Starting phenix.real_space_refine (version: dev) on Tue Apr 5 03:19:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/04_2022/6xeu_22150_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "G GLU 251": "OE1" <-> "OE2" Residue "G ASP 270": "OD1" <-> "OD2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 371": "OE1" <-> "OE2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 216": "NH1" <-> "NH2" Residue "J PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J GLU 251": "OE1" <-> "OE2" Residue "J ASP 270": "OD1" <-> "OD2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 302": "OE1" <-> "OE2" Residue "J TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 371": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10544 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "J" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 39 Unusual residues: {' K': 7, ' NA': 1, 'PIO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' NA': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.31, per 1000 atoms: 0.60 Number of scatterers: 10544 At special positions: 0 Unit cell: (89.25, 89.25, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 8 19.00 S 56 16.00 P 12 15.00 Na 4 11.00 O 1956 8.00 N 1716 7.00 C 6792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 166 " distance=2.04 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: 4.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 20 sheets defined 32.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 120 removed outlier: 3.816A pdb=" N LEU A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.812A pdb=" N SER A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 195 removed outlier: 3.619A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.968A pdb=" N ALA A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Proline residue: A 300 - end of helix No H-bonds generated for 'chain 'A' and resid 296 through 301' Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.537A pdb=" N SER A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 120 removed outlier: 3.816A pdb=" N LEU D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.812A pdb=" N SER D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 195 removed outlier: 3.619A pdb=" N ILE D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.968A pdb=" N ALA D 202 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Proline residue: D 300 - end of helix No H-bonds generated for 'chain 'D' and resid 296 through 301' Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.537A pdb=" N SER D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 82 through 88 Processing helix chain 'G' and resid 91 through 120 removed outlier: 3.816A pdb=" N LEU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 removed outlier: 3.812A pdb=" N SER G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 195 removed outlier: 3.619A pdb=" N ILE G 175 " --> pdb=" O ILE G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 204 removed outlier: 3.968A pdb=" N ALA G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Proline residue: G 300 - end of helix No H-bonds generated for 'chain 'G' and resid 296 through 301' Processing helix chain 'G' and resid 369 through 381 removed outlier: 3.537A pdb=" N SER G 381 " --> pdb=" O ASN G 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 Processing helix chain 'J' and resid 82 through 88 Processing helix chain 'J' and resid 91 through 120 removed outlier: 3.816A pdb=" N LEU J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE J 109 " --> pdb=" O THR J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 152 removed outlier: 3.812A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE J 149 " --> pdb=" O PHE J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 195 removed outlier: 3.619A pdb=" N ILE J 175 " --> pdb=" O ILE J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 204 removed outlier: 3.968A pdb=" N ALA J 202 " --> pdb=" O LYS J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Proline residue: J 300 - end of helix No H-bonds generated for 'chain 'J' and resid 296 through 301' Processing helix chain 'J' and resid 369 through 381 removed outlier: 3.537A pdb=" N SER J 381 " --> pdb=" O ASN J 377 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 205 through 207 Processing sheet with id= B, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.893A pdb=" N ALA A 211 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 258 through 261 Processing sheet with id= D, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= E, first strand: chain 'A' and resid 343 through 345 Processing sheet with id= F, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= G, first strand: chain 'D' and resid 332 through 334 removed outlier: 6.893A pdb=" N ALA D 211 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 258 through 261 Processing sheet with id= I, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= J, first strand: chain 'D' and resid 343 through 345 Processing sheet with id= K, first strand: chain 'G' and resid 205 through 207 Processing sheet with id= L, first strand: chain 'G' and resid 332 through 334 removed outlier: 6.893A pdb=" N ALA G 211 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 258 through 261 Processing sheet with id= N, first strand: chain 'G' and resid 336 through 338 Processing sheet with id= O, first strand: chain 'G' and resid 343 through 345 Processing sheet with id= P, first strand: chain 'J' and resid 205 through 207 Processing sheet with id= Q, first strand: chain 'J' and resid 332 through 334 removed outlier: 6.893A pdb=" N ALA J 211 " --> pdb=" O LEU J 333 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 258 through 261 Processing sheet with id= S, first strand: chain 'J' and resid 336 through 338 Processing sheet with id= T, first strand: chain 'J' and resid 343 through 345 424 hydrogen bonds defined for protein. 1140 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: 2.89 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3260 1.34 - 1.46: 2144 1.46 - 1.57: 5272 1.57 - 1.69: 16 1.69 - 1.81: 88 Bond restraints: 10780 Sorted by residual: bond pdb=" CA ASP A 352 " pdb=" C ASP A 352 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.08e-02 8.57e+03 5.73e+00 bond pdb=" CA ASP J 352 " pdb=" C ASP J 352 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.08e-02 8.57e+03 5.73e+00 bond pdb=" CA ASP D 352 " pdb=" C ASP D 352 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.08e-02 8.57e+03 5.73e+00 bond pdb=" CA ASP G 352 " pdb=" C ASP G 352 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.08e-02 8.57e+03 5.73e+00 bond pdb=" CA ILE J 126 " pdb=" C ILE J 126 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.27e-02 6.20e+03 4.42e+00 ... (remaining 10775 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 280 106.71 - 113.53: 6096 113.53 - 120.35: 4096 120.35 - 127.17: 4080 127.17 - 134.00: 120 Bond angle restraints: 14672 Sorted by residual: angle pdb=" N ASN G 354 " pdb=" CA ASN G 354 " pdb=" C ASN G 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN D 354 " pdb=" CA ASN D 354 " pdb=" C ASN D 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN A 354 " pdb=" CA ASN A 354 " pdb=" C ASN A 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN J 354 " pdb=" CA ASN J 354 " pdb=" C ASN J 354 " ideal model delta sigma weight residual 114.04 108.26 5.78 1.24e+00 6.50e-01 2.17e+01 angle pdb=" N ASN A 263 " pdb=" CA ASN A 263 " pdb=" C ASN A 263 " ideal model delta sigma weight residual 109.76 116.88 -7.12 1.59e+00 3.96e-01 2.00e+01 ... (remaining 14667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5560 17.72 - 35.44: 552 35.44 - 53.17: 132 53.17 - 70.89: 32 70.89 - 88.61: 8 Dihedral angle restraints: 6284 sinusoidal: 2448 harmonic: 3836 Sorted by residual: dihedral pdb=" C ILE D 126 " pdb=" N ILE D 126 " pdb=" CA ILE D 126 " pdb=" CB ILE D 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ILE G 126 " pdb=" N ILE G 126 " pdb=" CA ILE G 126 " pdb=" CB ILE G 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ILE J 126 " pdb=" N ILE J 126 " pdb=" CA ILE J 126 " pdb=" CB ILE J 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 6281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1479 0.072 - 0.144: 193 0.144 - 0.217: 20 0.217 - 0.289: 4 0.289 - 0.361: 4 Chirality restraints: 1700 Sorted by residual: chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ILE J 126 " pdb=" N ILE J 126 " pdb=" C ILE J 126 " pdb=" CB ILE J 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ILE G 126 " pdb=" N ILE G 126 " pdb=" C ILE G 126 " pdb=" CB ILE G 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1697 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 128 " -0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO A 129 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 128 " 0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO D 129 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 129 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 129 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 128 " 0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO G 129 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO G 129 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO G 129 " 0.051 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.94: 5095 2.94 - 3.49: 10499 3.49 - 4.04: 16322 4.04 - 4.59: 23430 4.59 - 5.14: 36328 Nonbonded interactions: 91674 Sorted by model distance: nonbonded pdb=" N ASP D 62 " pdb=" OD1 ASP D 62 " model vdw 2.387 2.520 nonbonded pdb=" N ASP J 62 " pdb=" OD1 ASP J 62 " model vdw 2.387 2.520 nonbonded pdb=" N ASP G 62 " pdb=" OD1 ASP G 62 " model vdw 2.387 2.520 nonbonded pdb=" N ASP A 62 " pdb=" OD1 ASP A 62 " model vdw 2.387 2.520 nonbonded pdb=" O THR G 154 " pdb=" K K A 404 " model vdw 2.426 2.850 ... (remaining 91669 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' and (resid 55 through 382 or resid 401)) selection = (chain 'D' and (resid 55 through 382 or resid 401)) selection = (chain 'G' and (resid 55 through 382 or resid 401)) selection = (chain 'J' and (resid 55 through 382 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 8 8.98 5 P 12 5.49 5 S 56 5.16 5 Na 4 4.78 5 C 6792 2.51 5 N 1716 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.680 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: 4.650 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 30.700 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.008 0.038 10780 Z= 0.521 Angle : 0.821 7.116 14672 Z= 0.490 Chirality : 0.056 0.361 1700 Planarity : 0.006 0.096 1796 Dihedral : 15.450 88.609 3800 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.32 % 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: -2.88 (0.22), residues: 1304 helix: -0.38 (0.24), residues: 424 sheet: -0.75 (0.31), residues: 288 loop : -3.82 (0.21), residues: 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.276 Fit side-chains outliers start: 32 outliers final: 8 residues processed: 110 average time/residue: 0.3045 time to fit residues: 44.3624 Evaluate side-chains 72 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2318 time to fit residues: 4.1850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 10780 Z= 0.335 Angle : 0.558 5.084 14672 Z= 0.307 Chirality : 0.044 0.141 1700 Planarity : 0.004 0.044 1796 Dihedral : 5.839 50.947 1444 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1304 helix: 0.57 (0.25), residues: 440 sheet: -0.30 (0.32), residues: 288 loop : -3.23 (0.22), residues: 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.293 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 0.2003 time to fit residues: 27.9453 Evaluate side-chains 72 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0972 time to fit residues: 3.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN D 322 GLN J 322 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 10780 Z= 0.206 Angle : 0.505 4.588 14672 Z= 0.275 Chirality : 0.042 0.137 1700 Planarity : 0.004 0.036 1796 Dihedral : 5.398 52.067 1444 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.71 % 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: -1.22 (0.24), residues: 1304 helix: 1.04 (0.26), residues: 440 sheet: -0.02 (0.32), residues: 288 loop : -2.86 (0.23), residues: 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.305 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 82 average time/residue: 0.2303 time to fit residues: 27.4622 Evaluate side-chains 68 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.0980 chunk 87 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 10780 Z= 0.113 Angle : 0.476 6.602 14672 Z= 0.249 Chirality : 0.043 0.240 1700 Planarity : 0.003 0.034 1796 Dihedral : 4.892 50.604 1444 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.41 % 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: -0.67 (0.24), residues: 1304 helix: 1.62 (0.27), residues: 440 sheet: 0.33 (0.32), residues: 288 loop : -2.67 (0.23), residues: 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.449 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 99 average time/residue: 0.2331 time to fit residues: 33.0161 Evaluate side-chains 76 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0966 time to fit residues: 3.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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: 0.8735 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 10780 Z= 0.219 Angle : 0.533 6.689 14672 Z= 0.275 Chirality : 0.043 0.137 1700 Planarity : 0.004 0.035 1796 Dihedral : 5.068 52.381 1444 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.06 % 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: -0.49 (0.24), residues: 1304 helix: 1.68 (0.27), residues: 440 sheet: 0.49 (0.32), residues: 288 loop : -2.51 (0.23), residues: 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.259 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.2113 time to fit residues: 29.7475 Evaluate side-chains 76 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0985 time to fit residues: 3.1462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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: 0.8711 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 10780 Z= 0.157 Angle : 0.503 7.889 14672 Z= 0.262 Chirality : 0.042 0.135 1700 Planarity : 0.003 0.034 1796 Dihedral : 4.956 52.627 1444 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.06 % 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: -0.38 (0.24), residues: 1304 helix: 1.80 (0.27), residues: 436 sheet: 0.57 (0.32), residues: 288 loop : -2.45 (0.23), residues: 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.321 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 88 average time/residue: 0.2065 time to fit residues: 27.6384 Evaluate side-chains 78 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0939 time to fit residues: 2.4493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8772 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 10780 Z= 0.296 Angle : 0.574 7.846 14672 Z= 0.298 Chirality : 0.043 0.137 1700 Planarity : 0.004 0.036 1796 Dihedral : 5.288 54.888 1444 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.44 % 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: -0.32 (0.24), residues: 1304 helix: 1.79 (0.26), residues: 428 sheet: 0.53 (0.32), residues: 288 loop : -2.26 (0.23), residues: 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.291 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 86 average time/residue: 0.2069 time to fit residues: 26.8676 Evaluate side-chains 69 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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: 0.8695 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10780 Z= 0.135 Angle : 0.506 8.787 14672 Z= 0.263 Chirality : 0.042 0.133 1700 Planarity : 0.004 0.034 1796 Dihedral : 4.893 54.751 1444 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.00 % 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: -0.18 (0.24), residues: 1304 helix: 1.96 (0.26), residues: 436 sheet: 0.64 (0.31), residues: 288 loop : -2.31 (0.23), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2109 time to fit residues: 23.1912 Evaluate side-chains 72 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10780 Z= 0.138 Angle : 0.524 9.639 14672 Z= 0.266 Chirality : 0.041 0.135 1700 Planarity : 0.003 0.034 1796 Dihedral : 4.787 54.253 1444 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.27 % 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: -0.06 (0.24), residues: 1304 helix: 2.11 (0.27), residues: 432 sheet: 0.73 (0.31), residues: 288 loop : -2.26 (0.23), residues: 584 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.395 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.2169 time to fit residues: 25.6939 Evaluate side-chains 75 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 2.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- 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: 0.8681 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 10780 Z= 0.135 Angle : 0.508 10.133 14672 Z= 0.262 Chirality : 0.041 0.135 1700 Planarity : 0.004 0.041 1796 Dihedral : 4.729 53.789 1444 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % 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: 0.02 (0.24), residues: 1304 helix: 2.10 (0.26), residues: 432 sheet: 0.86 (0.31), residues: 288 loop : -2.20 (0.23), residues: 584 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2156 time to fit residues: 27.0925 Evaluate side-chains 80 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3113 r_free = 0.3113 target = 0.076734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.058816 restraints weight = 23606.266| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.33 r_work: 0.2723 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work: 0.2703 rms_B_bonded: 3.06 restraints_weight: 0.1250 r_work: 0.2693 rms_B_bonded: 3.09 restraints_weight: 0.0625 r_work: 0.2683 rms_B_bonded: 3.14 restraints_weight: 0.0312 r_work: 0.2673 rms_B_bonded: 3.22 restraints_weight: 0.0156 r_work: 0.2662 rms_B_bonded: 3.31 restraints_weight: 0.0078 r_work: 0.2651 rms_B_bonded: 3.41 restraints_weight: 0.0039 r_work: 0.2640 rms_B_bonded: 3.54 restraints_weight: 0.0020 r_work: 0.2628 rms_B_bonded: 3.68 restraints_weight: 0.0010 r_work: 0.2617 rms_B_bonded: 3.83 restraints_weight: 0.0005 r_work: 0.2604 rms_B_bonded: 4.01 restraints_weight: 0.0002 r_work: 0.2592 rms_B_bonded: 4.20 restraints_weight: 0.0001 r_work: 0.2579 rms_B_bonded: 4.41 restraints_weight: 0.0001 r_work: 0.2566 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work: 0.2552 rms_B_bonded: 4.89 restraints_weight: 0.0000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10780 Z= 0.139 Angle : 0.505 10.021 14672 Z= 0.261 Chirality : 0.041 0.135 1700 Planarity : 0.003 0.034 1796 Dihedral : 4.696 53.440 1444 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.09 % 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: 0.13 (0.24), residues: 1304 helix: 2.08 (0.27), residues: 436 sheet: 1.02 (0.31), residues: 288 loop : -2.12 (0.23), residues: 580 =============================================================================== Job complete usr+sys time: 1740.81 seconds wall clock time: 32 minutes 39.66 seconds (1959.66 seconds total)