Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 22:56:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/10_2023/6xit_22200_updated.pdb" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9500 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 12 5.49 5 S 52 5.16 5 C 6704 2.51 5 N 1688 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D GLU 361": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10403 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 5.50, per 1000 atoms: 0.53 Number of scatterers: 10403 At special positions: 0 Unit cell: (87, 87, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 52 16.00 P 12 15.00 O 1944 8.00 N 1688 7.00 C 6704 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 B 134 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 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: 4.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 20 sheets defined 32.4% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 91 through 120 removed outlier: 3.612A pdb=" N TYR A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 117 " --> pdb=" O TRP A 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 118 " --> pdb=" O TRP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.549A pdb=" N SER A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 195 removed outlier: 3.504A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.120A pdb=" N ALA A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.516A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 84 through 87 No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 91 through 120 removed outlier: 3.612A pdb=" N TYR B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 117 " --> pdb=" O TRP B 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 118 " --> pdb=" O TRP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.549A pdb=" N SER B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 195 removed outlier: 3.505A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 4.119A pdb=" N ALA B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 353 through 356 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.515A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 84 through 87 No H-bonds generated for 'chain 'C' and resid 84 through 87' Processing helix chain 'C' and resid 91 through 120 removed outlier: 3.612A pdb=" N TYR C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 117 " --> pdb=" O TRP C 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.549A pdb=" N SER C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 195 removed outlier: 3.504A pdb=" N LEU C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 4.119A pdb=" N ALA C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.517A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 84 through 87 No H-bonds generated for 'chain 'D' and resid 84 through 87' Processing helix chain 'D' and resid 91 through 120 removed outlier: 3.613A pdb=" N TYR D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 117 " --> pdb=" O TRP D 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR D 118 " --> pdb=" O TRP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.549A pdb=" N SER D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 195 removed outlier: 3.505A pdb=" N LEU D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 4.119A pdb=" N ALA D 202 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 299 No H-bonds generated for 'chain 'D' and resid 296 through 299' Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.516A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 380 " --> pdb=" O ALA D 376 " (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 219 through 224 Processing sheet with id= C, first strand: chain 'A' and resid 258 through 262 removed outlier: 4.342A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) 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 342 through 345 Processing sheet with id= F, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= G, first strand: chain 'B' and resid 219 through 224 Processing sheet with id= H, first strand: chain 'B' and resid 258 through 262 removed outlier: 4.341A pdb=" N ALA B 241 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 336 through 338 Processing sheet with id= J, first strand: chain 'B' and resid 342 through 345 Processing sheet with id= K, first strand: chain 'C' and resid 205 through 207 Processing sheet with id= L, first strand: chain 'C' and resid 219 through 224 Processing sheet with id= M, first strand: chain 'C' and resid 258 through 262 removed outlier: 4.341A pdb=" N ALA C 241 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 336 through 338 Processing sheet with id= O, first strand: chain 'C' and resid 342 through 345 Processing sheet with id= P, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= Q, first strand: chain 'D' and resid 219 through 224 Processing sheet with id= R, first strand: chain 'D' and resid 258 through 262 removed outlier: 4.342A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= T, first strand: chain 'D' and resid 342 through 345 412 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2004 1.32 - 1.45: 2713 1.45 - 1.57: 5827 1.57 - 1.70: 16 1.70 - 1.82: 80 Bond restraints: 10640 Sorted by residual: bond pdb=" C1B PIO D 401 " pdb=" O3C PIO D 401 " ideal model delta sigma weight residual 1.399 1.327 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1B PIO A 401 " pdb=" O3C PIO A 401 " ideal model delta sigma weight residual 1.399 1.328 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1B PIO C 401 " pdb=" O3C PIO C 401 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1B PIO B 401 " pdb=" O3C PIO B 401 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PIO B 401 " pdb=" P4 PIO B 401 " ideal model delta sigma weight residual 1.648 1.585 0.063 2.00e-02 2.50e+03 9.86e+00 ... (remaining 10635 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.81: 271 106.81 - 113.62: 6144 113.62 - 120.44: 4089 120.44 - 127.25: 3878 127.25 - 134.06: 122 Bond angle restraints: 14504 Sorted by residual: angle pdb=" C HIS B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta sigma weight residual 121.41 131.06 -9.65 1.96e+00 2.60e-01 2.42e+01 angle pdb=" C HIS D 69 " pdb=" N GLY D 70 " pdb=" CA GLY D 70 " ideal model delta sigma weight residual 121.41 131.00 -9.59 1.96e+00 2.60e-01 2.39e+01 angle pdb=" C HIS A 69 " pdb=" N GLY A 70 " pdb=" CA GLY A 70 " ideal model delta sigma weight residual 121.41 130.97 -9.56 1.96e+00 2.60e-01 2.38e+01 angle pdb=" C HIS C 69 " pdb=" N GLY C 70 " pdb=" CA GLY C 70 " ideal model delta sigma weight residual 121.41 130.97 -9.56 1.96e+00 2.60e-01 2.38e+01 angle pdb=" N TRP A 91 " pdb=" CA TRP A 91 " pdb=" C TRP A 91 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 14499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5516 17.26 - 34.51: 555 34.51 - 51.77: 96 51.77 - 69.03: 9 69.03 - 86.29: 8 Dihedral angle restraints: 6184 sinusoidal: 2360 harmonic: 3824 Sorted by residual: dihedral pdb=" CA TYR C 159 " pdb=" C TYR C 159 " pdb=" N ARG C 160 " pdb=" CA ARG C 160 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TYR A 159 " pdb=" C TYR A 159 " pdb=" N ARG A 160 " pdb=" CA ARG A 160 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR D 159 " pdb=" C TYR D 159 " pdb=" N ARG D 160 " pdb=" CA ARG D 160 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1106 0.051 - 0.103: 436 0.103 - 0.154: 125 0.154 - 0.205: 18 0.205 - 0.257: 3 Chirality restraints: 1688 Sorted by residual: chirality pdb=" C1 PIO D 401 " pdb=" C2 PIO D 401 " pdb=" C6 PIO D 401 " pdb=" O1 PIO D 401 " both_signs ideal model delta sigma weight residual False 2.50 2.76 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 PIO A 401 " pdb=" C2 PIO A 401 " pdb=" C6 PIO A 401 " pdb=" O1 PIO A 401 " both_signs ideal model delta sigma weight residual False 2.50 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 PIO B 401 " pdb=" C2 PIO B 401 " pdb=" C6 PIO B 401 " pdb=" O1 PIO B 401 " both_signs ideal model delta sigma weight residual False 2.50 2.71 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1685 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 299 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 300 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 300 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 300 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 299 " -0.036 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO A 300 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 299 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 300 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " -0.030 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 153 2.54 - 3.19: 9242 3.19 - 3.84: 20888 3.84 - 4.49: 28255 4.49 - 5.14: 46149 Nonbonded interactions: 104687 Sorted by model distance: nonbonded pdb=" O52 PIO D 401 " pdb=" O6 PIO D 401 " model vdw 1.894 2.440 nonbonded pdb=" O52 PIO B 401 " pdb=" O6 PIO B 401 " model vdw 1.897 2.440 nonbonded pdb=" O52 PIO C 401 " pdb=" O6 PIO C 401 " model vdw 1.903 2.440 nonbonded pdb=" O12 PIO A 401 " pdb=" O2 PIO A 401 " model vdw 1.935 2.440 nonbonded pdb=" O52 PIO A 401 " pdb=" O6 PIO A 401 " model vdw 1.968 2.440 ... (remaining 104682 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 381 or resid 401)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 14.120 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.660 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.010 0.100 10640 Z= 0.606 Angle : 0.971 9.645 14504 Z= 0.518 Chirality : 0.059 0.257 1688 Planarity : 0.006 0.054 1788 Dihedral : 14.190 86.285 3708 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.74 % Allowed : 12.87 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.18), residues: 1300 helix: -4.27 (0.10), residues: 408 sheet: -1.49 (0.30), residues: 232 loop : -1.59 (0.20), residues: 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.351 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 195 average time/residue: 0.1815 time to fit residues: 54.1801 Evaluate side-chains 135 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1888 time to fit residues: 2.7642 ------------------------------------------------------------------------------- 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: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 176 GLN A 233 HIS A 258 ASN A 286 ASN B 68 HIS B 176 GLN B 233 HIS B 258 ASN B 286 ASN C 68 HIS C 176 GLN C 233 HIS C 258 ASN C 286 ASN C 322 GLN D 68 HIS D 176 GLN D 233 HIS D 258 ASN D 286 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10640 Z= 0.164 Angle : 0.538 6.578 14504 Z= 0.273 Chirality : 0.044 0.194 1688 Planarity : 0.004 0.034 1788 Dihedral : 6.324 54.318 1448 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.93 % Allowed : 17.74 % Favored : 80.33 % 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 (0.20), residues: 1300 helix: -1.63 (0.21), residues: 424 sheet: -1.15 (0.30), residues: 236 loop : -0.74 (0.21), residues: 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.238 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 216 average time/residue: 0.1699 time to fit residues: 56.6243 Evaluate side-chains 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0971 time to fit residues: 3.5313 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN D 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10640 Z= 0.358 Angle : 0.626 6.922 14504 Z= 0.321 Chirality : 0.049 0.218 1688 Planarity : 0.004 0.029 1788 Dihedral : 6.328 58.367 1448 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.78 % Allowed : 18.84 % Favored : 76.38 % 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: -0.63 (0.22), residues: 1300 helix: -0.11 (0.25), residues: 400 sheet: -1.02 (0.30), residues: 228 loop : -0.24 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.460 Fit side-chains outliers start: 52 outliers final: 44 residues processed: 201 average time/residue: 0.1899 time to fit residues: 56.6328 Evaluate side-chains 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.0940 time to fit residues: 9.4450 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN D 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10640 Z= 0.236 Angle : 0.533 7.042 14504 Z= 0.270 Chirality : 0.045 0.200 1688 Planarity : 0.003 0.023 1788 Dihedral : 6.068 57.892 1448 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.57 % Allowed : 20.68 % Favored : 76.75 % 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 (0.23), residues: 1300 helix: 0.28 (0.26), residues: 400 sheet: -1.06 (0.30), residues: 240 loop : -0.01 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.157 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 181 average time/residue: 0.1956 time to fit residues: 54.0656 Evaluate side-chains 159 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1047 time to fit residues: 3.5374 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 322 GLN C 94 ASN D 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10640 Z= 0.137 Angle : 0.479 6.870 14504 Z= 0.239 Chirality : 0.043 0.202 1688 Planarity : 0.003 0.024 1788 Dihedral : 5.617 54.718 1448 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.03 % Allowed : 22.15 % Favored : 74.82 % 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: 0.26 (0.23), residues: 1300 helix: 0.59 (0.26), residues: 404 sheet: -0.62 (0.31), residues: 232 loop : 0.40 (0.25), residues: 664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 203 average time/residue: 0.1809 time to fit residues: 55.6464 Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0971 time to fit residues: 3.7824 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10640 Z= 0.465 Angle : 0.675 7.007 14504 Z= 0.344 Chirality : 0.051 0.222 1688 Planarity : 0.004 0.030 1788 Dihedral : 6.266 58.271 1448 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.06 % Allowed : 20.22 % Favored : 74.72 % 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: -0.33 (0.23), residues: 1300 helix: 0.04 (0.25), residues: 412 sheet: -0.87 (0.29), residues: 232 loop : 0.05 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 157 time to evaluate : 1.269 Fit side-chains outliers start: 55 outliers final: 40 residues processed: 182 average time/residue: 0.1749 time to fit residues: 49.0126 Evaluate side-chains 187 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.0980 time to fit residues: 8.7009 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10640 Z= 0.198 Angle : 0.522 7.200 14504 Z= 0.262 Chirality : 0.045 0.194 1688 Planarity : 0.003 0.022 1788 Dihedral : 5.874 55.157 1448 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.65 % Allowed : 22.98 % Favored : 75.37 % 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: 0.09 (0.23), residues: 1300 helix: 0.38 (0.26), residues: 412 sheet: -0.65 (0.31), residues: 232 loop : 0.32 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.190 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 166 average time/residue: 0.1858 time to fit residues: 47.0929 Evaluate side-chains 156 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0973 time to fit residues: 2.9505 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10640 Z= 0.303 Angle : 0.583 7.116 14504 Z= 0.294 Chirality : 0.048 0.250 1688 Planarity : 0.004 0.027 1788 Dihedral : 6.006 56.545 1448 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.48 % Allowed : 23.62 % Favored : 73.90 % 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: -0.08 (0.23), residues: 1300 helix: 0.22 (0.25), residues: 412 sheet: -0.68 (0.30), residues: 232 loop : 0.19 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.404 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 162 average time/residue: 0.1858 time to fit residues: 45.6271 Evaluate side-chains 168 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0998 time to fit residues: 4.8538 ------------------------------------------------------------------------------- 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: 0.2980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 94 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10640 Z= 0.246 Angle : 0.547 7.092 14504 Z= 0.274 Chirality : 0.046 0.209 1688 Planarity : 0.003 0.023 1788 Dihedral : 5.922 56.432 1448 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.47 % Allowed : 24.26 % Favored : 74.26 % 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 (0.23), residues: 1300 helix: 0.32 (0.25), residues: 412 sheet: -0.59 (0.30), residues: 232 loop : 0.24 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.273 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 156 average time/residue: 0.1816 time to fit residues: 43.6326 Evaluate side-chains 156 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0999 time to fit residues: 3.7722 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 0.1980 chunk 117 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 0.0470 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10640 Z= 0.152 Angle : 0.508 8.083 14504 Z= 0.251 Chirality : 0.044 0.200 1688 Planarity : 0.003 0.025 1788 Dihedral : 5.627 53.448 1448 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.74 % Allowed : 25.55 % Favored : 73.71 % 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: 0.22 (0.23), residues: 1300 helix: 0.47 (0.26), residues: 412 sheet: -0.55 (0.31), residues: 240 loop : 0.41 (0.25), residues: 648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.156 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 173 average time/residue: 0.1786 time to fit residues: 47.5929 Evaluate side-chains 160 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1082 time to fit residues: 2.5306 ------------------------------------------------------------------------------- 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: 7.9990 chunk 93 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN D 94 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071013 restraints weight = 28984.420| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.41 r_work: 0.3030 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10640 Z= 0.138 Angle : 0.488 6.992 14504 Z= 0.243 Chirality : 0.043 0.199 1688 Planarity : 0.003 0.026 1788 Dihedral : 5.472 54.523 1448 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.37 % Allowed : 27.30 % Favored : 72.33 % 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: 0.40 (0.23), residues: 1300 helix: 0.52 (0.26), residues: 412 sheet: -0.33 (0.31), residues: 240 loop : 0.54 (0.25), residues: 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.89 seconds wall clock time: 41 minutes 36.23 seconds (2496.23 seconds total)