51 (0.20), residues: 621 loop : -0.30 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 50 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE D 301 TYR 0.024 0.002 TYR L 49 ARG 0.002 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 1.707 Fit side-chains REVERT: A 152 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: A 240 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: B 3 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: B 52 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8530 (ttmt) REVERT: C 3 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7959 (tp40) REVERT: C 105 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8234 (mm110) REVERT: D 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: D 410 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 103 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8133 (tttp) REVERT: F 103 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8059 (tttp) REVERT: G 139 LYS cc_start: 0.8429 (mptp) cc_final: 0.8225 (mmtm) REVERT: G 152 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: G 468 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: H 3 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8010 (tp40) outliers start: 59 outliers final: 31 residues processed: 278 average time/residue: 1.1931 time to fit residues: 369.6521 Evaluate side-chains 279 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16086 Z= 0.228 Angle : 0.596 6.201 21828 Z= 0.329 Chirality : 0.048 0.187 2574 Planarity : 0.004 0.039 2742 Dihedral : 5.815 51.483 2428 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.33 % Allowed : 13.48 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.79 (0.18), residues: 1992 helix: 2.10 (0.25), residues: 456 sheet: 0.51 (0.20), residues: 621 loop : -0.22 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 50 HIS 0.003 0.001 HIS G 102 PHE 0.013 0.001 PHE D 301 TYR 0.023 0.002 TYR L 49 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 235 time to evaluate : 1.913 Fit side-chains REVERT: A 152 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: A 240 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 3 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7977 (tp40) REVERT: B 52 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8534 (ttmt) REVERT: C 3 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7965 (tp40) REVERT: D 258 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8067 (tp30) REVERT: D 350 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8188 (t0) REVERT: D 410 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 103 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (tttp) REVERT: F 103 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8057 (tttp) REVERT: G 139 LYS cc_start: 0.8418 (mptp) cc_final: 0.8212 (mmtm) REVERT: G 152 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: G 468 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: H 3 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (tp40) outliers start: 59 outliers final: 37 residues processed: 270 average time/residue: 1.2292 time to fit residues: 368.0464 Evaluate side-chains 285 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 235 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN D 465 GLN G 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16086 Z= 0.217 Angle : 0.587 6.186 21828 Z= 0.324 Chirality : 0.048 0.188 2574 Planarity : 0.004 0.052 2742 Dihedral : 5.773 51.444 2428 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.05 % Allowed : 13.99 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.80 (0.18), residues: 1992 helix: 2.33 (0.26), residues: 438 sheet: 0.52 (0.20), residues: 621 loop : -0.29 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 50 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE D 301 TYR 0.023 0.002 TYR L 49 ARG 0.003 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 1.733 Fit side-chains REVERT: A 152 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: A 240 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: B 3 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (tp40) REVERT: B 52 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8531 (ttmt) REVERT: C 3 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: D 258 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: D 350 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8182 (t0) REVERT: E 103 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8108 (tttp) REVERT: F 103 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8015 (tttp) REVERT: G 139 LYS cc_start: 0.8416 (mptp) cc_final: 0.8210 (mmtm) REVERT: G 152 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: G 468 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: H 3 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8029 (tp40) outliers start: 54 outliers final: 36 residues processed: 273 average time/residue: 1.2241 time to fit residues: 370.1015 Evaluate side-chains 286 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN C 105 GLN D 465 GLN G 465 GLN H 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16086 Z= 0.209 Angle : 0.581 6.514 21828 Z= 0.319 Chirality : 0.047 0.186 2574 Planarity : 0.004 0.043 2742 Dihedral : 5.734 51.463 2428 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.82 % Allowed : 14.16 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.82 (0.18), residues: 1992 helix: 2.37 (0.26), residues: 438 sheet: 0.53 (0.20), residues: 621 loop : -0.28 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 50 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE D 301 TYR 0.023 0.002 TYR L 49 ARG 0.004 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 1.918 Fit side-chains REVERT: A 152 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: A 240 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 3 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: B 52 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8527 (ttmt) REVERT: C 3 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: C 105 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8236 (mm110) REVERT: D 258 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: D 350 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8176 (t0) REVERT: E 103 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8106 (tttp) REVERT: F 103 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (tttp) REVERT: G 139 LYS cc_start: 0.8412 (mptp) cc_final: 0.8207 (mmtm) REVERT: G 152 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: G 468 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6263 (mp10) REVERT: H 3 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8026 (tp40) outliers start: 50 outliers final: 35 residues processed: 269 average time/residue: 1.2928 time to fit residues: 386.1010 Evaluate side-chains 284 residues out of total 1773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN D 465 GLN G 102 HIS G 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099365 restraints weight = 17514.967| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.71 r_work: 0.3039 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16086 Z= 0.132 Angle : 0.486 6.543 21828 Z= 0.266 Chirality : 0.045 0.175 2574 Planarity : 0.004 0.038 2742 Dihedral : 5.314 51.112 2428 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.76 % Allowed : 14.21 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.01 (0.19), residues: 1992 helix: 2.57 (0.26), residues: 438 sheet: 0.69 (0.20), residues: 600 loop : -0.20 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 50 HIS 0.003 0.001 HIS G 102 PHE 0.011 0.001 PHE D 301 TYR 0.019 0.001 TYR F 49 ARG 0.003 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6712.22 seconds wall clock time: 122 minutes 22.84 seconds (7342.84 seconds total)