Starting phenix.real_space_refine on Wed Feb 14 23:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_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_22150/02_2024/6xeu_22150_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xeu_22150/02_2024/6xeu_22150_updated.pdb" } resolution = 3.2 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= 0.002 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.05, per 1000 atoms: 0.57 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: 3.95 Conformation dependent library (CDL) restraints added in 2.0 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: 2.35 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: 2.75 Time building geometry restraints manager: 4.31 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: 5592 17.72 - 35.44: 552 35.44 - 53.17: 140 53.17 - 70.89: 32 70.89 - 88.61: 8 Dihedral angle restraints: 6324 sinusoidal: 2488 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 6321 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 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: 1.340 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: 4.480 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.740 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 15.574 88.609 3840 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 % Allowed : 10.16 % Favored : 87.01 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 113 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.002 PHE J 224 TYR 0.010 0.001 TYR J 360 ARG 0.002 0.000 ARG J 225 *********************** 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 : 1.590 Fit side-chains REVERT: A 88 ASP cc_start: 0.8695 (t0) cc_final: 0.8465 (t0) REVERT: A 298 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8686 (tm-30) REVERT: D 88 ASP cc_start: 0.8698 (t0) cc_final: 0.8466 (t0) REVERT: D 298 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8687 (tm-30) REVERT: G 88 ASP cc_start: 0.8696 (t0) cc_final: 0.8462 (t0) REVERT: G 298 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8687 (tm-30) REVERT: J 88 ASP cc_start: 0.8696 (t0) cc_final: 0.8466 (t0) REVERT: J 298 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8686 (tm-30) outliers start: 32 outliers final: 8 residues processed: 110 average time/residue: 0.3186 time to fit residues: 46.1185 Evaluate side-chains 72 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 199 LYS 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: 2.9990 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: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 322 GLN J 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10780 Z= 0.373 Angle : 0.573 5.206 14672 Z= 0.314 Chirality : 0.045 0.144 1700 Planarity : 0.004 0.042 1796 Dihedral : 7.618 59.721 1508 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.12 % Allowed : 16.52 % Favored : 81.36 % 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 (0.23), residues: 1304 helix: 0.73 (0.25), residues: 428 sheet: -0.30 (0.32), residues: 288 loop : -3.14 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 113 HIS 0.003 0.001 HIS J 357 PHE 0.011 0.001 PHE J 274 TYR 0.010 0.001 TYR J 360 ARG 0.004 0.000 ARG J 378 *********************** 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 104 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.342 Fit side-chains REVERT: A 111 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8278 (tpp) REVERT: A 288 GLN cc_start: 0.9498 (mp10) cc_final: 0.9122 (mp10) REVERT: A 298 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8687 (tm-30) REVERT: D 88 ASP cc_start: 0.8644 (t0) cc_final: 0.8443 (t0) REVERT: D 111 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: D 288 GLN cc_start: 0.9498 (mp10) cc_final: 0.9120 (mp10) REVERT: D 298 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8685 (tm-30) REVERT: G 111 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8277 (tpp) REVERT: G 288 GLN cc_start: 0.9499 (mp10) cc_final: 0.9123 (mp10) REVERT: G 298 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8685 (tm-30) REVERT: J 111 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8278 (tpp) REVERT: J 288 GLN cc_start: 0.9500 (mp10) cc_final: 0.9126 (mp10) REVERT: J 298 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8688 (tm-30) outliers start: 24 outliers final: 12 residues processed: 100 average time/residue: 0.2052 time to fit residues: 30.8898 Evaluate side-chains 92 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 134 CYS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 134 CYS Chi-restraints excluded: chain J residue 210 HIS 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: 6.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8514 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10780 Z= 0.393 Angle : 0.576 5.198 14672 Z= 0.314 Chirality : 0.044 0.140 1700 Planarity : 0.004 0.038 1796 Dihedral : 6.982 59.006 1492 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.18 % Allowed : 17.58 % Favored : 79.24 % 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: -1.46 (0.23), residues: 1304 helix: 0.75 (0.25), residues: 440 sheet: -0.07 (0.32), residues: 288 loop : -2.96 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 113 HIS 0.003 0.001 HIS J 283 PHE 0.011 0.001 PHE J 274 TYR 0.011 0.001 TYR J 360 ARG 0.004 0.000 ARG J 378 *********************** 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 117 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 1.291 Fit side-chains REVERT: A 255 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8889 (mm) REVERT: A 288 GLN cc_start: 0.9488 (mp10) cc_final: 0.9106 (mp10) REVERT: A 298 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8624 (tm-30) REVERT: D 88 ASP cc_start: 0.8641 (t0) cc_final: 0.8432 (t0) REVERT: D 255 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8890 (mm) REVERT: D 288 GLN cc_start: 0.9488 (mp10) cc_final: 0.9105 (mp10) REVERT: D 298 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8622 (tm-30) REVERT: G 255 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8894 (mm) REVERT: G 288 GLN cc_start: 0.9489 (mp10) cc_final: 0.9107 (mp10) REVERT: G 298 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8622 (tm-30) REVERT: J 255 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8891 (mm) REVERT: J 288 GLN cc_start: 0.9488 (mp10) cc_final: 0.9225 (mp10) REVERT: J 298 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8618 (tm-30) outliers start: 36 outliers final: 20 residues processed: 117 average time/residue: 0.1956 time to fit residues: 34.4652 Evaluate side-chains 97 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 134 CYS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 134 CYS Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10780 Z= 0.195 Angle : 0.505 7.344 14672 Z= 0.270 Chirality : 0.042 0.135 1700 Planarity : 0.004 0.037 1796 Dihedral : 5.607 35.049 1484 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.18 % Allowed : 17.58 % Favored : 79.24 % 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: -0.92 (0.24), residues: 1304 helix: 1.38 (0.26), residues: 440 sheet: 0.12 (0.32), residues: 288 loop : -2.74 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 113 HIS 0.002 0.001 HIS A 357 PHE 0.024 0.001 PHE D 186 TYR 0.008 0.001 TYR J 360 ARG 0.005 0.000 ARG J 378 *********************** 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 117 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 1.133 Fit side-chains REVERT: A 111 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: A 288 GLN cc_start: 0.9477 (mp10) cc_final: 0.9250 (mp10) REVERT: A 298 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8541 (tm-30) REVERT: A 378 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8362 (ttp80) REVERT: D 111 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (tpp) REVERT: D 288 GLN cc_start: 0.9479 (mp10) cc_final: 0.9250 (mp10) REVERT: D 298 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8541 (tm-30) REVERT: D 378 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8365 (ttp80) REVERT: G 111 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: G 288 GLN cc_start: 0.9478 (mp10) cc_final: 0.9251 (mp10) REVERT: G 298 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8543 (tm-30) REVERT: G 378 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8367 (ttp80) REVERT: J 111 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: J 288 GLN cc_start: 0.9482 (mp10) cc_final: 0.9253 (mp10) REVERT: J 298 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8537 (tm-30) REVERT: J 378 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8219 (ttp80) outliers start: 36 outliers final: 16 residues processed: 109 average time/residue: 0.1962 time to fit residues: 31.7703 Evaluate side-chains 92 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.2980 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8441 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10780 Z= 0.168 Angle : 0.493 4.956 14672 Z= 0.263 Chirality : 0.042 0.136 1700 Planarity : 0.003 0.036 1796 Dihedral : 5.247 39.442 1484 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.77 % Allowed : 19.79 % Favored : 78.45 % 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: -0.53 (0.24), residues: 1304 helix: 1.74 (0.26), residues: 436 sheet: 0.38 (0.32), residues: 288 loop : -2.54 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 113 HIS 0.002 0.001 HIS J 357 PHE 0.018 0.001 PHE J 186 TYR 0.008 0.001 TYR D 360 ARG 0.004 0.000 ARG D 378 *********************** 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 101 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.274 Fit side-chains REVERT: A 111 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: A 288 GLN cc_start: 0.9483 (mp10) cc_final: 0.9283 (mp10) REVERT: A 298 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8450 (tm-30) REVERT: D 111 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: D 288 GLN cc_start: 0.9485 (mp10) cc_final: 0.9282 (mp10) REVERT: D 298 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8448 (tm-30) REVERT: G 111 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: G 288 GLN cc_start: 0.9485 (mp10) cc_final: 0.9284 (mp10) REVERT: G 298 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8450 (tm-30) REVERT: J 111 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: J 288 GLN cc_start: 0.9486 (mp10) cc_final: 0.9280 (mp10) REVERT: J 298 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8451 (tm-30) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.2186 time to fit residues: 30.0223 Evaluate side-chains 85 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10780 Z= 0.285 Angle : 0.522 4.869 14672 Z= 0.281 Chirality : 0.043 0.136 1700 Planarity : 0.004 0.037 1796 Dihedral : 5.479 39.971 1484 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.89 % Allowed : 17.76 % Favored : 78.36 % 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: 1.73 (0.26), residues: 436 sheet: 0.39 (0.32), residues: 288 loop : -2.47 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS A 283 PHE 0.024 0.001 PHE A 186 TYR 0.010 0.001 TYR J 360 ARG 0.006 0.000 ARG J 378 *********************** 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 115 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 71 time to evaluate : 1.403 Fit side-chains REVERT: A 111 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8314 (tpp) REVERT: A 288 GLN cc_start: 0.9495 (mp10) cc_final: 0.9290 (mp10) REVERT: A 298 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8449 (tm-30) REVERT: A 378 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8307 (ttp80) REVERT: D 111 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: D 288 GLN cc_start: 0.9498 (mp10) cc_final: 0.9290 (mp10) REVERT: D 298 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8447 (tm-30) REVERT: D 378 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8310 (ttp80) REVERT: G 111 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: G 288 GLN cc_start: 0.9496 (mp10) cc_final: 0.9291 (mp10) REVERT: G 298 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8452 (tm-30) REVERT: G 378 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8312 (ttp80) REVERT: J 111 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: J 288 GLN cc_start: 0.9497 (mp10) cc_final: 0.9289 (mp10) REVERT: J 298 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8451 (tm-30) REVERT: J 378 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8339 (ttp80) outliers start: 44 outliers final: 20 residues processed: 111 average time/residue: 0.2073 time to fit residues: 34.9264 Evaluate side-chains 99 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 134 CYS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 134 CYS Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.8454 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 10780 Z= 0.191 Angle : 0.494 5.318 14672 Z= 0.263 Chirality : 0.042 0.135 1700 Planarity : 0.004 0.035 1796 Dihedral : 5.261 43.266 1484 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.47 % Allowed : 19.52 % Favored : 78.00 % 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: -0.31 (0.24), residues: 1304 helix: 1.88 (0.26), residues: 436 sheet: 0.51 (0.32), residues: 288 loop : -2.36 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 113 HIS 0.002 0.001 HIS G 283 PHE 0.023 0.001 PHE G 186 TYR 0.008 0.001 TYR D 360 ARG 0.005 0.000 ARG J 378 *********************** 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 103 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 1.267 Fit side-chains REVERT: A 88 ASP cc_start: 0.8587 (t0) cc_final: 0.8357 (t0) REVERT: A 111 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8317 (tpp) REVERT: A 298 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8431 (tm-30) REVERT: A 378 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8288 (ttp80) REVERT: D 111 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: D 298 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8430 (tm-30) REVERT: D 378 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8288 (ttp80) REVERT: G 88 ASP cc_start: 0.8587 (t0) cc_final: 0.8355 (t0) REVERT: G 111 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: G 298 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8430 (tm-30) REVERT: G 378 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8289 (ttp80) REVERT: J 88 ASP cc_start: 0.8586 (t0) cc_final: 0.8357 (t0) REVERT: J 111 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: J 298 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8435 (tm-30) REVERT: J 378 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8315 (ttp80) outliers start: 28 outliers final: 16 residues processed: 99 average time/residue: 0.2064 time to fit residues: 30.9365 Evaluate side-chains 91 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 11 optimal weight: 0.0060 chunk 96 optimal weight: 0.0020 chunk 112 optimal weight: 0.0040 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.2515 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= 0.101 Angle : 0.457 5.024 14672 Z= 0.239 Chirality : 0.041 0.131 1700 Planarity : 0.003 0.033 1796 Dihedral : 4.705 51.191 1484 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.06 % Allowed : 20.67 % Favored : 78.27 % 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: -0.01 (0.24), residues: 1304 helix: 2.23 (0.26), residues: 436 sheet: 0.66 (0.31), residues: 288 loop : -2.27 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 114 HIS 0.001 0.000 HIS G 125 PHE 0.021 0.001 PHE J 186 TYR 0.007 0.001 TYR D 58 ARG 0.005 0.000 ARG D 378 *********************** 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 119 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.249 Fit side-chains REVERT: A 298 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8149 (tm-30) REVERT: A 378 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8403 (ttp80) REVERT: D 298 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8150 (tm-30) REVERT: D 378 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8402 (ttp80) REVERT: G 298 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8163 (tm-30) REVERT: G 378 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8403 (ttp80) REVERT: J 298 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8152 (tm-30) REVERT: J 378 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8411 (ttp80) outliers start: 12 outliers final: 4 residues processed: 115 average time/residue: 0.2367 time to fit residues: 39.0707 Evaluate side-chains 84 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain J residue 210 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN D 288 GLN G 288 GLN J 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2391 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= 0.136 Angle : 0.501 9.821 14672 Z= 0.253 Chirality : 0.041 0.134 1700 Planarity : 0.003 0.034 1796 Dihedral : 4.700 49.373 1484 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.71 % Allowed : 22.26 % Favored : 77.03 % 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: 0.03 (0.24), residues: 1304 helix: 2.17 (0.26), residues: 436 sheet: 0.80 (0.32), residues: 288 loop : -2.23 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 292 HIS 0.001 0.000 HIS J 283 PHE 0.027 0.001 PHE A 186 TYR 0.007 0.001 TYR J 360 ARG 0.004 0.000 ARG D 378 *********************** 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 80 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.239 Fit side-chains REVERT: A 298 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8118 (tm-30) REVERT: D 298 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8120 (tm-30) REVERT: G 298 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8127 (tm-30) REVERT: J 298 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8144 (tm-30) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.2343 time to fit residues: 27.6805 Evaluate side-chains 72 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain J residue 210 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 322 GLN J 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10780 Z= 0.350 Angle : 0.596 10.131 14672 Z= 0.308 Chirality : 0.044 0.135 1700 Planarity : 0.004 0.054 1796 Dihedral : 5.516 43.958 1484 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.80 % Allowed : 22.17 % Favored : 77.03 % 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: -0.15 (0.24), residues: 1304 helix: 1.94 (0.26), residues: 436 sheet: 0.60 (0.32), residues: 288 loop : -2.22 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.003 0.001 HIS J 283 PHE 0.025 0.002 PHE D 186 TYR 0.011 0.001 TYR G 360 ARG 0.009 0.001 ARG D 378 ********************** 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 73 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.278 Fit side-chains REVERT: A 287 GLN cc_start: 0.9169 (tt0) cc_final: 0.8823 (tm-30) REVERT: A 298 GLN cc_start: 0.8953 (tp-100) cc_final: 0.7997 (tm-30) REVERT: A 378 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8283 (ttp80) REVERT: D 287 GLN cc_start: 0.9169 (tt0) cc_final: 0.8821 (tm-30) REVERT: D 298 GLN cc_start: 0.8953 (tp-100) cc_final: 0.7998 (tm-30) REVERT: D 378 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8282 (ttp80) REVERT: G 287 GLN cc_start: 0.9167 (tt0) cc_final: 0.8821 (tm-30) REVERT: G 298 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8002 (tm-30) REVERT: G 378 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8282 (ttp80) REVERT: J 287 GLN cc_start: 0.9169 (tt0) cc_final: 0.8821 (tm-30) REVERT: J 298 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8006 (tm-30) REVERT: J 378 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8286 (ttp80) outliers start: 9 outliers final: 9 residues processed: 73 average time/residue: 0.2292 time to fit residues: 24.8898 Evaluate side-chains 73 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3064 r_free = 0.3064 target = 0.075048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.056814 restraints weight = 23814.987| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.40 r_work: 0.2554 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2110 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= 0.144 Angle : 0.518 9.862 14672 Z= 0.263 Chirality : 0.042 0.143 1700 Planarity : 0.004 0.038 1796 Dihedral : 5.026 48.754 1484 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.88 % Allowed : 22.08 % Favored : 77.03 % 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: -0.03 (0.24), residues: 1304 helix: 2.02 (0.26), residues: 436 sheet: 0.71 (0.32), residues: 288 loop : -2.15 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 113 HIS 0.001 0.000 HIS J 357 PHE 0.026 0.001 PHE D 186 TYR 0.008 0.001 TYR J 360 ARG 0.008 0.000 ARG J 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.30 seconds wall clock time: 36 minutes 25.81 seconds (2185.81 seconds total)