Starting phenix.real_space_refine on Thu Nov 16 20:37:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2023/8ozd_17305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2023/8ozd_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_2023/8ozd_17305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2023/8ozd_17305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2023/8ozd_17305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozd_17305/11_2023/8ozd_17305.pdb" } 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 Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 8.42, per 1000 atoms: 0.53 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 - 3.50 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: 6.41 Conformation dependent library (CDL) restraints added in 2.5 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: 5.32 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: 5.25 Time building geometry restraints manager: 6.94 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: 97.11 - 104.49: 437 104.49 - 111.87: 7959 111.87 - 119.25: 5654 119.25 - 126.63: 8099 126.63 - 134.01: 482 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: 9361 33.21 - 66.42: 322 66.42 - 99.62: 14 99.62 - 132.83: 1 132.83 - 166.04: 6 Dihedral angle restraints: 9704 sinusoidal: 4448 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 9701 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 2.520 nonbonded pdb=" OG SER D 493 " pdb=" OD1 ASP D 495 " model vdw 2.196 2.440 nonbonded pdb=" OG SER B 493 " pdb=" OD1 ASP B 495 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS C 24 " pdb=" O LEU D 29 " model vdw 2.224 2.520 nonbonded pdb=" O LEU C 227 " pdb=" OG1 THR C 230 " model vdw 2.229 2.440 ... (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 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 6.530 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.870 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.540 ------------------------------------------------------------------------------- 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 : 15.756 166.041 6308 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2899 time to fit residues: 106.7977 Evaluate side-chains 152 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3550 ------------------------------------------------------------------------------- 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: 0.6980 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 61 GLN B 360 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16533 Z= 0.206 Angle : 0.631 9.072 22631 Z= 0.327 Chirality : 0.042 0.154 2484 Planarity : 0.005 0.056 2620 Dihedral : 14.988 178.876 2664 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.03 % Favored : 94.52 % Rotamer: Outliers : 1.69 % Allowed : 9.64 % Favored : 88.67 % 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: 0.87 (0.22), residues: 590 sheet: -0.25 (0.31), residues: 290 loop : -0.78 (0.21), residues: 890 *********************** 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 191 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 180 average time/residue: 0.2522 time to fit residues: 71.9123 Evaluate side-chains 145 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1551 time to fit residues: 7.8775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 201 ASN D 329 HIS D 360 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16533 Z= 0.190 Angle : 0.584 8.741 22631 Z= 0.303 Chirality : 0.042 0.178 2484 Planarity : 0.005 0.052 2620 Dihedral : 14.883 174.435 2664 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.80 % Favored : 94.75 % Rotamer: Outliers : 1.06 % Allowed : 13.27 % Favored : 85.67 % 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: 1.03 (0.22), residues: 588 sheet: -0.21 (0.32), residues: 288 loop : -0.85 (0.21), residues: 894 *********************** 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 163 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 158 average time/residue: 0.2645 time to fit residues: 64.9570 Evaluate side-chains 137 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1474 time to fit residues: 5.6904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.0570 chunk 123 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 360 HIS ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16533 Z= 0.164 Angle : 0.574 8.893 22631 Z= 0.293 Chirality : 0.041 0.247 2484 Planarity : 0.004 0.053 2620 Dihedral : 14.803 173.845 2664 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.41 % Favored : 95.14 % Rotamer: Outliers : 1.38 % Allowed : 14.64 % Favored : 83.98 % 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: -0.16 (0.20), residues: 1770 helix: 1.10 (0.22), residues: 598 sheet: -0.16 (0.32), residues: 286 loop : -0.91 (0.21), residues: 886 *********************** 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 169 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.2465 time to fit residues: 61.8003 Evaluate side-chains 139 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1768 time to fit residues: 6.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN B 61 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 296 ASN D 360 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16533 Z= 0.249 Angle : 0.627 11.039 22631 Z= 0.326 Chirality : 0.043 0.227 2484 Planarity : 0.004 0.057 2620 Dihedral : 14.952 172.688 2664 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.08 % Favored : 94.46 % Rotamer: Outliers : 1.81 % Allowed : 16.46 % Favored : 81.73 % 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: -0.21 (0.20), residues: 1770 helix: 1.13 (0.22), residues: 590 sheet: -0.37 (0.30), residues: 310 loop : -0.92 (0.21), residues: 870 *********************** 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 166 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 159 average time/residue: 0.2533 time to fit residues: 63.7222 Evaluate side-chains 132 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1510 time to fit residues: 5.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 358 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 413 ASN D 360 HIS D 446 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 16533 Z= 0.421 Angle : 0.784 11.618 22631 Z= 0.413 Chirality : 0.047 0.290 2484 Planarity : 0.006 0.074 2620 Dihedral : 15.584 170.708 2664 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 2.32 % Allowed : 17.46 % Favored : 80.23 % 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: -0.82 (0.19), residues: 1770 helix: 0.54 (0.21), residues: 576 sheet: -0.73 (0.30), residues: 292 loop : -1.18 (0.20), residues: 902 *********************** 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 173 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 165 average time/residue: 0.2538 time to fit residues: 67.0673 Evaluate side-chains 137 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1950 time to fit residues: 7.7157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 105 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 overall best weight: 0.8764 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 207 HIS C 70 GLN C 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16533 Z= 0.201 Angle : 0.683 13.163 22631 Z= 0.346 Chirality : 0.044 0.253 2484 Planarity : 0.005 0.063 2620 Dihedral : 15.044 172.192 2664 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.41 % Rotamer: Outliers : 0.81 % Allowed : 19.46 % Favored : 79.72 % 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: -0.47 (0.20), residues: 1770 helix: 0.88 (0.21), residues: 588 sheet: -0.56 (0.31), residues: 270 loop : -1.02 (0.21), residues: 912 *********************** 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 161 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.786 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 154 average time/residue: 0.2550 time to fit residues: 62.6207 Evaluate side-chains 127 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1865 time to fit residues: 3.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16533 Z= 0.208 Angle : 0.667 13.285 22631 Z= 0.338 Chirality : 0.044 0.264 2484 Planarity : 0.005 0.063 2620 Dihedral : 14.941 171.543 2664 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.48 % Favored : 94.01 % Rotamer: Outliers : 1.13 % Allowed : 19.96 % 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: -0.47 (0.20), residues: 1770 helix: 0.86 (0.21), residues: 588 sheet: -0.76 (0.30), residues: 296 loop : -0.91 (0.21), residues: 886 *********************** 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 142 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.874 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 134 average time/residue: 0.2329 time to fit residues: 51.9095 Evaluate side-chains 128 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1478 time to fit residues: 5.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 0.0980 chunk 161 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16533 Z= 0.178 Angle : 0.676 13.973 22631 Z= 0.334 Chirality : 0.043 0.282 2484 Planarity : 0.004 0.061 2620 Dihedral : 14.811 170.613 2664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.92 % Favored : 94.69 % Rotamer: Outliers : 0.50 % Allowed : 21.40 % 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: -0.47 (0.20), residues: 1770 helix: 0.85 (0.21), residues: 592 sheet: -0.69 (0.31), residues: 280 loop : -0.94 (0.21), residues: 898 *********************** 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 147 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.746 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 140 average time/residue: 0.2262 time to fit residues: 52.2988 Evaluate side-chains 135 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1521 time to fit residues: 4.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.0270 chunk 113 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16533 Z= 0.189 Angle : 0.677 14.191 22631 Z= 0.337 Chirality : 0.043 0.280 2484 Planarity : 0.004 0.060 2620 Dihedral : 14.747 170.063 2664 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.25 % Favored : 94.35 % Rotamer: Outliers : 0.44 % Allowed : 21.90 % Favored : 77.66 % 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: -0.44 (0.20), residues: 1770 helix: 0.93 (0.21), residues: 590 sheet: -0.76 (0.30), residues: 296 loop : -0.93 (0.21), residues: 884 ********************** 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 140 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 137 average time/residue: 0.2430 time to fit residues: 54.6850 Evaluate side-chains 125 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1735 time to fit residues: 3.0434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.099505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078012 restraints weight = 67052.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080011 restraints weight = 41550.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.080828 restraints weight = 29959.009| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16533 Z= 0.211 Angle : 0.674 10.410 22631 Z= 0.338 Chirality : 0.044 0.332 2484 Planarity : 0.004 0.061 2620 Dihedral : 14.750 168.941 2664 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.31 % Favored : 94.29 % Rotamer: Outliers : 0.25 % Allowed : 21.96 % Favored : 77.78 % 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: -0.46 (0.20), residues: 1770 helix: 0.86 (0.21), residues: 592 sheet: -0.60 (0.31), residues: 282 loop : -0.97 (0.21), residues: 896 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2655.34 seconds wall clock time: 50 minutes 20.71 seconds (3020.71 seconds total)