Starting phenix.real_space_refine on Sun Apr 7 17:32:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jru_36606/04_2024/8jru_36606_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= 0.005 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3992 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 17 5.16 5 C 4571 2.51 5 N 1199 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 406": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7120 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2008 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 4, 'TRANS': 262} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TPO:plan-1': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2576 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 28, 'TRANS': 317} Chain breaks: 3 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 891 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.30, per 1000 atoms: 0.60 Number of scatterers: 7120 At special positions: 0 Unit cell: (73.899, 92.106, 154.224, 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) S 17 16.00 P 8 15.00 O 1325 8.00 N 1199 7.00 C 4571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 14 sheets defined 23.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'R' and resid 140 through 164 removed outlier: 3.506A pdb=" N MET R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR R 145 " --> pdb=" O PHE R 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.851A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 253 removed outlier: 4.172A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 272 removed outlier: 4.254A pdb=" N SER R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 284 removed outlier: 3.526A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 308 through 334 removed outlier: 3.709A pdb=" N GLN R 327 " --> pdb=" O VAL R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 366 removed outlier: 3.517A pdb=" N SER R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR R 353 " --> pdb=" O LYS R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix removed outlier: 3.588A pdb=" N GLU R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 363 " --> pdb=" O GLY R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 400 removed outlier: 3.503A pdb=" N ASP R 385 " --> pdb=" O LYS R 381 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE R 387 " --> pdb=" O PHE R 383 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU R 388 " --> pdb=" O PHE R 384 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER R 389 " --> pdb=" O ASP R 385 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER R 390 " --> pdb=" O LEU R 386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 425 removed outlier: 3.758A pdb=" N TRP R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.645A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.952A pdb=" N GLU A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 163 through 168 removed outlier: 3.529A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 57 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 80 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.764A pdb=" N ALA A 184 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 201 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 199 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 198 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 221 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 266 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.481A pdb=" N THR A 350 " --> pdb=" O TYR A 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 342 through 349 removed outlier: 4.255A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 258 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.574A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.803A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.579A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.731A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.662A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.631A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 72 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 49 through 51 250 hydrogen bonds defined for protein. 717 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: 1.90 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1189 1.32 - 1.45: 1971 1.45 - 1.57: 4072 1.57 - 1.69: 23 1.69 - 1.81: 26 Bond restraints: 7281 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O1P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O2P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C2C PIO A 701 " pdb=" O2C PIO A 701 " ideal model delta sigma weight residual 1.399 1.472 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 PIO A 701 " pdb=" O1 PIO A 701 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 7276 not shown) Histogram of bond angle deviations from ideal: 100.55 - 109.10: 530 109.10 - 117.66: 4974 117.66 - 126.22: 4320 126.22 - 134.78: 126 134.78 - 143.34: 1 Bond angle restraints: 9951 Sorted by residual: angle pdb=" C1 PIO A 701 " pdb=" O1 PIO A 701 " pdb=" P1 PIO A 701 " ideal model delta sigma weight residual 118.46 143.34 -24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" C1A PIO A 701 " pdb=" O2C PIO A 701 " pdb=" C2C PIO A 701 " ideal model delta sigma weight residual 113.89 127.52 -13.63 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C1A PIO A 701 " pdb=" C2A PIO A 701 " pdb=" C3A PIO A 701 " ideal model delta sigma weight residual 109.47 122.41 -12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB TPO R1360 " pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 119.31 106.98 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 9946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 3876 21.22 - 42.45: 315 42.45 - 63.67: 34 63.67 - 84.90: 8 84.90 - 106.12: 5 Dihedral angle restraints: 4238 sinusoidal: 1490 harmonic: 2748 Sorted by residual: dihedral pdb=" CA LEU A 243 " pdb=" C LEU A 243 " pdb=" N PHE A 244 " pdb=" CA PHE A 244 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C3 PIO A 701 " pdb=" C4 PIO A 701 " pdb=" C5 PIO A 701 " pdb=" C6 PIO A 701 " ideal model delta sinusoidal sigma weight residual 52.96 -53.16 106.12 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" CG ARG R 412 " pdb=" CD ARG R 412 " pdb=" NE ARG R 412 " pdb=" CZ ARG R 412 " ideal model delta sinusoidal sigma weight residual 90.00 131.84 -41.84 2 1.50e+01 4.44e-03 9.49e+00 ... (remaining 4235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1085 0.084 - 0.168: 79 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1165 Sorted by residual: chirality pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" C3C PIO A 701 " pdb=" O2C PIO A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.09 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CB VAL R 292 " pdb=" CA VAL R 292 " pdb=" CG1 VAL R 292 " pdb=" CG2 VAL R 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CG LEU B 102 " pdb=" CB LEU B 102 " pdb=" CD1 LEU B 102 " pdb=" CD2 LEU B 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1162 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 76 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASN B 76 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN B 76 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 77 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C THR B 56 " -0.031 2.00e-02 2.50e+03 pdb=" O THR B 56 " 0.012 2.00e-02 2.50e+03 pdb=" N THR B 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 44 " -0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 45 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.024 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1216 2.77 - 3.30: 6516 3.30 - 3.84: 11282 3.84 - 4.37: 12129 4.37 - 4.90: 22131 Nonbonded interactions: 53274 Sorted by model distance: nonbonded pdb=" OH TYR A 238 " pdb=" OE2 GLU A 346 " model vdw 2.241 2.440 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.269 2.440 nonbonded pdb=" OD2 ASP A 204 " pdb=" OG SER A 215 " model vdw 2.273 2.440 nonbonded pdb=" N GLU R 406 " pdb=" OE1 GLU R 406 " model vdw 2.304 2.520 nonbonded pdb=" N VAL H 5 " pdb=" O SER H 28 " model vdw 2.332 2.520 ... (remaining 53269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.860 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.004 0.107 7281 Z= 0.240 Angle : 0.709 24.877 9951 Z= 0.300 Chirality : 0.041 0.420 1165 Planarity : 0.004 0.043 1244 Dihedral : 15.228 106.121 2468 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.29 % Allowed : 12.86 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 912 helix: 1.45 (0.37), residues: 199 sheet: 1.00 (0.34), residues: 273 loop : -0.76 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 295 HIS 0.008 0.000 HIS R 361 PHE 0.016 0.001 PHE A 244 TYR 0.008 0.001 TYR B 79 ARG 0.006 0.000 ARG R 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.809 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1599 time to fit residues: 26.2193 Evaluate side-chains 110 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.0000 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 189 GLN A 219 HIS ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN B 44 HIS B 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7281 Z= 0.345 Angle : 0.657 7.988 9951 Z= 0.330 Chirality : 0.045 0.218 1165 Planarity : 0.005 0.038 1244 Dihedral : 8.220 96.717 1053 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.86 % Allowed : 14.57 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 912 helix: 1.35 (0.36), residues: 205 sheet: 0.34 (0.32), residues: 302 loop : -0.92 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.006 0.001 HIS H 38 PHE 0.019 0.002 PHE R 278 TYR 0.018 0.002 TYR H 107 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.851 Fit side-chains REVERT: H 106 TRP cc_start: 0.5837 (OUTLIER) cc_final: 0.3948 (t-100) REVERT: L 91 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8418 (pp30) REVERT: B 34 MET cc_start: 0.7990 (mmt) cc_final: 0.7461 (mmt) REVERT: B 79 TYR cc_start: 0.7456 (m-10) cc_final: 0.7221 (m-80) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1773 time to fit residues: 29.8143 Evaluate side-chains 108 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 219 HIS ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7281 Z= 0.242 Angle : 0.582 7.910 9951 Z= 0.290 Chirality : 0.042 0.165 1165 Planarity : 0.004 0.041 1244 Dihedral : 7.885 92.762 1049 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 4.14 % Allowed : 15.57 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 912 helix: 1.47 (0.37), residues: 205 sheet: 0.28 (0.32), residues: 299 loop : -0.94 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 305 HIS 0.008 0.001 HIS R 361 PHE 0.014 0.001 PHE R 387 TYR 0.017 0.001 TYR L 92 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.766 Fit side-chains REVERT: H 106 TRP cc_start: 0.6058 (OUTLIER) cc_final: 0.4120 (t-100) outliers start: 29 outliers final: 21 residues processed: 120 average time/residue: 0.1334 time to fit residues: 22.5920 Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 219 HIS A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7281 Z= 0.301 Angle : 0.611 8.444 9951 Z= 0.307 Chirality : 0.043 0.164 1165 Planarity : 0.004 0.043 1244 Dihedral : 7.906 91.028 1049 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.76 % Rotamer: Outliers : 5.00 % Allowed : 15.71 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.29), residues: 912 helix: 1.51 (0.37), residues: 203 sheet: 0.01 (0.32), residues: 300 loop : -1.04 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.008 0.001 HIS R 361 PHE 0.019 0.002 PHE A 244 TYR 0.019 0.001 TYR L 92 ARG 0.004 0.000 ARG R 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.807 Fit side-chains REVERT: R 343 TYR cc_start: 0.7508 (t80) cc_final: 0.7158 (t80) REVERT: A 192 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4914 (ppp) REVERT: H 106 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.4027 (t-100) outliers start: 35 outliers final: 20 residues processed: 123 average time/residue: 0.1736 time to fit residues: 29.9065 Evaluate side-chains 113 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7281 Z= 0.196 Angle : 0.571 8.930 9951 Z= 0.281 Chirality : 0.042 0.163 1165 Planarity : 0.004 0.041 1244 Dihedral : 7.750 89.984 1049 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.58 % Favored : 93.31 % Rotamer: Outliers : 4.14 % Allowed : 17.43 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 912 helix: 1.58 (0.38), residues: 204 sheet: 0.08 (0.32), residues: 300 loop : -1.02 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 241 HIS 0.008 0.001 HIS R 361 PHE 0.015 0.001 PHE R 387 TYR 0.020 0.001 TYR R 267 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7396 (m-80) cc_final: 0.7035 (m-80) REVERT: R 343 TYR cc_start: 0.7567 (t80) cc_final: 0.7272 (t80) REVERT: A 169 GLU cc_start: 0.7528 (mp0) cc_final: 0.7275 (mp0) REVERT: A 192 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.4925 (ppp) outliers start: 29 outliers final: 19 residues processed: 122 average time/residue: 0.1912 time to fit residues: 31.7400 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 362 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS R 392 GLN A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7281 Z= 0.197 Angle : 0.573 9.613 9951 Z= 0.280 Chirality : 0.041 0.159 1165 Planarity : 0.004 0.047 1244 Dihedral : 7.666 89.498 1049 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 4.14 % Allowed : 18.29 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 912 helix: 1.65 (0.38), residues: 203 sheet: 0.06 (0.32), residues: 300 loop : -0.92 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 241 HIS 0.009 0.001 HIS R 361 PHE 0.016 0.001 PHE R 230 TYR 0.015 0.001 TYR R 267 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7480 (m-80) cc_final: 0.7057 (m-80) REVERT: A 169 GLU cc_start: 0.7528 (mp0) cc_final: 0.7255 (mp0) REVERT: H 106 TRP cc_start: 0.6189 (OUTLIER) cc_final: 0.4039 (t60) outliers start: 29 outliers final: 21 residues processed: 119 average time/residue: 0.1791 time to fit residues: 29.3050 Evaluate side-chains 115 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS R 392 GLN A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN B 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7281 Z= 0.161 Angle : 0.576 10.195 9951 Z= 0.278 Chirality : 0.041 0.161 1165 Planarity : 0.004 0.056 1244 Dihedral : 7.573 89.103 1049 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 3.86 % Allowed : 19.00 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.29), residues: 912 helix: 1.68 (0.38), residues: 203 sheet: 0.11 (0.32), residues: 298 loop : -0.95 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 241 HIS 0.009 0.001 HIS R 361 PHE 0.012 0.001 PHE R 230 TYR 0.018 0.001 TYR R 233 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7468 (m-10) cc_final: 0.7003 (m-80) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.1570 time to fit residues: 25.7961 Evaluate side-chains 112 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS R 392 GLN A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7281 Z= 0.178 Angle : 0.582 10.795 9951 Z= 0.282 Chirality : 0.041 0.159 1165 Planarity : 0.004 0.041 1244 Dihedral : 7.499 88.396 1049 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 3.86 % Allowed : 19.57 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 912 helix: 1.78 (0.38), residues: 201 sheet: 0.09 (0.32), residues: 298 loop : -0.96 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 241 HIS 0.011 0.001 HIS R 361 PHE 0.011 0.001 PHE R 230 TYR 0.019 0.001 TYR R 233 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7478 (m-10) cc_final: 0.7068 (m-80) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.1564 time to fit residues: 26.3267 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7281 Z= 0.213 Angle : 0.605 10.568 9951 Z= 0.295 Chirality : 0.042 0.156 1165 Planarity : 0.004 0.042 1244 Dihedral : 7.528 87.382 1049 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 4.00 % Allowed : 19.86 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.29), residues: 912 helix: 1.67 (0.38), residues: 205 sheet: 0.05 (0.33), residues: 293 loop : -1.08 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 305 HIS 0.011 0.001 HIS R 361 PHE 0.012 0.001 PHE R 387 TYR 0.020 0.001 TYR R 233 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7434 (m-10) cc_final: 0.7004 (m-80) REVERT: R 304 TRP cc_start: 0.5424 (t60) cc_final: 0.4243 (m100) outliers start: 28 outliers final: 22 residues processed: 115 average time/residue: 0.1623 time to fit residues: 26.7376 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7281 Z= 0.285 Angle : 0.645 10.400 9951 Z= 0.319 Chirality : 0.043 0.158 1165 Planarity : 0.004 0.037 1244 Dihedral : 7.683 86.148 1049 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 3.86 % Allowed : 20.29 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 912 helix: 1.51 (0.37), residues: 204 sheet: -0.07 (0.32), residues: 303 loop : -1.06 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 305 HIS 0.011 0.001 HIS R 361 PHE 0.016 0.001 PHE R 230 TYR 0.028 0.002 TYR R 233 ARG 0.004 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7446 (m-10) cc_final: 0.7050 (m-80) outliers start: 27 outliers final: 23 residues processed: 113 average time/residue: 0.1740 time to fit residues: 27.3730 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS A 299 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096590 restraints weight = 13150.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098182 restraints weight = 8795.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098964 restraints weight = 7313.887| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7281 Z= 0.162 Angle : 0.602 10.655 9951 Z= 0.295 Chirality : 0.042 0.160 1165 Planarity : 0.004 0.039 1244 Dihedral : 7.537 86.512 1049 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.75 % Rotamer: Outliers : 3.57 % Allowed : 20.14 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 912 helix: 1.59 (0.38), residues: 206 sheet: -0.07 (0.32), residues: 301 loop : -0.97 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 305 HIS 0.010 0.001 HIS R 361 PHE 0.014 0.001 PHE R 230 TYR 0.030 0.001 TYR R 233 ARG 0.010 0.000 ARG R 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.03 seconds wall clock time: 34 minutes 35.51 seconds (2075.51 seconds total)