Starting phenix.real_space_refine on Thu Feb 15 20:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/02_2024/6vxz_21453_updated.pdb" } resolution = 3.42 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8876 2.51 5 N 2076 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ARG 330": "NH1" <-> "NH2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 7.44, per 1000 atoms: 0.56 Number of scatterers: 13324 At special positions: 0 Unit cell: (101.937, 101.937, 118.379, 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 28 16.00 P 12 15.00 O 2332 8.00 N 2076 7.00 C 8876 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: 5.54 Conformation dependent library (CDL) restraints added in 2.5 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 8 sheets defined 58.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 62 Proline residue: A 59 - end of helix removed outlier: 3.527A pdb=" N LEU A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 114 through 125 removed outlier: 4.171A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.526A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 222 removed outlier: 3.838A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 246 removed outlier: 4.072A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.549A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.826A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'B' and resid 11 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 62 Proline residue: B 59 - end of helix removed outlier: 3.527A pdb=" N LEU B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.171A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.526A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 222 removed outlier: 3.838A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 4.073A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.549A pdb=" N THR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.826A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 399 through 402 No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'C' and resid 11 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 62 Proline residue: C 59 - end of helix removed outlier: 3.528A pdb=" N LEU C 62 " --> pdb=" O ILE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 102 through 105 No H-bonds generated for 'chain 'C' and resid 102 through 105' Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.170A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 Processing helix chain 'C' and resid 166 through 181 removed outlier: 3.527A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 222 removed outlier: 3.838A pdb=" N LEU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 215 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 246 removed outlier: 4.073A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.549A pdb=" N THR C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.826A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 399 through 402 No H-bonds generated for 'chain 'C' and resid 399 through 402' Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'D' and resid 11 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 62 Proline residue: D 59 - end of helix removed outlier: 3.527A pdb=" N LEU D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 93 through 97 Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'D' and resid 108 through 111 Processing helix chain 'D' and resid 114 through 125 removed outlier: 4.172A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.526A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 222 removed outlier: 3.838A pdb=" N LEU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 246 removed outlier: 4.073A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.549A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.825A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 399 through 402 No H-bonds generated for 'chain 'D' and resid 399 through 402' Processing helix chain 'D' and resid 405 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 320 removed outlier: 3.668A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 346 through 349 Processing sheet with id= C, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.669A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 346 through 349 Processing sheet with id= E, first strand: chain 'C' and resid 318 through 320 removed outlier: 3.669A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 346 through 349 Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 removed outlier: 3.668A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 346 through 349 564 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2108 1.32 - 1.44: 3371 1.44 - 1.57: 8045 1.57 - 1.69: 20 1.69 - 1.81: 52 Bond restraints: 13596 Sorted by residual: bond pdb=" C5 CMP B 501 " pdb=" C6 CMP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C5 CMP A 501 " pdb=" C6 CMP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 CMP D 501 " pdb=" C6 CMP D 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C8 CMP D 501 " pdb=" N9 CMP D 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C8 CMP C 501 " pdb=" N9 CMP C 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 13591 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 465 106.57 - 113.43: 7658 113.43 - 120.29: 5063 120.29 - 127.15: 4954 127.15 - 134.02: 164 Bond angle restraints: 18304 Sorted by residual: angle pdb=" N GLU D 395 " pdb=" CA GLU D 395 " pdb=" C GLU D 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU C 395 " pdb=" CA GLU C 395 " pdb=" C GLU C 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU A 395 " pdb=" CA GLU A 395 " pdb=" C GLU A 395 " ideal model delta sigma weight residual 111.14 105.06 6.08 1.08e+00 8.57e-01 3.17e+01 angle pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" C GLU B 395 " ideal model delta sigma weight residual 111.14 105.09 6.05 1.08e+00 8.57e-01 3.14e+01 angle pdb=" C ASP B 393 " pdb=" N LYS B 394 " pdb=" CA LYS B 394 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.01e+01 ... (remaining 18299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 7872 34.43 - 68.85: 428 68.85 - 103.28: 56 103.28 - 137.70: 12 137.70 - 172.13: 32 Dihedral angle restraints: 8400 sinusoidal: 3824 harmonic: 4576 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.08 -108.08 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.04 -108.04 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 8397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1613 0.063 - 0.126: 412 0.126 - 0.188: 49 0.188 - 0.251: 14 0.251 - 0.314: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA ALA B 408 " pdb=" N ALA B 408 " pdb=" C ALA B 408 " pdb=" CB ALA B 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ALA A 408 " pdb=" N ALA A 408 " pdb=" C ALA A 408 " pdb=" CB ALA A 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ALA C 408 " pdb=" N ALA C 408 " pdb=" C ALA C 408 " pdb=" CB ALA C 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2089 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW A 502 " -0.199 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 502 " -0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW B 502 " 0.198 2.00e-02 2.50e+03 pdb=" C8 PGW B 502 " 0.076 2.00e-02 2.50e+03 pdb=" C9 PGW B 502 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW D 502 " -0.198 2.00e-02 2.50e+03 pdb=" C8 PGW D 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW D 502 " 0.198 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 10820 3.14 - 3.72: 18934 3.72 - 4.31: 26855 4.31 - 4.90: 45988 Nonbonded interactions: 102697 Sorted by model distance: nonbonded pdb=" O THR A 182 " pdb=" OG1 THR A 183 " model vdw 1.959 2.440 nonbonded pdb=" O THR D 182 " pdb=" OG1 THR D 183 " model vdw 1.959 2.440 nonbonded pdb=" O THR C 182 " pdb=" OG1 THR C 183 " model vdw 1.959 2.440 nonbonded pdb=" O THR B 182 " pdb=" OG1 THR B 183 " model vdw 1.959 2.440 nonbonded pdb=" ND1 HIS A 149 " pdb=" OH TYR A 170 " model vdw 2.260 2.520 ... (remaining 102692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.420 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.290 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.011 0.086 13596 Z= 0.715 Angle : 1.060 10.523 18304 Z= 0.561 Chirality : 0.057 0.314 2092 Planarity : 0.008 0.150 2196 Dihedral : 23.657 172.130 5448 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.40 % Allowed : 17.72 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.19), residues: 1540 helix: -2.12 (0.14), residues: 1032 sheet: -3.22 (0.43), residues: 120 loop : -3.24 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 18 HIS 0.003 0.001 HIS B 232 PHE 0.011 0.001 PHE A 397 TYR 0.014 0.001 TYR D 175 ARG 0.003 0.001 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4314 (pt) REVERT: A 393 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6186 (t0) REVERT: B 301 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4302 (pt) REVERT: B 393 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6223 (t0) REVERT: C 301 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4340 (pt) REVERT: C 329 ILE cc_start: 0.9037 (mt) cc_final: 0.8834 (mt) REVERT: C 393 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6229 (t0) REVERT: D 301 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4306 (pt) REVERT: D 393 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6196 (t0) outliers start: 32 outliers final: 13 residues processed: 178 average time/residue: 0.2647 time to fit residues: 67.7158 Evaluate side-chains 125 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13596 Z= 0.180 Angle : 0.666 8.627 18304 Z= 0.309 Chirality : 0.042 0.186 2092 Planarity : 0.004 0.040 2196 Dihedral : 25.498 169.206 2562 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 18.84 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1540 helix: -0.31 (0.17), residues: 1012 sheet: -1.76 (0.48), residues: 120 loop : -2.78 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 264 HIS 0.001 0.000 HIS D 232 PHE 0.006 0.001 PHE C 397 TYR 0.013 0.001 TYR A 25 ARG 0.003 0.000 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.8913 (mt) cc_final: 0.8676 (mt) REVERT: B 329 ILE cc_start: 0.8916 (mt) cc_final: 0.8679 (mt) REVERT: D 329 ILE cc_start: 0.8910 (mt) cc_final: 0.8667 (mt) outliers start: 40 outliers final: 8 residues processed: 154 average time/residue: 0.3062 time to fit residues: 65.9496 Evaluate side-chains 119 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13596 Z= 0.348 Angle : 0.720 9.010 18304 Z= 0.343 Chirality : 0.045 0.199 2092 Planarity : 0.005 0.046 2196 Dihedral : 23.971 176.816 2518 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.38 % Allowed : 19.97 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1540 helix: 0.13 (0.18), residues: 996 sheet: -1.37 (0.49), residues: 116 loop : -1.87 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 155 HIS 0.004 0.001 HIS D 281 PHE 0.005 0.001 PHE C 260 TYR 0.015 0.001 TYR B 175 ARG 0.006 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (t) REVERT: A 230 LEU cc_start: 0.8776 (mm) cc_final: 0.8495 (mt) REVERT: A 329 ILE cc_start: 0.9071 (mt) cc_final: 0.8841 (mt) REVERT: B 22 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 230 LEU cc_start: 0.8774 (mm) cc_final: 0.8495 (mt) REVERT: B 329 ILE cc_start: 0.9075 (mt) cc_final: 0.8844 (mt) REVERT: C 230 LEU cc_start: 0.8778 (mm) cc_final: 0.8499 (mt) REVERT: D 230 LEU cc_start: 0.8779 (mm) cc_final: 0.8500 (mt) REVERT: D 329 ILE cc_start: 0.9074 (mt) cc_final: 0.8844 (mt) outliers start: 45 outliers final: 26 residues processed: 154 average time/residue: 0.2499 time to fit residues: 56.7233 Evaluate side-chains 136 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13596 Z= 0.213 Angle : 0.643 9.934 18304 Z= 0.299 Chirality : 0.042 0.184 2092 Planarity : 0.004 0.058 2196 Dihedral : 22.189 176.136 2518 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.75 % Allowed : 20.05 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1540 helix: 0.50 (0.18), residues: 1000 sheet: -1.10 (0.48), residues: 116 loop : -1.37 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.002 0.001 HIS A 281 PHE 0.007 0.001 PHE D 36 TYR 0.011 0.001 TYR D 175 ARG 0.006 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 122 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8774 (mm) cc_final: 0.8503 (mt) REVERT: A 329 ILE cc_start: 0.9093 (mt) cc_final: 0.8876 (mt) REVERT: A 373 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.6003 (mt) REVERT: B 230 LEU cc_start: 0.8773 (mm) cc_final: 0.8504 (mt) REVERT: B 329 ILE cc_start: 0.9093 (mt) cc_final: 0.8873 (mt) REVERT: B 373 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6009 (mt) REVERT: C 22 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (t) REVERT: C 230 LEU cc_start: 0.8776 (mm) cc_final: 0.8508 (mt) REVERT: C 373 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6003 (mt) REVERT: D 22 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8077 (t) REVERT: D 230 LEU cc_start: 0.8776 (mm) cc_final: 0.8507 (mt) REVERT: D 329 ILE cc_start: 0.9092 (mt) cc_final: 0.8872 (mt) REVERT: D 373 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6014 (mt) outliers start: 50 outliers final: 26 residues processed: 166 average time/residue: 0.2443 time to fit residues: 60.0674 Evaluate side-chains 137 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13596 Z= 0.153 Angle : 0.606 10.636 18304 Z= 0.280 Chirality : 0.040 0.160 2092 Planarity : 0.004 0.054 2196 Dihedral : 19.319 154.948 2518 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.00 % Allowed : 21.85 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1540 helix: 0.85 (0.18), residues: 1000 sheet: -0.85 (0.47), residues: 116 loop : -1.01 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 264 HIS 0.001 0.000 HIS A 232 PHE 0.005 0.001 PHE B 36 TYR 0.007 0.001 TYR D 259 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8774 (mm) cc_final: 0.8523 (mt) REVERT: A 329 ILE cc_start: 0.9065 (mt) cc_final: 0.8848 (mt) REVERT: A 373 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.6007 (mt) REVERT: B 230 LEU cc_start: 0.8772 (mm) cc_final: 0.8520 (mt) REVERT: B 329 ILE cc_start: 0.9056 (mt) cc_final: 0.8840 (mt) REVERT: B 373 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.6015 (mt) REVERT: C 22 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 230 LEU cc_start: 0.8775 (mm) cc_final: 0.8525 (mt) REVERT: C 373 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5952 (mt) REVERT: D 22 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8063 (t) REVERT: D 230 LEU cc_start: 0.8776 (mm) cc_final: 0.8525 (mt) REVERT: D 329 ILE cc_start: 0.9058 (mt) cc_final: 0.8842 (mt) REVERT: D 373 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.6019 (mt) outliers start: 40 outliers final: 14 residues processed: 159 average time/residue: 0.2535 time to fit residues: 59.1551 Evaluate side-chains 133 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13596 Z= 0.162 Angle : 0.612 11.362 18304 Z= 0.282 Chirality : 0.040 0.151 2092 Planarity : 0.004 0.056 2196 Dihedral : 18.182 144.561 2518 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.08 % Allowed : 23.42 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1540 helix: 1.00 (0.18), residues: 1000 sheet: -0.65 (0.48), residues: 116 loop : -0.75 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 264 HIS 0.002 0.001 HIS B 281 PHE 0.007 0.001 PHE D 36 TYR 0.009 0.001 TYR D 175 ARG 0.004 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (t) REVERT: A 230 LEU cc_start: 0.8799 (mm) cc_final: 0.8596 (mt) REVERT: A 373 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.6015 (mt) REVERT: B 22 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8060 (t) REVERT: B 230 LEU cc_start: 0.8801 (mm) cc_final: 0.8596 (mt) REVERT: B 373 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.6019 (mt) REVERT: C 22 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8127 (t) REVERT: C 230 LEU cc_start: 0.8804 (mm) cc_final: 0.8597 (mt) REVERT: C 373 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5977 (mt) REVERT: D 22 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.8050 (t) REVERT: D 230 LEU cc_start: 0.8810 (mm) cc_final: 0.8604 (mt) REVERT: D 373 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5971 (mt) outliers start: 41 outliers final: 21 residues processed: 167 average time/residue: 0.2466 time to fit residues: 61.0745 Evaluate side-chains 139 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13596 Z= 0.206 Angle : 0.640 11.289 18304 Z= 0.293 Chirality : 0.041 0.154 2092 Planarity : 0.004 0.056 2196 Dihedral : 18.136 145.162 2518 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.28 % Allowed : 22.60 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1540 helix: 1.11 (0.18), residues: 988 sheet: -0.62 (0.49), residues: 116 loop : -0.57 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS B 281 PHE 0.006 0.001 PHE D 36 TYR 0.012 0.001 TYR D 175 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 120 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8847 (mm) cc_final: 0.8633 (mt) REVERT: A 373 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5969 (mt) REVERT: B 230 LEU cc_start: 0.8842 (mm) cc_final: 0.8632 (mt) REVERT: B 373 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5972 (mt) REVERT: C 22 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8091 (t) REVERT: C 230 LEU cc_start: 0.8849 (mm) cc_final: 0.8581 (mt) REVERT: C 373 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5940 (mt) REVERT: D 22 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8072 (t) REVERT: D 230 LEU cc_start: 0.8853 (mm) cc_final: 0.8581 (mt) REVERT: D 373 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5974 (mt) outliers start: 57 outliers final: 27 residues processed: 166 average time/residue: 0.2280 time to fit residues: 57.2606 Evaluate side-chains 149 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13596 Z= 0.176 Angle : 0.626 11.084 18304 Z= 0.286 Chirality : 0.040 0.164 2092 Planarity : 0.004 0.058 2196 Dihedral : 17.748 142.284 2518 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.68 % Allowed : 23.05 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1540 helix: 1.23 (0.18), residues: 988 sheet: -0.63 (0.49), residues: 116 loop : -0.48 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 264 HIS 0.002 0.001 HIS C 281 PHE 0.006 0.001 PHE D 36 TYR 0.010 0.001 TYR C 175 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8267 (t) cc_final: 0.8065 (t) REVERT: A 373 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5957 (mt) REVERT: B 373 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5953 (mt) REVERT: C 22 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8082 (t) REVERT: D 22 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (t) REVERT: D 373 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5965 (mt) outliers start: 49 outliers final: 33 residues processed: 156 average time/residue: 0.2365 time to fit residues: 55.6195 Evaluate side-chains 145 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13596 Z= 0.189 Angle : 0.637 11.061 18304 Z= 0.292 Chirality : 0.041 0.154 2092 Planarity : 0.004 0.058 2196 Dihedral : 17.697 141.889 2518 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.75 % Allowed : 23.72 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1540 helix: 1.28 (0.18), residues: 988 sheet: -0.54 (0.49), residues: 116 loop : -0.36 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS D 281 PHE 0.006 0.001 PHE C 36 TYR 0.010 0.001 TYR B 175 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8270 (t) cc_final: 0.8055 (t) REVERT: A 373 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5936 (mt) REVERT: B 22 VAL cc_start: 0.8270 (t) cc_final: 0.8060 (t) REVERT: B 373 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5930 (mt) REVERT: C 22 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8081 (t) REVERT: D 22 VAL cc_start: 0.8262 (t) cc_final: 0.8055 (t) REVERT: D 373 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5946 (mt) outliers start: 50 outliers final: 35 residues processed: 148 average time/residue: 0.2343 time to fit residues: 52.4236 Evaluate side-chains 148 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.0010 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 0.0770 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13596 Z= 0.143 Angle : 0.623 11.053 18304 Z= 0.281 Chirality : 0.040 0.138 2092 Planarity : 0.004 0.060 2196 Dihedral : 16.970 137.235 2518 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.48 % Allowed : 25.23 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1540 helix: 1.48 (0.18), residues: 988 sheet: -0.62 (0.47), residues: 116 loop : -0.23 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 264 HIS 0.001 0.000 HIS B 292 PHE 0.007 0.001 PHE A 36 TYR 0.008 0.001 TYR A 259 ARG 0.004 0.000 ARG C 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5953 (mt) REVERT: B 373 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5947 (mt) REVERT: D 373 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5954 (mt) outliers start: 33 outliers final: 21 residues processed: 146 average time/residue: 0.2470 time to fit residues: 53.6976 Evaluate side-chains 130 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.0060 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117373 restraints weight = 15801.180| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.42 r_work: 0.2874 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13596 Z= 0.171 Angle : 0.634 11.272 18304 Z= 0.289 Chirality : 0.040 0.166 2092 Planarity : 0.005 0.061 2196 Dihedral : 16.993 137.317 2518 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.10 % Allowed : 25.45 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1540 helix: 1.48 (0.18), residues: 988 sheet: -0.54 (0.48), residues: 116 loop : -0.15 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 15 HIS 0.002 0.000 HIS B 281 PHE 0.006 0.001 PHE A 36 TYR 0.009 0.001 TYR D 175 ARG 0.005 0.000 ARG C 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.92 seconds wall clock time: 45 minutes 42.64 seconds (2742.64 seconds total)