Starting phenix.real_space_refine on Fri Mar 15 23:23:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xkv_22226/03_2024/6xkv_22226_updated.pdb" } resolution = 3.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "P ARG 85": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1801 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "Q" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1794 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "R" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11016 SG CYS E 133 31.625 67.838 38.027 0.25105.87 S ATOM 11162 SG CYS E 153 30.491 64.409 37.476 0.25107.21 S ATOM 12381 SG CYS R 133 82.719 27.940 38.570 0.25105.87 S ATOM 12527 SG CYS R 153 83.841 31.371 38.015 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 52 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 40 not shown) Time building chain proxies: 6.88, per 1000 atoms: 0.53 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 96.56, 107.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 501 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 135 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 156 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 133 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 45.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.900A pdb=" N HIS C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.975A pdb=" N MET C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 147 Processing helix chain 'C' and resid 154 through 168 removed outlier: 4.863A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 269 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.557A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 348 removed outlier: 3.848A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 361 through 380 Processing helix chain 'C' and resid 389 through 414 removed outlier: 5.577A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 221 through 249 Processing helix chain 'P' and resid 15 through 20 removed outlier: 4.900A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 32 Processing helix chain 'P' and resid 47 through 67 removed outlier: 3.975A pdb=" N MET P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 85 Processing helix chain 'P' and resid 90 through 117 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 147 Processing helix chain 'P' and resid 154 through 168 removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 181 Processing helix chain 'P' and resid 188 through 198 Processing helix chain 'P' and resid 201 through 218 removed outlier: 3.586A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 269 Processing helix chain 'P' and resid 277 through 280 Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'P' and resid 317 through 322 removed outlier: 4.558A pdb=" N THR P 322 " --> pdb=" O VAL P 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 348 removed outlier: 3.847A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Proline residue: P 347 - end of helix Processing helix chain 'P' and resid 357 through 359 No H-bonds generated for 'chain 'P' and resid 357 through 359' Processing helix chain 'P' and resid 361 through 380 Processing helix chain 'P' and resid 389 through 414 removed outlier: 5.576A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 45 through 48 removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 45 through 48' Processing helix chain 'Q' and resid 58 through 66 Processing helix chain 'Q' and resid 128 through 135 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 221 through 249 Processing helix chain 'E' and resid 12 through 36 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'R' and resid 12 through 36 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 79 through 86 Processing helix chain 'R' and resid 110 through 113 No H-bonds generated for 'chain 'R' and resid 110 through 113' Processing sheet with id= A, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= B, first strand: chain 'Q' and resid 153 through 155 Processing sheet with id= C, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.606A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 64 through 67 Processing sheet with id= E, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 64 through 67 540 hydrogen bonds defined for protein. 1581 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: 3.39 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5786 1.41 - 1.61: 7561 1.61 - 1.80: 99 1.80 - 2.00: 35 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 86.91 - 105.46: 401 105.46 - 124.01: 17343 124.01 - 142.56: 764 142.56 - 161.12: 0 161.12 - 179.67: 12 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.10 -13.44 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.79 13.54 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6978 17.90 - 35.80: 536 35.80 - 53.69: 79 53.69 - 71.59: 10 71.59 - 89.49: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.24 82.24 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.11 82.11 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.15 77.15 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1911 0.146 - 0.292: 46 0.292 - 0.439: 1 0.439 - 0.585: 10 0.585 - 0.731: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.009 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.110 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.009 2.00e-02 2.50e+03 4.11e-02 3.79e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 158 2.57 - 3.15: 11818 3.15 - 3.73: 19602 3.73 - 4.32: 27571 4.32 - 4.90: 45683 Nonbonded interactions: 104832 Sorted by model distance: nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 2.440 nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 2.440 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 2.520 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.006 2.520 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 2.520 ... (remaining 104827 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 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 257 or resid 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } 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=0.25 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.020 Extract box with map and model: 3.480 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.620 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.009 0.220 13509 Z= 0.617 Angle : 1.018 15.793 18520 Z= 0.636 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.755 89.490 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.41 % Favored : 83.17 % Rotamer: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % 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: -4.31 (0.17), residues: 1658 helix: -1.65 (0.16), residues: 784 sheet: -3.39 (0.48), residues: 64 loop : -4.22 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 296 HIS 0.010 0.001 HIS C 111 PHE 0.021 0.001 PHE P 104 TYR 0.010 0.001 TYR C 297 ARG 0.002 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8212 (ptp-170) REVERT: C 351 THR cc_start: 0.8113 (p) cc_final: 0.7549 (p) REVERT: D 14 ILE cc_start: 0.8784 (mp) cc_final: 0.8577 (mt) REVERT: D 165 ASP cc_start: 0.6750 (m-30) cc_final: 0.6381 (m-30) REVERT: D 196 ASP cc_start: 0.8044 (p0) cc_final: 0.7757 (p0) REVERT: P 222 ASN cc_start: 0.7704 (t0) cc_final: 0.7276 (t0) REVERT: P 334 ILE cc_start: 0.8882 (mt) cc_final: 0.8667 (mt) REVERT: Q 14 ILE cc_start: 0.8568 (mp) cc_final: 0.8364 (mt) REVERT: E 13 ASP cc_start: 0.5978 (p0) cc_final: 0.5733 (m-30) REVERT: E 94 ARG cc_start: 0.6015 (ttm-80) cc_final: 0.5510 (mpt180) REVERT: E 118 PHE cc_start: 0.5907 (m-80) cc_final: 0.5507 (m-80) REVERT: E 119 ASP cc_start: 0.5752 (t0) cc_final: 0.4514 (m-30) REVERT: E 165 ARG cc_start: 0.5899 (mtm-85) cc_final: 0.5616 (mtm-85) REVERT: R 139 VAL cc_start: 0.6400 (t) cc_final: 0.5308 (t) REVERT: R 158 SER cc_start: 0.1845 (m) cc_final: 0.1597 (m) REVERT: R 161 ASP cc_start: 0.6263 (p0) cc_final: 0.6009 (p0) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.2713 time to fit residues: 111.3736 Evaluate side-chains 190 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 153 GLN D 20 GLN D 159 GLN D 177 HIS P 68 HIS P 99 ASN P 153 GLN E 17 HIS E 100 ASN R 17 HIS R 100 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13509 Z= 0.262 Angle : 0.704 10.880 18520 Z= 0.343 Chirality : 0.045 0.180 1970 Planarity : 0.006 0.077 2327 Dihedral : 8.501 85.624 1861 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.34 % Favored : 88.42 % Rotamer: Outliers : 2.48 % Allowed : 11.21 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.16 (0.20), residues: 1658 helix: 0.38 (0.18), residues: 796 sheet: -2.24 (0.59), residues: 70 loop : -3.46 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 180 HIS 0.004 0.001 HIS P 97 PHE 0.022 0.002 PHE P 113 TYR 0.029 0.001 TYR C 199 ARG 0.005 0.001 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: C 349 LEU cc_start: 0.8975 (mt) cc_final: 0.8698 (mp) REVERT: C 351 THR cc_start: 0.8216 (p) cc_final: 0.7809 (p) REVERT: D 14 ILE cc_start: 0.8734 (mp) cc_final: 0.8532 (mt) REVERT: D 167 CYS cc_start: 0.6960 (m) cc_final: 0.6606 (m) REVERT: P 42 ASN cc_start: 0.7921 (m-40) cc_final: 0.7714 (m110) REVERT: P 349 LEU cc_start: 0.8828 (mt) cc_final: 0.8594 (mp) REVERT: Q 14 ILE cc_start: 0.8696 (mp) cc_final: 0.8495 (mt) REVERT: Q 79 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7155 (mm-30) REVERT: Q 87 MET cc_start: 0.8713 (mtt) cc_final: 0.8204 (mtt) REVERT: Q 99 ASP cc_start: 0.8175 (t0) cc_final: 0.7662 (t70) REVERT: Q 218 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7950 (tp30) REVERT: E 68 ARG cc_start: 0.6843 (ttt180) cc_final: 0.6626 (ttt180) REVERT: R 53 ASP cc_start: 0.5942 (t70) cc_final: 0.5378 (m-30) outliers start: 31 outliers final: 18 residues processed: 244 average time/residue: 0.2499 time to fit residues: 87.4736 Evaluate side-chains 202 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS C 99 ASN C 276 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN P 42 ASN P 82 HIS R 36 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13509 Z= 0.459 Angle : 0.790 13.810 18520 Z= 0.382 Chirality : 0.049 0.189 1970 Planarity : 0.006 0.066 2327 Dihedral : 8.579 87.803 1858 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.61 % Favored : 87.15 % Rotamer: Outliers : 3.92 % Allowed : 14.89 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.73 (0.20), residues: 1658 helix: 0.50 (0.18), residues: 806 sheet: -1.10 (0.65), residues: 62 loop : -3.08 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 67 HIS 0.009 0.002 HIS P 97 PHE 0.028 0.003 PHE P 104 TYR 0.022 0.002 TYR C 199 ARG 0.005 0.001 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: C 351 THR cc_start: 0.8344 (p) cc_final: 0.7935 (p) REVERT: D 50 ASP cc_start: 0.7997 (m-30) cc_final: 0.7642 (m-30) REVERT: P 93 MET cc_start: 0.8437 (mmt) cc_final: 0.8203 (mmt) REVERT: P 351 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7812 (p) REVERT: Q 62 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: Q 79 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6994 (mm-30) REVERT: Q 87 MET cc_start: 0.8880 (mtt) cc_final: 0.8431 (mtt) REVERT: Q 167 CYS cc_start: 0.8204 (m) cc_final: 0.7862 (m) REVERT: E 167 ARG cc_start: 0.6172 (mtp180) cc_final: 0.5906 (mtp85) outliers start: 49 outliers final: 33 residues processed: 249 average time/residue: 0.2282 time to fit residues: 83.9309 Evaluate side-chains 207 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 351 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 158 SER Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 72 optimal weight: 0.0030 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 0.0980 chunk 43 optimal weight: 0.0980 overall best weight: 0.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN P 42 ASN R 36 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13509 Z= 0.180 Angle : 0.623 11.040 18520 Z= 0.304 Chirality : 0.043 0.175 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.101 83.363 1858 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.19 % Favored : 89.69 % Rotamer: Outliers : 2.08 % Allowed : 18.09 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.08 (0.21), residues: 1658 helix: 1.15 (0.19), residues: 796 sheet: -0.79 (0.67), residues: 62 loop : -2.85 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 296 HIS 0.003 0.001 HIS C 212 PHE 0.015 0.001 PHE P 216 TYR 0.015 0.001 TYR D 153 ARG 0.002 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.458 Fit side-chains REVERT: C 351 THR cc_start: 0.8229 (p) cc_final: 0.7869 (p) REVERT: D 50 ASP cc_start: 0.7912 (m-30) cc_final: 0.7612 (m-30) REVERT: D 183 MET cc_start: 0.8563 (ttp) cc_final: 0.8190 (ttm) REVERT: D 248 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7172 (ttt180) REVERT: Q 62 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: Q 79 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6930 (mm-30) REVERT: Q 87 MET cc_start: 0.8817 (mtt) cc_final: 0.8323 (mtt) REVERT: Q 183 MET cc_start: 0.8479 (ttp) cc_final: 0.7916 (ttm) REVERT: Q 248 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7166 (ttt180) REVERT: E 68 ARG cc_start: 0.6839 (ttt180) cc_final: 0.6434 (ttt180) REVERT: E 167 ARG cc_start: 0.6152 (mtp180) cc_final: 0.5914 (mtp85) REVERT: R 127 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5498 (tt) REVERT: R 167 ARG cc_start: 0.6320 (mtp180) cc_final: 0.5941 (mtp85) outliers start: 26 outliers final: 14 residues processed: 231 average time/residue: 0.2607 time to fit residues: 85.4882 Evaluate side-chains 201 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 127 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 42 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13509 Z= 0.231 Angle : 0.631 10.001 18520 Z= 0.307 Chirality : 0.043 0.166 1970 Planarity : 0.005 0.054 2327 Dihedral : 8.022 81.634 1858 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.52 % Favored : 88.36 % Rotamer: Outliers : 2.40 % Allowed : 19.22 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.87 (0.21), residues: 1658 helix: 1.31 (0.18), residues: 796 sheet: -0.62 (0.68), residues: 64 loop : -2.72 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 400 HIS 0.005 0.001 HIS P 212 PHE 0.016 0.001 PHE P 104 TYR 0.016 0.001 TYR D 153 ARG 0.010 0.000 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 1.313 Fit side-chains REVERT: D 248 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7173 (ttt180) REVERT: P 180 LEU cc_start: 0.9444 (tp) cc_final: 0.9088 (mt) REVERT: Q 79 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6937 (mm-30) REVERT: Q 87 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: Q 183 MET cc_start: 0.8595 (ttp) cc_final: 0.8096 (ttm) REVERT: Q 248 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7175 (ttt180) REVERT: E 167 ARG cc_start: 0.6018 (mtp180) cc_final: 0.5781 (mtp85) REVERT: R 127 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5508 (tt) outliers start: 30 outliers final: 21 residues processed: 221 average time/residue: 0.2550 time to fit residues: 81.1218 Evaluate side-chains 194 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13509 Z= 0.275 Angle : 0.658 15.126 18520 Z= 0.318 Chirality : 0.044 0.211 1970 Planarity : 0.005 0.053 2327 Dihedral : 8.045 81.947 1858 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.58 % Favored : 88.30 % Rotamer: Outliers : 2.64 % Allowed : 20.02 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.76 (0.21), residues: 1658 helix: 1.34 (0.18), residues: 800 sheet: -0.31 (0.69), residues: 64 loop : -2.63 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 400 HIS 0.006 0.001 HIS C 212 PHE 0.015 0.002 PHE C 104 TYR 0.016 0.001 TYR D 153 ARG 0.005 0.000 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: C 180 LEU cc_start: 0.9449 (tp) cc_final: 0.9109 (mt) REVERT: D 87 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8637 (mmm) REVERT: D 183 MET cc_start: 0.8585 (ttp) cc_final: 0.8174 (ttm) REVERT: D 248 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7200 (ttt180) REVERT: P 180 LEU cc_start: 0.9453 (tp) cc_final: 0.9095 (mt) REVERT: Q 79 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6884 (mm-30) REVERT: Q 87 MET cc_start: 0.8845 (mtt) cc_final: 0.8235 (mtt) REVERT: Q 248 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7201 (ttt180) REVERT: E 167 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5819 (mtp85) REVERT: R 113 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6494 (tpt-90) outliers start: 33 outliers final: 25 residues processed: 215 average time/residue: 0.2428 time to fit residues: 76.4071 Evaluate side-chains 203 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 100 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13509 Z= 0.214 Angle : 0.626 14.728 18520 Z= 0.303 Chirality : 0.042 0.164 1970 Planarity : 0.005 0.051 2327 Dihedral : 7.896 78.913 1858 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 2.08 % Allowed : 21.14 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.62 (0.21), residues: 1658 helix: 1.45 (0.18), residues: 798 sheet: -0.20 (0.69), residues: 64 loop : -2.56 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 296 HIS 0.005 0.001 HIS C 212 PHE 0.014 0.001 PHE P 216 TYR 0.016 0.001 TYR D 153 ARG 0.004 0.000 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.687 Fit side-chains REVERT: C 180 LEU cc_start: 0.9436 (tp) cc_final: 0.9105 (mt) REVERT: D 140 GLU cc_start: 0.7700 (mp0) cc_final: 0.7479 (mp0) REVERT: D 183 MET cc_start: 0.8545 (ttp) cc_final: 0.8138 (ttm) REVERT: D 248 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7194 (ttt180) REVERT: P 180 LEU cc_start: 0.9431 (tp) cc_final: 0.9085 (mt) REVERT: Q 79 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6921 (mm-30) REVERT: Q 87 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: Q 248 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7193 (ttt180) REVERT: E 53 ASP cc_start: 0.5157 (t0) cc_final: 0.4818 (m-30) REVERT: E 99 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: E 167 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5863 (mtp85) REVERT: R 113 ARG cc_start: 0.6687 (tpt-90) cc_final: 0.6410 (tpt-90) outliers start: 26 outliers final: 20 residues processed: 229 average time/residue: 0.2521 time to fit residues: 83.3078 Evaluate side-chains 202 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13509 Z= 0.245 Angle : 0.645 13.610 18520 Z= 0.311 Chirality : 0.043 0.177 1970 Planarity : 0.005 0.055 2327 Dihedral : 7.890 78.211 1858 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.94 % Favored : 87.94 % Rotamer: Outliers : 2.40 % Allowed : 21.06 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.58 (0.21), residues: 1658 helix: 1.46 (0.18), residues: 798 sheet: -0.52 (0.62), residues: 84 loop : -2.51 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 400 HIS 0.005 0.001 HIS C 212 PHE 0.014 0.001 PHE P 216 TYR 0.015 0.001 TYR D 153 ARG 0.007 0.000 ARG P 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.373 Fit side-chains REVERT: C 180 LEU cc_start: 0.9444 (tp) cc_final: 0.9099 (mt) REVERT: D 87 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8611 (mmm) REVERT: D 183 MET cc_start: 0.8585 (ttp) cc_final: 0.8166 (ttm) REVERT: D 248 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7198 (ttt180) REVERT: P 180 LEU cc_start: 0.9424 (tp) cc_final: 0.9108 (mt) REVERT: Q 79 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6861 (mm-30) REVERT: Q 87 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8263 (mtt) REVERT: Q 183 MET cc_start: 0.8486 (ttm) cc_final: 0.7723 (ttm) REVERT: Q 248 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7550 (ttt180) REVERT: E 99 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: E 167 ARG cc_start: 0.6129 (mtp180) cc_final: 0.5782 (mtp85) REVERT: R 113 ARG cc_start: 0.6776 (tpt-90) cc_final: 0.6443 (tpt-90) outliers start: 30 outliers final: 20 residues processed: 220 average time/residue: 0.2535 time to fit residues: 80.0352 Evaluate side-chains 195 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13509 Z= 0.287 Angle : 0.674 13.111 18520 Z= 0.325 Chirality : 0.044 0.174 1970 Planarity : 0.005 0.053 2327 Dihedral : 7.931 78.864 1858 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.70 % Favored : 88.18 % Rotamer: Outliers : 2.48 % Allowed : 21.30 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.60 (0.21), residues: 1658 helix: 1.42 (0.18), residues: 798 sheet: -0.38 (0.63), residues: 82 loop : -2.52 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 400 HIS 0.005 0.001 HIS C 212 PHE 0.014 0.002 PHE P 216 TYR 0.015 0.001 TYR D 153 ARG 0.007 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.293 Fit side-chains REVERT: C 180 LEU cc_start: 0.9444 (tp) cc_final: 0.9078 (mt) REVERT: D 87 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: D 183 MET cc_start: 0.8653 (ttp) cc_final: 0.8204 (ttm) REVERT: D 248 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7199 (ttt180) REVERT: P 180 LEU cc_start: 0.9414 (tp) cc_final: 0.9064 (mt) REVERT: Q 79 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6796 (mm-30) REVERT: Q 87 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: Q 183 MET cc_start: 0.8562 (ttm) cc_final: 0.7860 (ttm) REVERT: Q 248 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7511 (ttt180) REVERT: E 99 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: R 113 ARG cc_start: 0.6770 (tpt-90) cc_final: 0.6435 (tpt-90) outliers start: 31 outliers final: 24 residues processed: 206 average time/residue: 0.2696 time to fit residues: 79.2966 Evaluate side-chains 197 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 378 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 165 optimal weight: 0.0670 chunk 152 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13509 Z= 0.226 Angle : 0.642 12.560 18520 Z= 0.310 Chirality : 0.043 0.177 1970 Planarity : 0.005 0.054 2327 Dihedral : 7.847 76.614 1858 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.40 % Favored : 88.48 % Rotamer: Outliers : 2.32 % Allowed : 21.38 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.21), residues: 1658 helix: 1.49 (0.18), residues: 798 sheet: -0.35 (0.63), residues: 82 loop : -2.48 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 296 HIS 0.005 0.001 HIS P 212 PHE 0.014 0.001 PHE P 216 TYR 0.014 0.001 TYR D 153 ARG 0.007 0.000 ARG C 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.465 Fit side-chains REVERT: C 180 LEU cc_start: 0.9429 (tp) cc_final: 0.9099 (mt) REVERT: D 87 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8642 (mmm) REVERT: D 99 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7885 (t70) REVERT: D 183 MET cc_start: 0.8618 (ttp) cc_final: 0.8194 (ttm) REVERT: D 248 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7565 (ttt180) REVERT: P 180 LEU cc_start: 0.9399 (tp) cc_final: 0.9089 (mt) REVERT: Q 79 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6809 (mm-30) REVERT: Q 87 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: Q 183 MET cc_start: 0.8390 (ttm) cc_final: 0.7673 (ttm) REVERT: Q 248 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7578 (ttt180) REVERT: R 113 ARG cc_start: 0.6962 (tpt-90) cc_final: 0.6535 (tpt-90) outliers start: 29 outliers final: 22 residues processed: 202 average time/residue: 0.2599 time to fit residues: 75.3477 Evaluate side-chains 194 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain E residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.150976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117580 restraints weight = 17363.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116135 restraints weight = 18446.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116614 restraints weight = 16988.170| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13509 Z= 0.223 Angle : 0.638 12.928 18520 Z= 0.308 Chirality : 0.042 0.168 1970 Planarity : 0.005 0.053 2327 Dihedral : 7.805 76.621 1858 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.22 % Favored : 88.66 % Rotamer: Outliers : 2.24 % Allowed : 21.94 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.44 (0.21), residues: 1658 helix: 1.54 (0.18), residues: 796 sheet: -0.44 (0.61), residues: 84 loop : -2.40 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 296 HIS 0.005 0.001 HIS P 212 PHE 0.014 0.001 PHE P 216 TYR 0.014 0.001 TYR D 153 ARG 0.007 0.000 ARG P 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.31 seconds wall clock time: 46 minutes 0.45 seconds (2760.45 seconds total)