Starting phenix.real_space_refine on Mon Nov 18 14:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2024/8ozd_17305.cif" } resolution = 3.89 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 609 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 48 5.16 5 C 10118 2.51 5 N 2650 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16001 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "F" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Time building chain proxies: 9.63, per 1000 atoms: 0.60 Number of scatterers: 16001 At special positions: 0 Unit cell: (153.67, 128.26, 117.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 66 15.00 O 3119 8.00 N 2650 7.00 C 10118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 40.1% alpha, 17.5% beta 11 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.774A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.505A pdb=" N LYS A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.252A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.101A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.700A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.530A pdb=" N ILE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.689A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 367 removed outlier: 4.348A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.953A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.669A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.949A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.670A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.603A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.884A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.858A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.795A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 451 through 463 removed outlier: 4.044A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.774A pdb=" N GLU C 50 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.505A pdb=" N LYS C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.251A pdb=" N ARG C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.100A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 224 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.700A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.531A pdb=" N ILE C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.690A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 353 through 367 removed outlier: 4.348A pdb=" N ASN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 384 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 3.953A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.668A pdb=" N ILE D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.950A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 removed outlier: 3.671A pdb=" N TYR D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.604A pdb=" N LEU D 214 " --> pdb=" O PHE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.884A pdb=" N ASP D 233 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.795A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 451 through 463 removed outlier: 4.045A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 Processing helix chain 'D' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.421A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU B 3 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 414 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 167 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 4.817A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.610A pdb=" N GLY A 312 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 319 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.836A pdb=" N ILE B 12 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.541A pdb=" N GLY B 45 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.421A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS D 279 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS D 360 " --> pdb=" O CYS D 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS D 279 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS D 360 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY D 385 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL D 412 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU D 3 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN C 413 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR D 6 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N SER C 415 " --> pdb=" O TYR D 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 414 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS C 167 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 180 removed outlier: 4.817A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AB7, first strand: chain 'C' and resid 283 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.609A pdb=" N GLY C 312 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 319 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.836A pdb=" N ILE D 12 " --> pdb=" O CYS D 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.541A pdb=" N GLY D 45 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 139 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE D 224 " --> pdb=" O TRP D 139 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 141 " --> pdb=" O PHE D 224 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3882 1.33 - 1.45: 3661 1.45 - 1.57: 8786 1.57 - 1.69: 130 1.69 - 1.81: 74 Bond restraints: 16533 Sorted by residual: bond pdb=" CG ARG C 374 " pdb=" CD ARG C 374 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG ARG A 374 " pdb=" CD ARG A 374 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB ASP C 40 " pdb=" CG ASP C 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.42e-01 bond pdb=" CB ASP A 40 " pdb=" CG ASP A 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.22e-01 bond pdb=" CA ASP A 146 " pdb=" C ASP A 146 " ideal model delta sigma weight residual 1.519 1.530 -0.010 1.14e-02 7.69e+03 8.38e-01 ... (remaining 16528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 22229 1.89 - 3.78: 343 3.78 - 5.68: 49 5.68 - 7.57: 4 7.57 - 9.46: 6 Bond angle restraints: 22631 Sorted by residual: angle pdb=" C LEU C 39 " pdb=" N ASP C 40 " pdb=" CA ASP C 40 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C LEU A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.20e+01 angle pdb=" C TRP A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 120.65 124.79 -4.14 1.32e+00 5.74e-01 9.85e+00 angle pdb=" C TRP C 369 " pdb=" N ASN C 370 " pdb=" CA ASN C 370 " ideal model delta sigma weight residual 120.65 124.75 -4.10 1.32e+00 5.74e-01 9.63e+00 angle pdb=" C LYS A 86 " pdb=" N GLN A 87 " pdb=" CA GLN A 87 " ideal model delta sigma weight residual 121.14 116.10 5.04 1.75e+00 3.27e-01 8.29e+00 ... (remaining 22626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 9523 33.21 - 66.42: 428 66.42 - 99.62: 14 99.62 - 132.83: 1 132.83 - 166.04: 6 Dihedral angle restraints: 9972 sinusoidal: 4716 harmonic: 5256 Sorted by residual: dihedral pdb=" O4' U F 31 " pdb=" C1' U F 31 " pdb=" N1 U F 31 " pdb=" C2 U F 31 " ideal model delta sinusoidal sigma weight residual 200.00 33.96 166.04 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U I 13 " pdb=" C1' U I 13 " pdb=" N1 U I 13 " pdb=" C2 U I 13 " ideal model delta sinusoidal sigma weight residual 200.00 39.42 160.58 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U F 27 " pdb=" C1' U F 27 " pdb=" N1 U F 27 " pdb=" C2 U F 27 " ideal model delta sinusoidal sigma weight residual -160.00 -24.95 -135.05 1 1.50e+01 4.44e-03 7.29e+01 ... (remaining 9969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1819 0.039 - 0.078: 449 0.078 - 0.117: 189 0.117 - 0.156: 25 0.156 - 0.195: 2 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB ILE D 223 " pdb=" CA ILE D 223 " pdb=" CG1 ILE D 223 " pdb=" CG2 ILE D 223 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA GLN C 156 " pdb=" N GLN C 156 " pdb=" C GLN C 156 " pdb=" CB GLN C 156 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2481 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 437 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO B 438 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 437 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 438 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 438 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 438 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 132 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU C 132 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU C 132 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 133 " -0.010 2.00e-02 2.50e+03 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 850 2.72 - 3.27: 16505 3.27 - 3.81: 27878 3.81 - 4.36: 33721 4.36 - 4.90: 54779 Nonbonded interactions: 133733 Sorted by model distance: nonbonded pdb=" NZ LYS A 162 " pdb=" O PRO B 427 " model vdw 2.178 3.120 nonbonded pdb=" OG SER D 493 " pdb=" OD1 ASP D 495 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 493 " pdb=" OD1 ASP B 495 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS C 24 " pdb=" O LEU D 29 " model vdw 2.224 3.120 nonbonded pdb=" O LEU C 227 " pdb=" OG1 THR C 230 " model vdw 2.229 3.040 ... (remaining 133728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'F' selection = (chain 'I' and (name P or name OP1 or name OP2 or name O5' or name C5' or name C \ 4' or name O4' or name C3' or name O3' or name C2' or name O2' or name C1' or na \ me N1 or name C2 or name O2 or name N3 or name C4 or name O4 or name C5 or name \ C6 )) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.680 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 0.033 16533 Z= 0.165 Angle : 0.589 9.461 22631 Z= 0.313 Chirality : 0.041 0.195 2484 Planarity : 0.004 0.077 2620 Dihedral : 16.885 166.041 6576 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.75 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.29 (0.20), residues: 1770 helix: 0.76 (0.22), residues: 582 sheet: -0.35 (0.31), residues: 292 loop : -0.72 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 231 HIS 0.004 0.001 HIS B 217 PHE 0.018 0.001 PHE C 273 TYR 0.007 0.001 TYR A 251 ARG 0.010 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.4934 (ttm110) cc_final: 0.4672 (ttm170) REVERT: A 277 MET cc_start: 0.6731 (mtp) cc_final: 0.5977 (mmp) REVERT: A 279 ASP cc_start: 0.7655 (t70) cc_final: 0.7181 (m-30) REVERT: A 364 GLN cc_start: 0.6917 (tp40) cc_final: 0.6049 (tp40) REVERT: A 395 MET cc_start: 0.7309 (ppp) cc_final: 0.6913 (ppp) REVERT: B 58 ASP cc_start: 0.8369 (p0) cc_final: 0.8093 (m-30) REVERT: B 474 ASP cc_start: 0.8353 (t70) cc_final: 0.7954 (t70) REVERT: C 193 MET cc_start: 0.6223 (ttt) cc_final: 0.5262 (tmm) REVERT: D 64 ILE cc_start: 0.8955 (mm) cc_final: 0.8543 (mm) REVERT: D 247 LYS cc_start: 0.8805 (mppt) cc_final: 0.8515 (mtmt) REVERT: D 309 ASP cc_start: 0.7700 (p0) cc_final: 0.7370 (p0) REVERT: D 362 LYS cc_start: 0.8377 (pptt) cc_final: 0.7899 (ptpt) REVERT: D 466 ASN cc_start: 0.8318 (t0) cc_final: 0.7675 (t0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3074 time to fit residues: 113.1484 Evaluate side-chains 159 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0670 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS B 446 ASN D 154 ASN D 360 HIS D 446 ASN D 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16533 Z= 0.198 Angle : 0.637 9.298 22631 Z= 0.331 Chirality : 0.043 0.151 2484 Planarity : 0.005 0.058 2620 Dihedral : 17.258 178.865 2932 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.03 % Favored : 94.52 % Rotamer: Outliers : 1.25 % Allowed : 9.95 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.20), residues: 1770 helix: 0.86 (0.22), residues: 590 sheet: -0.21 (0.32), residues: 286 loop : -0.79 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 368 HIS 0.016 0.001 HIS A 9 PHE 0.016 0.001 PHE A 380 TYR 0.020 0.001 TYR D 397 ARG 0.010 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.4999 (ttm110) cc_final: 0.4681 (ttm110) REVERT: A 277 MET cc_start: 0.7040 (mtp) cc_final: 0.6570 (ttm) REVERT: A 279 ASP cc_start: 0.7843 (t70) cc_final: 0.7315 (m-30) REVERT: A 364 GLN cc_start: 0.7708 (tp40) cc_final: 0.7219 (mm-40) REVERT: A 395 MET cc_start: 0.7715 (ppp) cc_final: 0.7233 (ppp) REVERT: B 1 MET cc_start: 0.5115 (mmp) cc_final: 0.4641 (mmp) REVERT: B 92 THR cc_start: 0.8619 (m) cc_final: 0.8278 (p) REVERT: B 474 ASP cc_start: 0.8427 (t70) cc_final: 0.8105 (t70) REVERT: C 20 TRP cc_start: 0.7499 (t60) cc_final: 0.7200 (t60) REVERT: C 87 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8543 (pp30) REVERT: D 12 ILE cc_start: 0.8778 (pt) cc_final: 0.8538 (mm) REVERT: D 56 TYR cc_start: 0.8841 (t80) cc_final: 0.8546 (t80) REVERT: D 123 ASP cc_start: 0.8401 (p0) cc_final: 0.8135 (p0) REVERT: D 161 MET cc_start: 0.2508 (ppp) cc_final: 0.2239 (ppp) REVERT: D 247 LYS cc_start: 0.8762 (mppt) cc_final: 0.8501 (mtmt) REVERT: D 303 MET cc_start: 0.8594 (tmm) cc_final: 0.8226 (tmm) REVERT: D 309 ASP cc_start: 0.7734 (p0) cc_final: 0.7400 (p0) REVERT: D 466 ASN cc_start: 0.8130 (t0) cc_final: 0.7622 (t0) outliers start: 20 outliers final: 13 residues processed: 196 average time/residue: 0.2723 time to fit residues: 83.3935 Evaluate side-chains 153 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 0.0010 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 70 GLN D 59 HIS D 329 HIS D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16533 Z= 0.215 Angle : 0.616 8.941 22631 Z= 0.321 Chirality : 0.043 0.199 2484 Planarity : 0.005 0.053 2620 Dihedral : 17.282 175.878 2932 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.92 % Favored : 94.63 % Rotamer: Outliers : 1.50 % Allowed : 13.27 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.19 (0.20), residues: 1770 helix: 1.09 (0.22), residues: 584 sheet: -0.28 (0.32), residues: 280 loop : -0.86 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 368 HIS 0.021 0.001 HIS B 360 PHE 0.015 0.001 PHE C 273 TYR 0.011 0.001 TYR B 280 ARG 0.007 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.5124 (ttm110) cc_final: 0.4865 (ttm110) REVERT: A 277 MET cc_start: 0.7163 (mtp) cc_final: 0.6943 (mtm) REVERT: A 279 ASP cc_start: 0.7810 (t70) cc_final: 0.7277 (m-30) REVERT: A 291 THR cc_start: 0.2960 (m) cc_final: 0.2728 (m) REVERT: A 364 GLN cc_start: 0.8030 (tp40) cc_final: 0.7693 (tp40) REVERT: A 395 MET cc_start: 0.7635 (ppp) cc_final: 0.6956 (ppp) REVERT: B 92 THR cc_start: 0.8621 (m) cc_final: 0.8265 (p) REVERT: B 474 ASP cc_start: 0.8412 (t70) cc_final: 0.7962 (t0) REVERT: C 20 TRP cc_start: 0.7801 (t60) cc_final: 0.7557 (t60) REVERT: C 87 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8493 (pp30) REVERT: D 56 TYR cc_start: 0.8879 (t80) cc_final: 0.8650 (t80) REVERT: D 123 ASP cc_start: 0.8566 (p0) cc_final: 0.8300 (p0) REVERT: D 247 LYS cc_start: 0.8887 (mppt) cc_final: 0.8682 (mtmt) REVERT: D 303 MET cc_start: 0.8740 (tmm) cc_final: 0.8294 (tmm) REVERT: D 309 ASP cc_start: 0.7883 (p0) cc_final: 0.7675 (p0) REVERT: D 456 LEU cc_start: 0.9339 (mm) cc_final: 0.8996 (mm) REVERT: D 466 ASN cc_start: 0.8276 (t0) cc_final: 0.7729 (t0) REVERT: D 468 ASN cc_start: 0.8244 (t0) cc_final: 0.7861 (t0) REVERT: D 476 GLU cc_start: 0.8091 (pm20) cc_final: 0.7744 (pm20) outliers start: 24 outliers final: 20 residues processed: 164 average time/residue: 0.2619 time to fit residues: 67.3830 Evaluate side-chains 153 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 360 HIS C 226 HIS D 201 ASN D 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16533 Z= 0.176 Angle : 0.594 10.554 22631 Z= 0.305 Chirality : 0.042 0.252 2484 Planarity : 0.004 0.054 2620 Dihedral : 17.230 174.570 2932 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.18 % Favored : 95.37 % Rotamer: Outliers : 2.19 % Allowed : 14.08 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.20), residues: 1770 helix: 1.16 (0.22), residues: 590 sheet: -0.33 (0.31), residues: 288 loop : -0.89 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 368 HIS 0.027 0.001 HIS D 59 PHE 0.014 0.001 PHE A 45 TYR 0.009 0.001 TYR D 397 ARG 0.006 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.5195 (ttm110) cc_final: 0.4947 (ttm110) REVERT: A 85 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8063 (tptt) REVERT: A 217 PHE cc_start: 0.6452 (m-80) cc_final: 0.6165 (m-10) REVERT: A 279 ASP cc_start: 0.7806 (t70) cc_final: 0.7305 (m-30) REVERT: A 291 THR cc_start: 0.3159 (m) cc_final: 0.2894 (m) REVERT: A 364 GLN cc_start: 0.8079 (tp40) cc_final: 0.7633 (tp40) REVERT: A 395 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7112 (ppp) REVERT: B 1 MET cc_start: 0.5275 (mmp) cc_final: 0.4840 (mmp) REVERT: B 92 THR cc_start: 0.8607 (m) cc_final: 0.8245 (p) REVERT: B 303 MET cc_start: 0.8493 (tmm) cc_final: 0.8234 (tmm) REVERT: B 474 ASP cc_start: 0.8340 (t70) cc_final: 0.7982 (t0) REVERT: C 87 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8528 (pp30) REVERT: C 154 TYR cc_start: 0.6336 (t80) cc_final: 0.5948 (t80) REVERT: C 156 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5603 (pt0) REVERT: C 309 MET cc_start: 0.8464 (tpp) cc_final: 0.8244 (tpp) REVERT: C 395 MET cc_start: 0.8590 (ppp) cc_final: 0.8308 (ppp) REVERT: D 44 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9122 (tp) REVERT: D 123 ASP cc_start: 0.8566 (p0) cc_final: 0.8283 (p0) REVERT: D 161 MET cc_start: 0.2271 (tmm) cc_final: 0.1187 (ppp) REVERT: D 309 ASP cc_start: 0.7903 (p0) cc_final: 0.7688 (p0) REVERT: D 466 ASN cc_start: 0.8370 (t0) cc_final: 0.7758 (t0) REVERT: D 476 GLU cc_start: 0.8031 (pm20) cc_final: 0.6157 (pm20) outliers start: 35 outliers final: 19 residues processed: 180 average time/residue: 0.2706 time to fit residues: 76.0768 Evaluate side-chains 157 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 0.3980 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 357 GLN B 129 ASN B 329 HIS D 59 HIS D 129 ASN D 131 ASN D 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16533 Z= 0.288 Angle : 0.668 12.036 22631 Z= 0.348 Chirality : 0.044 0.257 2484 Planarity : 0.005 0.059 2620 Dihedral : 17.476 173.650 2932 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.97 % Favored : 94.58 % Rotamer: Outliers : 2.75 % Allowed : 14.96 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.31 (0.20), residues: 1770 helix: 1.18 (0.22), residues: 584 sheet: -0.71 (0.29), residues: 322 loop : -0.93 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 20 HIS 0.005 0.001 HIS A 9 PHE 0.017 0.002 PHE D 419 TYR 0.018 0.002 TYR C 154 ARG 0.009 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8179 (tptt) REVERT: A 217 PHE cc_start: 0.6528 (m-80) cc_final: 0.6228 (m-10) REVERT: A 279 ASP cc_start: 0.7805 (t70) cc_final: 0.7273 (m-30) REVERT: A 332 PHE cc_start: 0.8456 (m-80) cc_final: 0.8092 (m-10) REVERT: A 352 ASP cc_start: 0.6100 (p0) cc_final: 0.4680 (t0) REVERT: A 395 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7264 (ppp) REVERT: B 92 THR cc_start: 0.8706 (m) cc_final: 0.8361 (p) REVERT: B 254 TRP cc_start: 0.9513 (m100) cc_final: 0.9056 (m100) REVERT: B 303 MET cc_start: 0.8451 (tmm) cc_final: 0.7958 (tmm) REVERT: B 360 HIS cc_start: 0.8656 (m90) cc_final: 0.8396 (m90) REVERT: C 20 TRP cc_start: 0.7961 (t60) cc_final: 0.7697 (t60) REVERT: C 287 MET cc_start: 0.8010 (tpt) cc_final: 0.7711 (tpt) REVERT: C 309 MET cc_start: 0.8470 (tpp) cc_final: 0.8215 (tpp) REVERT: C 395 MET cc_start: 0.8812 (ppp) cc_final: 0.8586 (ppp) REVERT: D 123 ASP cc_start: 0.8621 (p0) cc_final: 0.8413 (p0) REVERT: D 309 ASP cc_start: 0.8159 (p0) cc_final: 0.7940 (p0) REVERT: D 466 ASN cc_start: 0.8584 (t0) cc_final: 0.8202 (t0) REVERT: D 468 ASN cc_start: 0.8279 (t0) cc_final: 0.7918 (t0) outliers start: 44 outliers final: 23 residues processed: 170 average time/residue: 0.2514 time to fit residues: 67.6133 Evaluate side-chains 150 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN D 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16533 Z= 0.181 Angle : 0.616 9.166 22631 Z= 0.315 Chirality : 0.042 0.270 2484 Planarity : 0.005 0.063 2620 Dihedral : 17.332 173.643 2932 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.35 % Favored : 95.20 % Rotamer: Outliers : 2.25 % Allowed : 17.15 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.22 (0.20), residues: 1770 helix: 1.22 (0.22), residues: 590 sheet: -0.49 (0.30), residues: 310 loop : -0.95 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 46 HIS 0.009 0.001 HIS D 59 PHE 0.029 0.001 PHE A 17 TYR 0.011 0.001 TYR A 213 ARG 0.005 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8158 (tptt) REVERT: A 279 ASP cc_start: 0.7686 (t70) cc_final: 0.7184 (m-30) REVERT: A 332 PHE cc_start: 0.8388 (m-80) cc_final: 0.7952 (m-10) REVERT: A 352 ASP cc_start: 0.6112 (p0) cc_final: 0.4702 (t0) REVERT: A 395 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7238 (ppp) REVERT: B 92 THR cc_start: 0.8628 (m) cc_final: 0.8265 (p) REVERT: B 303 MET cc_start: 0.8395 (tmm) cc_final: 0.7975 (tmm) REVERT: B 360 HIS cc_start: 0.8607 (m90) cc_final: 0.8356 (m90) REVERT: B 396 LEU cc_start: 0.8078 (pp) cc_final: 0.7873 (pp) REVERT: B 435 MET cc_start: 0.4186 (mmt) cc_final: 0.3504 (mmp) REVERT: C 20 TRP cc_start: 0.8113 (t60) cc_final: 0.7887 (t60) REVERT: C 156 GLN cc_start: 0.6121 (OUTLIER) cc_final: 0.5495 (pt0) REVERT: C 309 MET cc_start: 0.8554 (tpp) cc_final: 0.8287 (tpp) REVERT: D 78 PHE cc_start: 0.8299 (t80) cc_final: 0.8010 (t80) REVERT: D 123 ASP cc_start: 0.8543 (p0) cc_final: 0.8329 (p0) REVERT: D 309 ASP cc_start: 0.8089 (p0) cc_final: 0.7877 (p0) REVERT: D 466 ASN cc_start: 0.8521 (t0) cc_final: 0.8078 (t0) REVERT: D 468 ASN cc_start: 0.8184 (t0) cc_final: 0.7787 (t0) outliers start: 36 outliers final: 21 residues processed: 174 average time/residue: 0.2348 time to fit residues: 65.3301 Evaluate side-chains 153 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16533 Z= 0.168 Angle : 0.625 10.007 22631 Z= 0.316 Chirality : 0.042 0.274 2484 Planarity : 0.004 0.060 2620 Dihedral : 17.144 174.251 2932 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.29 % Favored : 95.31 % Rotamer: Outliers : 2.25 % Allowed : 17.83 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.15 (0.20), residues: 1770 helix: 1.27 (0.22), residues: 588 sheet: -0.44 (0.32), residues: 278 loop : -0.90 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 46 HIS 0.007 0.001 HIS D 59 PHE 0.019 0.001 PHE A 17 TYR 0.013 0.001 TYR A 293 ARG 0.008 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7624 (t70) cc_final: 0.7119 (m-30) REVERT: A 352 ASP cc_start: 0.6222 (p0) cc_final: 0.4820 (t0) REVERT: A 395 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7498 (ppp) REVERT: B 92 THR cc_start: 0.8653 (m) cc_final: 0.8281 (p) REVERT: B 303 MET cc_start: 0.8410 (tmm) cc_final: 0.7996 (tmm) REVERT: B 360 HIS cc_start: 0.8564 (m90) cc_final: 0.8311 (m90) REVERT: B 435 MET cc_start: 0.4339 (mmt) cc_final: 0.3378 (mmp) REVERT: C 193 MET cc_start: 0.6807 (ttt) cc_final: 0.6050 (tmm) REVERT: C 309 MET cc_start: 0.8590 (tpp) cc_final: 0.8324 (tpp) REVERT: D 123 ASP cc_start: 0.8526 (p0) cc_final: 0.8276 (p0) REVERT: D 309 ASP cc_start: 0.8149 (p0) cc_final: 0.7935 (p0) REVERT: D 466 ASN cc_start: 0.8420 (t0) cc_final: 0.7974 (t0) outliers start: 36 outliers final: 25 residues processed: 176 average time/residue: 0.2452 time to fit residues: 68.9346 Evaluate side-chains 156 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 0.3980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 109 ASN D 59 HIS D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16533 Z= 0.170 Angle : 0.630 10.178 22631 Z= 0.316 Chirality : 0.042 0.293 2484 Planarity : 0.004 0.055 2620 Dihedral : 17.023 173.792 2932 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.18 % Favored : 95.48 % Rotamer: Outliers : 2.13 % Allowed : 18.96 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.19 (0.20), residues: 1770 helix: 1.20 (0.22), residues: 592 sheet: -0.45 (0.32), residues: 278 loop : -0.90 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 20 HIS 0.008 0.001 HIS D 59 PHE 0.021 0.001 PHE A 17 TYR 0.011 0.001 TYR A 213 ARG 0.004 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7627 (t70) cc_final: 0.7140 (m-30) REVERT: A 332 PHE cc_start: 0.8352 (m-80) cc_final: 0.7912 (m-10) REVERT: A 352 ASP cc_start: 0.6234 (p0) cc_final: 0.4846 (t0) REVERT: A 364 GLN cc_start: 0.7795 (tp40) cc_final: 0.7313 (mm-40) REVERT: A 395 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7425 (ppp) REVERT: B 92 THR cc_start: 0.8599 (m) cc_final: 0.8250 (p) REVERT: B 145 ASP cc_start: 0.8696 (m-30) cc_final: 0.8389 (p0) REVERT: B 303 MET cc_start: 0.8475 (tmm) cc_final: 0.7998 (tmm) REVERT: B 360 HIS cc_start: 0.8534 (m90) cc_final: 0.8292 (m90) REVERT: B 435 MET cc_start: 0.4486 (mmt) cc_final: 0.3870 (mmp) REVERT: B 470 CYS cc_start: 0.8040 (t) cc_final: 0.7288 (p) REVERT: C 193 MET cc_start: 0.6934 (ttt) cc_final: 0.6177 (tmm) REVERT: C 309 MET cc_start: 0.8584 (tpp) cc_final: 0.8307 (tpp) REVERT: D 11 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7089 (tptp) REVERT: D 123 ASP cc_start: 0.8524 (p0) cc_final: 0.8279 (p0) REVERT: D 309 ASP cc_start: 0.8125 (p0) cc_final: 0.7913 (p0) REVERT: D 466 ASN cc_start: 0.8442 (t0) cc_final: 0.7931 (t0) outliers start: 34 outliers final: 27 residues processed: 171 average time/residue: 0.2365 time to fit residues: 65.1116 Evaluate side-chains 161 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.0570 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 106 optimal weight: 0.0980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 207 HIS B 446 ASN D 59 HIS D 302 GLN D 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16533 Z= 0.172 Angle : 0.647 10.971 22631 Z= 0.321 Chirality : 0.042 0.285 2484 Planarity : 0.004 0.054 2620 Dihedral : 16.935 173.619 2932 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.41 % Favored : 95.31 % Rotamer: Outliers : 2.25 % Allowed : 19.09 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.23 (0.20), residues: 1770 helix: 1.13 (0.22), residues: 590 sheet: -0.45 (0.33), residues: 264 loop : -0.90 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 20 HIS 0.007 0.001 HIS D 59 PHE 0.018 0.001 PHE C 273 TYR 0.014 0.001 TYR A 293 ARG 0.007 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6560 (ptp) REVERT: A 279 ASP cc_start: 0.7801 (t70) cc_final: 0.7332 (m-30) REVERT: A 352 ASP cc_start: 0.6127 (p0) cc_final: 0.4757 (t0) REVERT: A 364 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7283 (mm-40) REVERT: A 395 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7495 (ppp) REVERT: B 92 THR cc_start: 0.8551 (m) cc_final: 0.8206 (p) REVERT: B 145 ASP cc_start: 0.8722 (m-30) cc_final: 0.8402 (p0) REVERT: B 303 MET cc_start: 0.8565 (tmm) cc_final: 0.8120 (tmm) REVERT: B 360 HIS cc_start: 0.8467 (m90) cc_final: 0.8215 (m90) REVERT: B 435 MET cc_start: 0.4450 (mmt) cc_final: 0.3768 (mmp) REVERT: B 470 CYS cc_start: 0.7914 (t) cc_final: 0.7225 (p) REVERT: C 193 MET cc_start: 0.6928 (ttt) cc_final: 0.6160 (tmm) REVERT: C 287 MET cc_start: 0.7261 (tpt) cc_final: 0.6702 (tpt) REVERT: C 309 MET cc_start: 0.8579 (tpp) cc_final: 0.8309 (tpp) REVERT: D 11 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7317 (tptp) REVERT: D 123 ASP cc_start: 0.8566 (p0) cc_final: 0.8289 (p0) REVERT: D 466 ASN cc_start: 0.8438 (t0) cc_final: 0.7886 (t0) outliers start: 36 outliers final: 29 residues processed: 166 average time/residue: 0.2474 time to fit residues: 65.2349 Evaluate side-chains 166 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 364 GLN B 207 HIS D 59 HIS D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16533 Z= 0.179 Angle : 0.650 10.598 22631 Z= 0.324 Chirality : 0.043 0.288 2484 Planarity : 0.004 0.055 2620 Dihedral : 16.884 173.441 2932 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 2.32 % Allowed : 19.40 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.20), residues: 1770 helix: 1.10 (0.22), residues: 590 sheet: -0.45 (0.33), residues: 264 loop : -0.90 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 20 HIS 0.008 0.001 HIS D 59 PHE 0.015 0.001 PHE A 17 TYR 0.011 0.001 TYR C 293 ARG 0.007 0.001 ARG A 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6630 (mtp) REVERT: A 279 ASP cc_start: 0.7778 (t70) cc_final: 0.7308 (m-30) REVERT: A 332 PHE cc_start: 0.8379 (m-80) cc_final: 0.7950 (m-10) REVERT: A 352 ASP cc_start: 0.6163 (p0) cc_final: 0.4816 (t0) REVERT: A 364 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7284 (mm-40) REVERT: A 395 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7525 (ppp) REVERT: B 92 THR cc_start: 0.8597 (m) cc_final: 0.8253 (p) REVERT: B 145 ASP cc_start: 0.8752 (m-30) cc_final: 0.8439 (p0) REVERT: B 303 MET cc_start: 0.8477 (tmm) cc_final: 0.8080 (tmm) REVERT: B 360 HIS cc_start: 0.8475 (m90) cc_final: 0.8226 (m90) REVERT: B 435 MET cc_start: 0.4580 (mmt) cc_final: 0.3912 (mmp) REVERT: B 470 CYS cc_start: 0.7797 (t) cc_final: 0.7095 (p) REVERT: C 193 MET cc_start: 0.7002 (ttt) cc_final: 0.6235 (tmm) REVERT: C 287 MET cc_start: 0.7306 (tpt) cc_final: 0.6601 (tpt) REVERT: C 309 MET cc_start: 0.8581 (tpp) cc_final: 0.8303 (tpp) REVERT: D 11 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7352 (tptp) REVERT: D 123 ASP cc_start: 0.8559 (p0) cc_final: 0.8300 (p0) REVERT: D 466 ASN cc_start: 0.8498 (t0) cc_final: 0.7965 (t0) outliers start: 37 outliers final: 30 residues processed: 161 average time/residue: 0.2415 time to fit residues: 62.8957 Evaluate side-chains 167 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 390 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 207 HIS B 329 HIS B 446 ASN D 59 HIS D 154 ASN D 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.098971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.076893 restraints weight = 68069.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078777 restraints weight = 42139.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079580 restraints weight = 30731.007| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 16533 Z= 0.326 Angle : 0.724 9.794 22631 Z= 0.373 Chirality : 0.046 0.323 2484 Planarity : 0.005 0.072 2620 Dihedral : 16.989 172.965 2932 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.54 % Favored : 94.24 % Rotamer: Outliers : 2.38 % Allowed : 19.52 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.41 (0.20), residues: 1770 helix: 0.95 (0.21), residues: 588 sheet: -0.77 (0.30), residues: 298 loop : -0.89 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 46 HIS 0.022 0.002 HIS D 360 PHE 0.022 0.002 PHE B 206 TYR 0.019 0.002 TYR D 65 ARG 0.010 0.001 ARG A 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.12 seconds wall clock time: 54 minutes 9.88 seconds (3249.88 seconds total)