Starting phenix.real_space_refine on Thu Feb 15 18:25:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi0_22189/02_2024/6xi0_22189_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= 0.005 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 "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" 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 "D ASP 203": "OD1" <-> "OD2" 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 "Q ASP 203": "OD1" <-> "OD2" 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-5238/modules/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 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: "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: 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: "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: 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: "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: "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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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: "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 933 SG CYS E 133 30.849 65.240 37.564 0.25105.87 S ATOM 1079 SG CYS E 153 29.828 61.763 37.104 0.25107.21 S ATOM 12381 SG CYS R 133 83.431 27.174 37.574 0.25105.87 S ATOM 12527 SG CYS R 153 84.451 30.652 37.124 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: 7.40, per 1000 atoms: 0.57 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 93.84, 106.08, 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: 6.01 Conformation dependent library (CDL) restraints added in 2.7 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 133 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " 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: 2.72 Creating SS restraints... 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 '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 91 through 117 removed outlier: 3.756A 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: 5.576A 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: 3.976A 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: 3.541A 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: 5.575A 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 '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 'E' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 64 through 67 Processing sheet with id= C, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= D, first strand: chain 'Q' and resid 153 through 155 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 67 539 hydrogen bonds defined for protein. 1578 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: 3.18 Time building geometry restraints manager: 6.28 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: 103 1.80 - 2.00: 31 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 1.20e+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 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=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 86.92 - 105.46: 400 105.46 - 124.00: 17341 124.00 - 142.54: 767 142.54 - 161.08: 0 161.08 - 179.62: 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 89.11 -13.45 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 89.09 -13.43 1.14e+00 7.69e-01 1.39e+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 90.91 13.42 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 90.94 13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.80 13.53 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6979 17.90 - 35.79: 535 35.79 - 53.69: 79 53.69 - 71.58: 10 71.58 - 89.48: 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 -22.29 82.29 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 -22.15 82.15 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 -17.14 77.14 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: 1912 0.146 - 0.292: 45 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 1.32e+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 0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.010 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 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 " -0.010 2.00e-02 2.50e+03 4.10e-02 3.78e+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 4.27e-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: 162 2.57 - 3.15: 11825 3.15 - 3.73: 19606 3.73 - 4.32: 27618 4.32 - 4.90: 45739 Nonbonded interactions: 104950 Sorted by model distance: nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 2.440 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 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 2.007 2.520 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 2.520 ... (remaining 104945 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.760 Find NCS groups from input model: 0.720 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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= 0.637 Angle : 1.015 15.809 18520 Z= 0.635 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.757 89.475 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.34 % Favored : 83.23 % 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: -3.37 (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 P 296 HIS 0.010 0.001 HIS P 111 PHE 0.021 0.001 PHE P 104 TYR 0.010 0.001 TYR C 297 ARG 0.002 0.000 ARG P 85 *********************** 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 217 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.1777 (t70) cc_final: 0.1459 (t70) REVERT: E 113 ARG cc_start: 0.7350 (tpt90) cc_final: 0.7095 (ttt90) REVERT: D 218 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8112 (tp30) REVERT: P 305 LEU cc_start: 0.8858 (tp) cc_final: 0.8566 (tt) REVERT: Q 74 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7263 (tttt) REVERT: Q 218 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7916 (tp30) REVERT: Q 247 LYS cc_start: 0.7812 (tttt) cc_final: 0.7557 (tttt) REVERT: R 81 ASP cc_start: 0.1993 (t70) cc_final: 0.1623 (t70) REVERT: R 113 ARG cc_start: 0.7393 (tpt90) cc_final: 0.7086 (ttt90) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.3316 time to fit residues: 98.2737 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 0.9980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS E 100 ASN C 68 HIS C 82 HIS C 99 ASN D 177 HIS P 68 HIS P 82 HIS P 99 ASN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 159 GLN Q 177 HIS R 17 HIS R 100 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13509 Z= 0.252 Angle : 0.735 12.317 18520 Z= 0.345 Chirality : 0.045 0.185 1970 Planarity : 0.006 0.077 2327 Dihedral : 8.492 87.500 1861 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.86 % Favored : 88.96 % Rotamer: Outliers : 1.04 % Allowed : 9.29 % Favored : 89.67 % 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: -2.07 (0.20), residues: 1658 helix: 0.41 (0.18), residues: 786 sheet: -2.28 (0.62), residues: 54 loop : -3.30 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 400 HIS 0.006 0.001 HIS C 97 PHE 0.022 0.001 PHE C 113 TYR 0.026 0.001 TYR C 199 ARG 0.008 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 182 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: E 115 LEU cc_start: 0.6584 (pp) cc_final: 0.6271 (pt) REVERT: C 305 LEU cc_start: 0.9024 (tp) cc_final: 0.8800 (tt) REVERT: D 248 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7337 (ttt180) REVERT: P 18 TRP cc_start: 0.6351 (t-100) cc_final: 0.5887 (t-100) REVERT: P 305 LEU cc_start: 0.9021 (tp) cc_final: 0.8783 (tt) REVERT: Q 74 LYS cc_start: 0.7264 (ttpt) cc_final: 0.7040 (tttt) REVERT: Q 155 ASN cc_start: 0.8804 (t0) cc_final: 0.8489 (t0) REVERT: Q 248 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7377 (ttt180) REVERT: R 66 LYS cc_start: 0.7998 (tptm) cc_final: 0.7772 (tptp) REVERT: R 100 ASN cc_start: 0.7719 (p0) cc_final: 0.7364 (p0) REVERT: R 115 LEU cc_start: 0.7373 (pp) cc_final: 0.6908 (pt) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.2733 time to fit residues: 69.9532 Evaluate side-chains 159 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 151 optimal weight: 0.0570 chunk 163 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 159 GLN P 72 HIS ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13509 Z= 0.190 Angle : 0.658 13.049 18520 Z= 0.300 Chirality : 0.043 0.165 1970 Planarity : 0.005 0.065 2327 Dihedral : 8.086 81.769 1858 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.94 % Favored : 87.94 % Rotamer: Outliers : 1.84 % Allowed : 11.21 % Favored : 86.95 % 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: -1.40 (0.20), residues: 1658 helix: 1.02 (0.18), residues: 802 sheet: -2.05 (0.58), residues: 74 loop : -3.10 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 400 HIS 0.005 0.001 HIS P 212 PHE 0.015 0.001 PHE C 113 TYR 0.012 0.001 TYR C 199 ARG 0.003 0.000 ARG C 231 *********************** 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 201 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: E 100 ASN cc_start: 0.7375 (p0) cc_final: 0.7143 (p0) REVERT: C 252 ASP cc_start: 0.7673 (m-30) cc_final: 0.7473 (m-30) REVERT: D 205 MET cc_start: 0.8677 (mtm) cc_final: 0.8397 (mtm) REVERT: D 248 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7409 (ttt-90) REVERT: P 18 TRP cc_start: 0.6459 (t-100) cc_final: 0.6057 (t-100) REVERT: Q 79 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6777 (mm-30) REVERT: Q 155 ASN cc_start: 0.8849 (t0) cc_final: 0.8599 (t0) REVERT: Q 156 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8497 (ttpt) REVERT: Q 205 MET cc_start: 0.8685 (mtm) cc_final: 0.8427 (mtm) REVERT: Q 248 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7409 (ttt180) REVERT: R 66 LYS cc_start: 0.7977 (tptm) cc_final: 0.7742 (tptp) REVERT: R 100 ASN cc_start: 0.7438 (p0) cc_final: 0.7137 (p0) REVERT: R 115 LEU cc_start: 0.7030 (pp) cc_final: 0.6704 (pt) outliers start: 23 outliers final: 17 residues processed: 191 average time/residue: 0.2579 time to fit residues: 70.9173 Evaluate side-chains 166 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 ASN D 204 GLN Q 28 GLN Q 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13509 Z= 0.240 Angle : 0.684 15.395 18520 Z= 0.312 Chirality : 0.044 0.175 1970 Planarity : 0.005 0.066 2327 Dihedral : 8.079 88.323 1858 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.96 % Rotamer: Outliers : 2.32 % Allowed : 13.29 % Favored : 84.39 % 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: -1.10 (0.21), residues: 1658 helix: 1.25 (0.18), residues: 796 sheet: -1.33 (0.62), residues: 76 loop : -2.97 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 126 HIS 0.006 0.001 HIS C 97 PHE 0.016 0.001 PHE C 113 TYR 0.013 0.001 TYR P 199 ARG 0.004 0.000 ARG Q 46 *********************** 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 183 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.585 Fit side-chains REVERT: E 100 ASN cc_start: 0.7411 (p0) cc_final: 0.7054 (p0) REVERT: D 205 MET cc_start: 0.8819 (mtm) cc_final: 0.8593 (mtm) REVERT: D 248 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7365 (ttt-90) REVERT: Q 155 ASN cc_start: 0.8917 (t0) cc_final: 0.8690 (t0) REVERT: Q 205 MET cc_start: 0.8831 (mtm) cc_final: 0.8607 (mtm) REVERT: Q 248 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7372 (ttt180) REVERT: R 100 ASN cc_start: 0.7381 (p0) cc_final: 0.7073 (p0) outliers start: 29 outliers final: 22 residues processed: 173 average time/residue: 0.2279 time to fit residues: 59.8656 Evaluate side-chains 163 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 0.0470 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13509 Z= 0.208 Angle : 0.640 13.849 18520 Z= 0.294 Chirality : 0.043 0.166 1970 Planarity : 0.005 0.060 2327 Dihedral : 7.937 85.909 1858 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 1.68 % Allowed : 15.93 % Favored : 82.39 % 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: -0.83 (0.21), residues: 1658 helix: 1.42 (0.18), residues: 794 sheet: -1.01 (0.64), residues: 76 loop : -2.77 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 400 HIS 0.004 0.001 HIS C 97 PHE 0.014 0.001 PHE C 113 TYR 0.011 0.001 TYR P 199 ARG 0.004 0.000 ARG Q 46 *********************** 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 187 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 100 ASN cc_start: 0.7296 (p0) cc_final: 0.6872 (p0) REVERT: C 351 THR cc_start: 0.8240 (p) cc_final: 0.7904 (p) REVERT: D 79 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7350 (mm-30) REVERT: D 205 MET cc_start: 0.8818 (mtm) cc_final: 0.8570 (mtm) REVERT: D 248 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7293 (ttt-90) REVERT: P 351 THR cc_start: 0.8354 (p) cc_final: 0.8046 (p) REVERT: Q 79 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6970 (mm-30) REVERT: Q 248 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7305 (ttt-90) REVERT: R 100 ASN cc_start: 0.7414 (p0) cc_final: 0.7128 (p0) outliers start: 21 outliers final: 20 residues processed: 181 average time/residue: 0.2393 time to fit residues: 64.2168 Evaluate side-chains 174 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL 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 C residue 32 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 154 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13509 Z= 0.234 Angle : 0.671 15.511 18520 Z= 0.300 Chirality : 0.043 0.177 1970 Planarity : 0.005 0.056 2327 Dihedral : 7.862 81.552 1858 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 2.08 % Allowed : 16.49 % Favored : 81.43 % 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: -0.75 (0.21), residues: 1658 helix: 1.38 (0.18), residues: 796 sheet: -0.71 (0.67), residues: 76 loop : -2.64 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 400 HIS 0.006 0.001 HIS C 97 PHE 0.014 0.001 PHE C 113 TYR 0.013 0.001 TYR C 399 ARG 0.009 0.000 ARG P 193 *********************** 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 180 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.449 Fit side-chains REVERT: E 100 ASN cc_start: 0.7429 (p0) cc_final: 0.6842 (p0) REVERT: C 351 THR cc_start: 0.8435 (p) cc_final: 0.8130 (p) REVERT: D 183 MET cc_start: 0.8636 (ttt) cc_final: 0.8007 (ttt) REVERT: D 205 MET cc_start: 0.8809 (mtm) cc_final: 0.8594 (mtm) REVERT: D 248 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7288 (ttt-90) REVERT: P 351 THR cc_start: 0.8435 (p) cc_final: 0.8136 (p) REVERT: Q 191 GLN cc_start: 0.8826 (tt0) cc_final: 0.8437 (tt0) REVERT: Q 248 ARG cc_start: 0.8051 (ttm170) cc_final: 0.7357 (ttt-90) REVERT: R 100 ASN cc_start: 0.7370 (p0) cc_final: 0.6791 (p0) outliers start: 26 outliers final: 22 residues processed: 172 average time/residue: 0.2450 time to fit residues: 61.9719 Evaluate side-chains 170 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.0470 chunk 91 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN R 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13509 Z= 0.193 Angle : 0.626 13.278 18520 Z= 0.287 Chirality : 0.042 0.164 1970 Planarity : 0.005 0.051 2327 Dihedral : 7.751 78.506 1858 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.49 % Favored : 89.38 % Rotamer: Outliers : 2.40 % Allowed : 16.57 % Favored : 81.02 % 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: 1.54 (0.18), residues: 792 sheet: -0.60 (0.68), residues: 76 loop : -2.59 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 400 HIS 0.004 0.001 HIS C 97 PHE 0.013 0.001 PHE P 216 TYR 0.011 0.001 TYR C 399 ARG 0.009 0.000 ARG P 193 *********************** 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 199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.442 Fit side-chains REVERT: E 100 ASN cc_start: 0.7485 (p0) cc_final: 0.6887 (p0) REVERT: C 351 THR cc_start: 0.8331 (p) cc_final: 0.8050 (p) REVERT: D 79 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7500 (mm-30) REVERT: D 183 MET cc_start: 0.8665 (ttt) cc_final: 0.8099 (ttt) REVERT: D 248 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7404 (ttt-90) REVERT: P 351 THR cc_start: 0.8336 (p) cc_final: 0.8065 (p) REVERT: Q 183 MET cc_start: 0.8504 (ttt) cc_final: 0.7965 (ttt) REVERT: Q 191 GLN cc_start: 0.8817 (tt0) cc_final: 0.8454 (tt0) REVERT: Q 248 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7311 (ttt-90) REVERT: R 100 ASN cc_start: 0.7431 (p0) cc_final: 0.6839 (p0) outliers start: 30 outliers final: 25 residues processed: 188 average time/residue: 0.2340 time to fit residues: 65.8599 Evaluate side-chains 179 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 101 optimal weight: 0.6980 chunk 109 optimal weight: 0.0170 chunk 79 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13509 Z= 0.170 Angle : 0.609 12.129 18520 Z= 0.279 Chirality : 0.041 0.169 1970 Planarity : 0.005 0.049 2327 Dihedral : 7.652 78.668 1858 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.07 % Favored : 89.81 % Rotamer: Outliers : 2.40 % Allowed : 17.05 % Favored : 80.54 % 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: -0.49 (0.21), residues: 1658 helix: 1.63 (0.18), residues: 790 sheet: -0.55 (0.67), residues: 76 loop : -2.52 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 18 HIS 0.003 0.001 HIS P 111 PHE 0.013 0.001 PHE C 216 TYR 0.010 0.001 TYR C 399 ARG 0.003 0.000 ARG Q 46 *********************** 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 189 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.499 Fit side-chains REVERT: E 100 ASN cc_start: 0.7282 (p0) cc_final: 0.6920 (p0) REVERT: C 351 THR cc_start: 0.8235 (p) cc_final: 0.7993 (p) REVERT: D 79 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7324 (mm-30) REVERT: D 183 MET cc_start: 0.8494 (ttt) cc_final: 0.8001 (ttt) REVERT: D 248 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7323 (ttt-90) REVERT: P 351 THR cc_start: 0.8334 (p) cc_final: 0.8105 (p) REVERT: Q 183 MET cc_start: 0.8543 (ttt) cc_final: 0.8006 (ttt) REVERT: Q 191 GLN cc_start: 0.8791 (tt0) cc_final: 0.8389 (tt0) REVERT: Q 248 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7362 (ttt-90) REVERT: R 100 ASN cc_start: 0.7448 (p0) cc_final: 0.6846 (p0) outliers start: 30 outliers final: 23 residues processed: 181 average time/residue: 0.2279 time to fit residues: 62.2254 Evaluate side-chains 171 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL 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: 9.9990 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13509 Z= 0.198 Angle : 0.635 14.022 18520 Z= 0.285 Chirality : 0.042 0.164 1970 Planarity : 0.005 0.048 2327 Dihedral : 7.628 76.921 1858 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 2.16 % Allowed : 17.85 % Favored : 79.98 % 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: -0.45 (0.21), residues: 1658 helix: 1.60 (0.19), residues: 792 sheet: -0.42 (0.67), residues: 76 loop : -2.45 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 18 HIS 0.004 0.001 HIS C 97 PHE 0.012 0.001 PHE C 113 TYR 0.012 0.001 TYR C 399 ARG 0.003 0.000 ARG Q 46 *********************** 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 176 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.427 Fit side-chains REVERT: E 100 ASN cc_start: 0.7375 (p0) cc_final: 0.6707 (p0) REVERT: E 127 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5918 (tt) REVERT: C 351 THR cc_start: 0.8217 (p) cc_final: 0.7986 (p) REVERT: D 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7493 (mm-30) REVERT: D 183 MET cc_start: 0.8730 (ttt) cc_final: 0.8117 (ttt) REVERT: D 248 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7341 (ttt-90) REVERT: P 351 THR cc_start: 0.8201 (p) cc_final: 0.7985 (p) REVERT: Q 183 MET cc_start: 0.8718 (ttt) cc_final: 0.8086 (ttt) REVERT: Q 191 GLN cc_start: 0.8720 (tt0) cc_final: 0.8361 (tt0) REVERT: Q 248 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7349 (ttt-90) REVERT: R 100 ASN cc_start: 0.7490 (p0) cc_final: 0.6859 (p0) REVERT: R 115 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7115 (pt) outliers start: 27 outliers final: 23 residues processed: 170 average time/residue: 0.2331 time to fit residues: 59.3113 Evaluate side-chains 173 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL 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: 0.9990 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 165 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 ASN C 99 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 ASN P 222 ASN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13509 Z= 0.309 Angle : 0.715 16.427 18520 Z= 0.319 Chirality : 0.044 0.183 1970 Planarity : 0.005 0.048 2327 Dihedral : 7.767 76.045 1858 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.88 % Favored : 88.00 % Rotamer: Outliers : 2.08 % Allowed : 17.69 % Favored : 80.22 % 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: -0.66 (0.21), residues: 1658 helix: 1.31 (0.18), residues: 798 sheet: -0.38 (0.68), residues: 76 loop : -2.46 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 18 HIS 0.008 0.001 HIS C 97 PHE 0.016 0.002 PHE C 113 TYR 0.017 0.001 TYR C 199 ARG 0.005 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 165 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.448 Fit side-chains REVERT: E 100 ASN cc_start: 0.7436 (p0) cc_final: 0.6771 (p0) REVERT: C 351 THR cc_start: 0.8600 (p) cc_final: 0.8367 (p) REVERT: D 183 MET cc_start: 0.8950 (ttt) cc_final: 0.8069 (ttt) REVERT: D 248 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7276 (ttt-90) REVERT: P 351 THR cc_start: 0.8599 (p) cc_final: 0.8379 (p) REVERT: Q 19 ASP cc_start: 0.7420 (t0) cc_final: 0.7162 (t70) REVERT: Q 183 MET cc_start: 0.8903 (ttt) cc_final: 0.8060 (ttt) REVERT: Q 191 GLN cc_start: 0.8767 (tt0) cc_final: 0.8423 (tt0) REVERT: Q 248 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7282 (ttt-90) REVERT: R 100 ASN cc_start: 0.7570 (p0) cc_final: 0.7041 (p0) REVERT: R 115 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7192 (pt) outliers start: 26 outliers final: 23 residues processed: 159 average time/residue: 0.2397 time to fit residues: 57.0369 Evaluate side-chains 161 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 131 optimal weight: 0.0870 chunk 55 optimal weight: 0.0000 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131298 restraints weight = 15626.059| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.63 r_work: 0.2999 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13509 Z= 0.169 Angle : 0.605 11.299 18520 Z= 0.281 Chirality : 0.041 0.163 1970 Planarity : 0.005 0.047 2327 Dihedral : 7.684 78.631 1858 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.83 % Favored : 90.05 % Rotamer: Outliers : 1.76 % Allowed : 18.01 % Favored : 80.22 % 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: -0.43 (0.21), residues: 1658 helix: 1.58 (0.18), residues: 790 sheet: 0.43 (0.85), residues: 52 loop : -2.40 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 18 HIS 0.003 0.001 HIS P 212 PHE 0.012 0.001 PHE C 113 TYR 0.010 0.001 TYR C 399 ARG 0.006 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.07 seconds wall clock time: 51 minutes 0.02 seconds (3060.02 seconds total)