Starting phenix.real_space_refine on Sat Mar 16 18:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upk_26668/03_2024/7upk_26668.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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 84 5.16 5 C 9654 2.51 5 N 2514 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15276 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 7.75, per 1000 atoms: 0.51 Number of scatterers: 15276 At special positions: 0 Unit cell: (144.18, 132.84, 103.68, 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 84 16.00 O 3024 8.00 N 2514 7.00 C 9654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 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=2.02 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 C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.6 seconds 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 31 sheets defined 27.7% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.565A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 Proline residue: D 89 - end of helix removed outlier: 3.911A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 146 removed outlier: 4.438A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.812A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.718A 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 246 removed outlier: 3.568A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 358 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 452 through 471 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.733A pdb=" N VAL L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 65 through 72 removed outlier: 5.773A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.878A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.441A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 192 through 215 removed outlier: 4.128A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.612A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.749A pdb=" N VAL F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.540A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 3.916A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.442A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.093A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.571A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.710A pdb=" N VAL G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 158 through 162 removed outlier: 18.193A pdb=" N THR D 168 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N THR D 54 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N TYR D 170 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP D 56 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE D 172 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 58 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (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=AA2, first strand: chain 'D' and resid 226 through 227 removed outlier: 3.885A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (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=AA3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'D' and resid 301 through 302 removed outlier: 5.915A pdb=" N ARG D 365 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'D' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.101A pdb=" N PHE L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 158 through 162 removed outlier: 18.099A pdb=" N THR A 168 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N THR A 54 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N PHE A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 58 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'A' and resid 263 through 270 removed outlier: 6.227A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.825A pdb=" N MET A 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 425 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AB8, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.885A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.090A pdb=" N PHE F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 158 through 162 removed outlier: 18.067A pdb=" N THR B 168 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N THR B 54 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N PHE B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 58 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AC6, first strand: chain 'B' and resid 263 through 270 removed outlier: 6.233A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 303 removed outlier: 5.979A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.434A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP E 33 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.434A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.153A pdb=" N PHE G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 33 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.153A pdb=" N PHE G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1668 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: 5.05 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4912 1.34 - 1.46: 3581 1.46 - 1.58: 6933 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 15546 Sorted by residual: bond pdb=" CB THR B 250 " pdb=" CG2 THR B 250 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" N GLU D 95 " pdb=" CA GLU D 95 " ideal model delta sigma weight residual 1.458 1.471 -0.014 1.42e-02 4.96e+03 9.06e-01 bond pdb=" CD GLU D 95 " pdb=" OE1 GLU D 95 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 7.83e-01 bond pdb=" CB VAL B 449 " pdb=" CG1 VAL B 449 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.78e-01 bond pdb=" CB THR A 245 " pdb=" CG2 THR A 245 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.71e-01 ... (remaining 15541 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 333 106.47 - 113.35: 8701 113.35 - 120.23: 5232 120.23 - 127.11: 6720 127.11 - 134.00: 119 Bond angle restraints: 21105 Sorted by residual: angle pdb=" N GLU D 95 " pdb=" CA GLU D 95 " pdb=" CB GLU D 95 " ideal model delta sigma weight residual 110.42 115.36 -4.94 1.76e+00 3.23e-01 7.87e+00 angle pdb=" CA TRP F 96 " pdb=" CB TRP F 96 " pdb=" CG TRP F 96 " ideal model delta sigma weight residual 113.60 109.60 4.00 1.90e+00 2.77e-01 4.44e+00 angle pdb=" C VAL D 39 " pdb=" N LYS D 40 " pdb=" CA LYS D 40 " ideal model delta sigma weight residual 120.87 117.95 2.92 1.42e+00 4.96e-01 4.22e+00 angle pdb=" CA TRP L 96 " pdb=" CB TRP L 96 " pdb=" CG TRP L 96 " ideal model delta sigma weight residual 113.60 109.71 3.89 1.90e+00 2.77e-01 4.19e+00 angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 119.07 -4.67 2.30e+00 1.89e-01 4.12e+00 ... (remaining 21100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8767 17.95 - 35.90: 478 35.90 - 53.85: 96 53.85 - 71.80: 28 71.80 - 89.75: 18 Dihedral angle restraints: 9387 sinusoidal: 3642 harmonic: 5745 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -142.13 56.13 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.66 48.66 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 9384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1896 0.047 - 0.095: 418 0.095 - 0.142: 155 0.142 - 0.190: 5 0.190 - 0.237: 1 Chirality restraints: 2475 Sorted by residual: chirality pdb=" CA GLU D 95 " pdb=" N GLU D 95 " pdb=" C GLU D 95 " pdb=" CB GLU D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA CYS A 71 " pdb=" N CYS A 71 " pdb=" C CYS A 71 " pdb=" CB CYS A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA CYS A 192 " pdb=" N CYS A 192 " pdb=" C CYS A 192 " pdb=" CB CYS A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2472 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 68 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C MET A 68 " -0.050 2.00e-02 2.50e+03 pdb=" O MET A 68 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 69 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 66 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C SER A 66 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 66 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 67 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 23 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.55e+00 pdb=" C LYS H 23 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS H 23 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA H 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 442 2.70 - 3.25: 14981 3.25 - 3.80: 25731 3.80 - 4.35: 34521 4.35 - 4.90: 57512 Nonbonded interactions: 133187 Sorted by model distance: nonbonded pdb=" OG SER B 50 " pdb=" OG1 THR B 286 " model vdw 2.156 2.440 nonbonded pdb=" O ASP H 50 " pdb=" OG1 THR H 57 " model vdw 2.242 2.440 nonbonded pdb=" NZ LYS D 148 " pdb=" OD2 ASP D 270 " model vdw 2.252 2.520 nonbonded pdb=" O MET B 61 " pdb=" OH TYR B 79 " model vdw 2.264 2.440 nonbonded pdb=" O MET A 61 " pdb=" OH TYR A 79 " model vdw 2.273 2.440 ... (remaining 133182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' 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: 3.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.740 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 39.460 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 0.035 15546 Z= 0.211 Angle : 0.566 6.970 21105 Z= 0.307 Chirality : 0.045 0.237 2475 Planarity : 0.004 0.044 2670 Dihedral : 12.649 89.751 5637 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.19), residues: 1959 helix: 0.47 (0.23), residues: 462 sheet: -0.31 (0.21), residues: 636 loop : 0.18 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 96 HIS 0.003 0.001 HIS B 372 PHE 0.012 0.001 PHE F 11 TYR 0.031 0.002 TYR C 52 ARG 0.004 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.561 Fit side-chains REVERT: D 209 ASP cc_start: 0.8023 (m-30) cc_final: 0.7716 (m-30) REVERT: L 27 GLU cc_start: 0.7645 (pt0) cc_final: 0.7289 (pt0) REVERT: F 27 GLU cc_start: 0.7638 (pt0) cc_final: 0.7233 (pt0) REVERT: B 415 THR cc_start: 0.8220 (p) cc_final: 0.7988 (p) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 1.1491 time to fit residues: 371.3833 Evaluate side-chains 224 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN D 351 ASN L 38 GLN A 64 ASN A 305 ASN A 341 ASN A 351 ASN C 39 GLN F 38 GLN B 64 ASN B 217 ASN B 351 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15546 Z= 0.246 Angle : 0.535 6.585 21105 Z= 0.281 Chirality : 0.045 0.151 2475 Planarity : 0.004 0.043 2670 Dihedral : 4.943 25.862 2121 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.62 % Allowed : 8.90 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.19), residues: 1959 helix: 1.03 (0.24), residues: 465 sheet: -0.31 (0.22), residues: 606 loop : 0.10 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 96 HIS 0.002 0.000 HIS B 372 PHE 0.011 0.002 PHE C 29 TYR 0.036 0.002 TYR C 52 ARG 0.005 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 1.621 Fit side-chains REVERT: D 209 ASP cc_start: 0.8014 (m-30) cc_final: 0.7722 (m-30) REVERT: D 251 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: D 406 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6583 (pt0) REVERT: L 27 GLU cc_start: 0.7761 (pt0) cc_final: 0.7395 (pt0) REVERT: A 156 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 388 ILE cc_start: 0.8630 (mm) cc_final: 0.8427 (mm) REVERT: A 406 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6493 (pt0) REVERT: C 58 ASN cc_start: 0.7446 (t0) cc_final: 0.7238 (t0) REVERT: F 3 GLN cc_start: 0.7250 (mp10) cc_final: 0.6651 (mp10) REVERT: F 27 GLU cc_start: 0.7610 (pt0) cc_final: 0.7217 (pt0) REVERT: B 61 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: B 406 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: B 415 THR cc_start: 0.8248 (p) cc_final: 0.7969 (p) outliers start: 28 outliers final: 10 residues processed: 256 average time/residue: 1.1600 time to fit residues: 330.0633 Evaluate side-chains 240 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN A 305 ASN F 6 GLN B 314 ASN G 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15546 Z= 0.438 Angle : 0.644 7.763 21105 Z= 0.333 Chirality : 0.049 0.200 2475 Planarity : 0.004 0.048 2670 Dihedral : 5.403 27.417 2121 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.24 % Allowed : 10.34 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.19), residues: 1959 helix: 1.05 (0.24), residues: 465 sheet: -0.36 (0.21), residues: 591 loop : -0.15 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 96 HIS 0.003 0.001 HIS E 43 PHE 0.013 0.002 PHE C 29 TYR 0.046 0.002 TYR H 52 ARG 0.006 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 233 time to evaluate : 1.739 Fit side-chains REVERT: D 160 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: D 209 ASP cc_start: 0.8039 (m-30) cc_final: 0.7717 (m-30) REVERT: D 251 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: D 406 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: L 27 GLU cc_start: 0.7722 (pt0) cc_final: 0.7368 (pt0) REVERT: A 156 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 251 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: A 406 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6519 (pt0) REVERT: C 80 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (ttm) REVERT: F 27 GLU cc_start: 0.7687 (pt0) cc_final: 0.7178 (pt0) REVERT: B 61 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8176 (mtp) REVERT: B 258 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7091 (tp30) REVERT: B 375 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6433 (mpp-170) REVERT: B 406 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: B 415 THR cc_start: 0.8256 (p) cc_final: 0.8032 (p) outliers start: 56 outliers final: 23 residues processed: 270 average time/residue: 1.1619 time to fit residues: 348.4192 Evaluate side-chains 259 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 226 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.0980 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 175 optimal weight: 0.0980 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 58 ASN L 38 GLN A 305 ASN A 351 ASN F 37 GLN B 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15546 Z= 0.169 Angle : 0.490 6.819 21105 Z= 0.256 Chirality : 0.043 0.150 2475 Planarity : 0.003 0.043 2670 Dihedral : 4.790 23.787 2121 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.60 % Allowed : 12.36 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.19), residues: 1959 helix: 1.36 (0.24), residues: 465 sheet: -0.30 (0.21), residues: 591 loop : -0.00 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.002 0.001 HIS B 372 PHE 0.011 0.001 PHE E 29 TYR 0.016 0.001 TYR F 91 ARG 0.005 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 233 time to evaluate : 1.915 Fit side-chains REVERT: D 209 ASP cc_start: 0.7995 (m-30) cc_final: 0.7669 (m-30) REVERT: D 293 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8761 (mm) REVERT: D 380 ASN cc_start: 0.8188 (m-40) cc_final: 0.7953 (m-40) REVERT: D 406 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6594 (pt0) REVERT: L 27 GLU cc_start: 0.7668 (pt0) cc_final: 0.7225 (pt0) REVERT: A 156 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: A 293 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8702 (mm) REVERT: A 406 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6559 (pt0) REVERT: F 27 GLU cc_start: 0.7727 (pt0) cc_final: 0.7243 (pt0) REVERT: B 61 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: B 293 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 406 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6413 (pt0) outliers start: 45 outliers final: 14 residues processed: 262 average time/residue: 1.1380 time to fit residues: 331.2393 Evaluate side-chains 235 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 314 ASN F 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15546 Z= 0.265 Angle : 0.533 6.291 21105 Z= 0.275 Chirality : 0.045 0.143 2475 Planarity : 0.003 0.042 2670 Dihedral : 4.879 23.250 2121 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.77 % Allowed : 13.29 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.19), residues: 1959 helix: 1.42 (0.24), residues: 465 sheet: -0.28 (0.21), residues: 588 loop : -0.05 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 96 HIS 0.002 0.001 HIS E 43 PHE 0.011 0.001 PHE C 29 TYR 0.020 0.002 TYR H 52 ARG 0.006 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.8004 (m-30) cc_final: 0.7674 (m-30) REVERT: D 293 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8766 (mm) REVERT: D 380 ASN cc_start: 0.8270 (m-40) cc_final: 0.8024 (m-40) REVERT: D 406 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: L 27 GLU cc_start: 0.7680 (pt0) cc_final: 0.7185 (pt0) REVERT: A 156 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 293 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8698 (mm) REVERT: A 406 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6508 (pt0) REVERT: F 27 GLU cc_start: 0.7632 (pt0) cc_final: 0.7085 (pt0) REVERT: B 61 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: B 293 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 375 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6387 (mpp-170) REVERT: B 406 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6449 (pt0) outliers start: 48 outliers final: 23 residues processed: 253 average time/residue: 1.1778 time to fit residues: 330.4656 Evaluate side-chains 244 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15546 Z= 0.238 Angle : 0.517 6.377 21105 Z= 0.267 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.039 2670 Dihedral : 4.811 23.057 2121 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.06 % Allowed : 13.46 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.19), residues: 1959 helix: 1.46 (0.24), residues: 465 sheet: -0.27 (0.21), residues: 588 loop : -0.04 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 96 HIS 0.002 0.000 HIS E 43 PHE 0.011 0.001 PHE C 29 TYR 0.018 0.002 TYR F 91 ARG 0.008 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.7976 (m-30) cc_final: 0.7658 (m-30) REVERT: D 293 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8769 (mm) REVERT: D 380 ASN cc_start: 0.8265 (m-40) cc_final: 0.8022 (m-40) REVERT: D 406 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6609 (pt0) REVERT: H 46 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: L 27 GLU cc_start: 0.7702 (pt0) cc_final: 0.7180 (pt0) REVERT: A 156 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 251 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: A 293 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8703 (mm) REVERT: A 406 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6546 (pt0) REVERT: C 46 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: F 27 GLU cc_start: 0.7606 (pt0) cc_final: 0.7082 (pt0) REVERT: B 61 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8235 (mtp) REVERT: B 74 SER cc_start: 0.7951 (p) cc_final: 0.7630 (m) REVERT: B 293 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8825 (mm) REVERT: B 375 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.6460 (mpp-170) REVERT: B 406 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: E 46 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7139 (mt-10) outliers start: 53 outliers final: 27 residues processed: 250 average time/residue: 1.1646 time to fit residues: 322.9174 Evaluate side-chains 256 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15546 Z= 0.224 Angle : 0.513 6.295 21105 Z= 0.265 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.045 2670 Dihedral : 4.792 21.868 2121 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.29 % Allowed : 13.63 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.19), residues: 1959 helix: 1.48 (0.24), residues: 465 sheet: -0.25 (0.21), residues: 588 loop : -0.03 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 96 HIS 0.002 0.000 HIS E 43 PHE 0.011 0.001 PHE C 29 TYR 0.018 0.001 TYR F 91 ARG 0.013 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 222 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.7966 (m-30) cc_final: 0.7641 (m-30) REVERT: D 293 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8763 (mm) REVERT: D 406 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6615 (pt0) REVERT: L 27 GLU cc_start: 0.7739 (pt0) cc_final: 0.7232 (pt0) REVERT: A 156 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 251 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: A 293 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8702 (mm) REVERT: A 406 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: C 46 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: F 27 GLU cc_start: 0.7637 (pt0) cc_final: 0.7112 (pt0) REVERT: B 61 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: B 293 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8816 (mm) REVERT: B 375 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6189 (mpp-170) REVERT: B 406 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6491 (pt0) REVERT: E 46 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7133 (mt-10) outliers start: 57 outliers final: 29 residues processed: 261 average time/residue: 1.1522 time to fit residues: 335.0619 Evaluate side-chains 255 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15546 Z= 0.202 Angle : 0.501 6.046 21105 Z= 0.258 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.046 2670 Dihedral : 4.702 21.624 2121 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.24 % Allowed : 13.81 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.19), residues: 1959 helix: 1.50 (0.24), residues: 465 sheet: -0.22 (0.21), residues: 588 loop : 0.03 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 96 HIS 0.001 0.000 HIS E 43 PHE 0.010 0.001 PHE C 29 TYR 0.017 0.001 TYR F 91 ARG 0.009 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 219 time to evaluate : 1.805 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.7973 (m-30) cc_final: 0.7642 (m-30) REVERT: D 293 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8763 (mm) REVERT: D 406 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: H 46 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: L 27 GLU cc_start: 0.7769 (pt0) cc_final: 0.7250 (pt0) REVERT: A 156 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 251 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: A 293 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 406 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6583 (pt0) REVERT: C 46 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: F 27 GLU cc_start: 0.7610 (pt0) cc_final: 0.7067 (pt0) REVERT: F 70 ASP cc_start: 0.7733 (m-30) cc_final: 0.7452 (m-30) REVERT: B 61 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8237 (mtp) REVERT: B 293 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 375 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6172 (mpp-170) REVERT: B 406 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6488 (pt0) REVERT: E 46 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7133 (mt-10) outliers start: 56 outliers final: 32 residues processed: 255 average time/residue: 1.1539 time to fit residues: 327.5436 Evaluate side-chains 260 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 215 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15546 Z= 0.210 Angle : 0.502 5.876 21105 Z= 0.259 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.041 2670 Dihedral : 4.685 20.809 2121 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.00 % Allowed : 14.33 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.19), residues: 1959 helix: 1.48 (0.24), residues: 465 sheet: -0.20 (0.21), residues: 588 loop : 0.05 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 96 HIS 0.001 0.000 HIS E 43 PHE 0.010 0.001 PHE H 29 TYR 0.017 0.001 TYR F 91 ARG 0.009 0.001 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 216 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.7983 (m-30) cc_final: 0.7626 (m-30) REVERT: D 293 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8765 (mm) REVERT: D 406 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: H 46 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: L 27 GLU cc_start: 0.7759 (pt0) cc_final: 0.7252 (pt0) REVERT: A 156 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: A 251 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: A 293 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 406 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: C 46 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: F 27 GLU cc_start: 0.7603 (pt0) cc_final: 0.7068 (pt0) REVERT: F 70 ASP cc_start: 0.7904 (m-30) cc_final: 0.7662 (m-30) REVERT: B 61 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: B 293 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 375 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6220 (mpp-170) REVERT: B 406 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: E 46 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7130 (mt-10) outliers start: 52 outliers final: 32 residues processed: 251 average time/residue: 1.1403 time to fit residues: 319.2674 Evaluate side-chains 257 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 176 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN A 305 ASN F 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15546 Z= 0.180 Angle : 0.485 6.013 21105 Z= 0.250 Chirality : 0.043 0.142 2475 Planarity : 0.003 0.038 2670 Dihedral : 4.575 20.615 2121 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.48 % Allowed : 14.96 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.19), residues: 1959 helix: 1.51 (0.24), residues: 465 sheet: -0.14 (0.21), residues: 573 loop : 0.10 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 96 HIS 0.001 0.000 HIS E 43 PHE 0.010 0.001 PHE H 29 TYR 0.016 0.001 TYR F 91 ARG 0.009 0.000 ARG E 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.7963 (m-30) cc_final: 0.7615 (m-30) REVERT: D 293 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8761 (mm) REVERT: D 406 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6609 (pt0) REVERT: H 46 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: L 27 GLU cc_start: 0.7741 (pt0) cc_final: 0.7247 (pt0) REVERT: A 156 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 293 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 406 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6599 (pt0) REVERT: C 46 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: F 27 GLU cc_start: 0.7640 (pt0) cc_final: 0.7081 (pt0) REVERT: F 70 ASP cc_start: 0.7873 (m-30) cc_final: 0.7614 (m-30) REVERT: B 61 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8151 (mtp) REVERT: B 293 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8804 (mm) REVERT: B 375 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.6188 (mpp-170) REVERT: B 406 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: E 46 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7094 (mt-10) outliers start: 43 outliers final: 29 residues processed: 241 average time/residue: 1.1384 time to fit residues: 306.6136 Evaluate side-chains 247 residues out of total 1731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 156 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN A 305 ASN F 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118933 restraints weight = 15407.044| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.41 r_work: 0.3116 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15546 Z= 0.216 Angle : 0.507 5.940 21105 Z= 0.261 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.037 2670 Dihedral : 4.639 20.595 2121 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.00 % Allowed : 14.38 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.19), residues: 1959 helix: 1.50 (0.24), residues: 465 sheet: -0.14 (0.21), residues: 573 loop : 0.08 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 96 HIS 0.002 0.001 HIS E 43 PHE 0.010 0.001 PHE C 29 TYR 0.018 0.001 TYR F 91 ARG 0.009 0.001 ARG E 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5731.29 seconds wall clock time: 102 minutes 13.25 seconds (6133.25 seconds total)