Starting phenix.real_space_refine on Sat Apr 6 05:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv8_36671/04_2024/8jv8_36671_updated.pdb" } resolution = 3.34 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= 0.001 sd= 0.038 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 P 3 5.49 5 S 45 5.16 5 C 4638 2.51 5 N 1221 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7245 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.62 Number of scatterers: 7245 At special positions: 0 Unit cell: (87.98, 85.49, 108.73, 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 45 16.00 P 3 15.00 O 1338 8.00 N 1221 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.02 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.01 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 187 " " NAG A 402 " - " ASN A 213 " " NAG B 401 " - " ASN B 187 " " NAG B 402 " - " ASN B 213 " " NAG C 401 " - " ASN C 187 " " NAG C 402 " - " ASN C 213 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 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: 18 helices and 21 sheets defined 18.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.969A pdb=" N PHE A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.862A pdb=" N GLU A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.664A pdb=" N THR A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 330 through 349 removed outlier: 4.114A pdb=" N SER A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 removed outlier: 4.100A pdb=" N PHE B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.853A pdb=" N GLU B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.745A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 330 through 349 removed outlier: 4.316A pdb=" N SER B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 48 removed outlier: 4.021A pdb=" N PHE C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.868A pdb=" N GLU C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.651A pdb=" N THR C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 330 through 349 removed outlier: 4.094A pdb=" N SER C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 348 " --> pdb=" O PHE C 344 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 58 through 66 removed outlier: 3.678A pdb=" N THR A 189 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 203 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 69 through 77 Processing sheet with id= C, first strand: chain 'A' and resid 115 through 119 Processing sheet with id= D, first strand: chain 'A' and resid 316 through 326 removed outlier: 3.556A pdb=" N GLY A 326 " --> pdb=" O CYS A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 292 through 295 Processing sheet with id= F, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= G, first strand: chain 'A' and resid 152 through 156 removed outlier: 6.464A pdb=" N LEU A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 66 removed outlier: 3.582A pdb=" N THR B 189 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR B 203 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 69 through 77 Processing sheet with id= J, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 152 through 154 Processing sheet with id= L, first strand: chain 'B' and resid 271 through 277 removed outlier: 7.490A pdb=" N MET B 252 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG B 316 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE B 254 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 318 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE B 256 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 320 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TRP B 258 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE B 322 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N CYS B 260 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 324 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 315 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 105 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE B 317 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 103 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 319 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B 101 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 292 through 295 Processing sheet with id= N, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= O, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.667A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR C 203 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 69 through 77 Processing sheet with id= Q, first strand: chain 'C' and resid 115 through 119 Processing sheet with id= R, first strand: chain 'C' and resid 152 through 154 Processing sheet with id= S, first strand: chain 'C' and resid 316 through 326 removed outlier: 3.515A pdb=" N GLY C 326 " --> pdb=" O CYS C 260 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 292 through 295 Processing sheet with id= U, first strand: chain 'C' and resid 298 through 301 249 hydrogen bonds defined for protein. 675 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: 1.91 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.43: 3287 1.43 - 1.69: 4098 1.69 - 1.95: 51 1.95 - 2.20: 0 2.20 - 2.46: 1 Bond restraints: 7437 Sorted by residual: bond pdb=" CB PRO C 56 " pdb=" CG PRO C 56 " ideal model delta sigma weight residual 1.492 2.462 -0.970 5.00e-02 4.00e+02 3.76e+02 bond pdb=" C GLU C 55 " pdb=" N PRO C 56 " ideal model delta sigma weight residual 1.334 1.530 -0.197 2.34e-02 1.83e+03 7.06e+01 bond pdb=" CA PRO C 56 " pdb=" CB PRO C 56 " ideal model delta sigma weight residual 1.533 1.457 0.076 1.42e-02 4.96e+03 2.89e+01 bond pdb=" CAQ 20V C 403 " pdb=" CBB 20V C 403 " ideal model delta sigma weight residual 1.394 1.500 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CAQ 20V B 403 " pdb=" CBB 20V B 403 " ideal model delta sigma weight residual 1.394 1.500 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 7432 not shown) Histogram of bond angle deviations from ideal: 54.92 - 72.68: 1 72.68 - 90.43: 1 90.43 - 108.19: 486 108.19 - 125.94: 9565 125.94 - 143.70: 123 Bond angle restraints: 10176 Sorted by residual: angle pdb=" CB PRO C 56 " pdb=" CG PRO C 56 " pdb=" CD PRO C 56 " ideal model delta sigma weight residual 106.10 54.92 51.18 3.20e+00 9.77e-02 2.56e+02 angle pdb=" CAQ 20V A 403 " pdb=" CBG 20V A 403 " pdb=" SBM 20V A 403 " ideal model delta sigma weight residual 80.58 117.97 -37.39 3.00e+00 1.11e-01 1.55e+02 angle pdb=" CAQ 20V B 403 " pdb=" CBG 20V B 403 " pdb=" SBM 20V B 403 " ideal model delta sigma weight residual 80.58 117.84 -37.26 3.00e+00 1.11e-01 1.54e+02 angle pdb=" CAQ 20V C 403 " pdb=" CBG 20V C 403 " pdb=" SBM 20V C 403 " ideal model delta sigma weight residual 80.58 117.63 -37.05 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CA PRO C 56 " pdb=" N PRO C 56 " pdb=" CD PRO C 56 " ideal model delta sigma weight residual 112.00 97.86 14.14 1.40e+00 5.10e-01 1.02e+02 ... (remaining 10171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.57: 4027 27.57 - 55.14: 277 55.14 - 82.72: 27 82.72 - 110.29: 4 110.29 - 137.86: 3 Dihedral angle restraints: 4338 sinusoidal: 1569 harmonic: 2769 Sorted by residual: dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual 93.00 -176.63 -90.37 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 175.65 -82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual 93.00 172.59 -79.59 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 941 0.082 - 0.165: 174 0.165 - 0.247: 12 0.247 - 0.329: 0 0.329 - 0.411: 1 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PRO C 56 " pdb=" N PRO C 56 " pdb=" C PRO C 56 " pdb=" CB PRO C 56 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLU C 55 " pdb=" N GLU C 55 " pdb=" C GLU C 55 " pdb=" CB GLU C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL B 212 " pdb=" N VAL B 212 " pdb=" C VAL B 212 " pdb=" CB VAL B 212 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1125 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 55 " -0.107 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 56 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 56 " -0.029 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C PRO C 56 " 0.110 2.00e-02 2.50e+03 pdb=" O PRO C 56 " -0.043 2.00e-02 2.50e+03 pdb=" N LEU C 57 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 232 " -0.031 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C GLY C 232 " 0.110 2.00e-02 2.50e+03 pdb=" O GLY C 232 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP C 233 " -0.037 2.00e-02 2.50e+03 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 70 2.57 - 3.15: 5944 3.15 - 3.74: 10707 3.74 - 4.32: 14074 4.32 - 4.90: 23548 Nonbonded interactions: 54343 Sorted by model distance: nonbonded pdb=" OH TYR B 343 " pdb=" O ALA C 334 " model vdw 1.988 2.440 nonbonded pdb=" NH2 ARG A 277 " pdb=" OD2 ASP A 279 " model vdw 2.133 2.520 nonbonded pdb=" O ALA A 334 " pdb=" OH TYR C 343 " model vdw 2.147 2.440 nonbonded pdb=" NH2 ARG B 277 " pdb=" OD2 ASP B 279 " model vdw 2.150 2.520 nonbonded pdb=" OH TYR A 343 " pdb=" O ALA B 334 " model vdw 2.230 2.440 ... (remaining 54338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.820 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.090 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.015 0.970 7437 Z= 1.190 Angle : 1.474 51.175 10176 Z= 0.723 Chirality : 0.059 0.411 1128 Planarity : 0.011 0.164 1302 Dihedral : 17.534 137.860 2523 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 3.55 % Allowed : 31.48 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.23 (0.27), residues: 954 helix: -0.10 (0.43), residues: 135 sheet: -0.47 (0.28), residues: 342 loop : -1.23 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP C 258 HIS 0.045 0.004 HIS C 34 PHE 0.035 0.004 PHE C 313 TYR 0.089 0.004 TYR C 336 ARG 0.008 0.002 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.863 Fit side-chains REVERT: A 195 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 267 HIS cc_start: 0.8141 (t-90) cc_final: 0.7766 (t70) REVERT: B 40 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: B 195 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7550 (t0) REVERT: B 288 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6753 (p90) REVERT: C 195 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7651 (t0) outliers start: 23 outliers final: 11 residues processed: 127 average time/residue: 0.1530 time to fit residues: 27.8935 Evaluate side-chains 108 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 0.0870 chunk 45 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7437 Z= 0.260 Angle : 0.699 14.214 10176 Z= 0.337 Chirality : 0.045 0.130 1128 Planarity : 0.005 0.086 1302 Dihedral : 11.265 133.937 1206 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.17 % Allowed : 28.55 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.57 (0.28), residues: 954 helix: 1.53 (0.46), residues: 132 sheet: -0.34 (0.29), residues: 324 loop : -0.90 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS C 34 PHE 0.016 0.002 PHE A 242 TYR 0.013 0.001 TYR A 93 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 0.958 Fit side-chains REVERT: A 201 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6746 (m-70) REVERT: B 195 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7726 (t0) REVERT: B 201 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6792 (m-70) REVERT: C 201 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6454 (m-70) REVERT: C 332 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6465 (tm-30) outliers start: 40 outliers final: 24 residues processed: 127 average time/residue: 0.1442 time to fit residues: 26.6973 Evaluate side-chains 116 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7437 Z= 0.340 Angle : 0.730 16.029 10176 Z= 0.359 Chirality : 0.046 0.162 1128 Planarity : 0.004 0.061 1302 Dihedral : 10.796 128.248 1183 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 7.56 % Allowed : 28.40 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.59 (0.28), residues: 954 helix: 1.32 (0.41), residues: 150 sheet: -0.27 (0.29), residues: 324 loop : -1.00 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 258 HIS 0.003 0.001 HIS A 34 PHE 0.021 0.002 PHE C 242 TYR 0.019 0.002 TYR C 291 ARG 0.004 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 92 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7658 (mmm160) REVERT: A 201 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6979 (m-70) REVERT: B 178 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7755 (mmm160) REVERT: B 251 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7371 (mt) REVERT: C 201 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.7044 (m-70) REVERT: C 332 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6592 (tm-30) outliers start: 49 outliers final: 32 residues processed: 135 average time/residue: 0.1693 time to fit residues: 32.6695 Evaluate side-chains 118 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7437 Z= 0.172 Angle : 0.632 12.463 10176 Z= 0.304 Chirality : 0.044 0.143 1128 Planarity : 0.003 0.047 1302 Dihedral : 10.217 127.816 1175 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.48 % Allowed : 32.72 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.34 (0.29), residues: 954 helix: 2.10 (0.48), residues: 123 sheet: -0.41 (0.28), residues: 339 loop : -0.63 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.003 0.001 HIS A 34 PHE 0.025 0.001 PHE B 38 TYR 0.016 0.001 TYR A 93 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6822 (m-70) REVERT: A 327 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7983 (mtpp) REVERT: C 178 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7682 (mmm160) REVERT: C 201 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6777 (m-70) REVERT: C 252 MET cc_start: 0.7937 (tpt) cc_final: 0.7711 (tpt) REVERT: C 327 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7966 (mtpp) outliers start: 29 outliers final: 19 residues processed: 131 average time/residue: 0.1707 time to fit residues: 31.8711 Evaluate side-chains 122 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.0010 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7437 Z= 0.150 Angle : 0.622 13.138 10176 Z= 0.294 Chirality : 0.044 0.142 1128 Planarity : 0.003 0.037 1302 Dihedral : 9.933 124.503 1173 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.94 % Allowed : 33.02 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.19 (0.29), residues: 954 helix: 2.14 (0.48), residues: 126 sheet: -0.18 (0.28), residues: 333 loop : -0.64 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.002 0.000 HIS A 34 PHE 0.025 0.001 PHE B 38 TYR 0.015 0.001 TYR A 93 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: A 327 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7936 (mtpp) REVERT: C 178 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7582 (mmm160) REVERT: C 201 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6816 (m-70) REVERT: C 327 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7956 (mtpp) outliers start: 32 outliers final: 22 residues processed: 136 average time/residue: 0.1756 time to fit residues: 34.0293 Evaluate side-chains 130 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7437 Z= 0.373 Angle : 0.737 14.270 10176 Z= 0.360 Chirality : 0.047 0.157 1128 Planarity : 0.004 0.039 1302 Dihedral : 10.145 122.879 1173 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 8.49 % Allowed : 30.86 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.29), residues: 954 helix: 1.59 (0.42), residues: 150 sheet: -0.24 (0.29), residues: 324 loop : -0.92 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 258 HIS 0.004 0.001 HIS C 34 PHE 0.026 0.002 PHE B 38 TYR 0.019 0.002 TYR C 291 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 92 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7580 (mmm160) REVERT: A 201 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7079 (m-70) REVERT: A 252 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7493 (tpt) REVERT: A 327 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7956 (mtpp) REVERT: C 178 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7706 (mmm160) REVERT: C 201 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7137 (m-70) REVERT: C 327 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8126 (mtpp) REVERT: C 332 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6608 (tm-30) outliers start: 55 outliers final: 36 residues processed: 137 average time/residue: 0.1665 time to fit residues: 32.1119 Evaluate side-chains 127 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 83 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7437 Z= 0.198 Angle : 0.658 13.063 10176 Z= 0.313 Chirality : 0.045 0.144 1128 Planarity : 0.003 0.035 1302 Dihedral : 9.944 123.154 1173 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.02 % Allowed : 34.26 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.28 (0.29), residues: 954 helix: 2.22 (0.48), residues: 123 sheet: -0.19 (0.29), residues: 324 loop : -0.76 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.003 0.001 HIS C 34 PHE 0.027 0.002 PHE B 38 TYR 0.015 0.001 TYR A 93 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 96 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6988 (m-70) REVERT: A 327 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7999 (mtpp) REVERT: B 178 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7710 (mmm160) REVERT: C 178 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7695 (mmm160) REVERT: C 201 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.7084 (m-70) REVERT: C 327 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8118 (mtpp) outliers start: 39 outliers final: 28 residues processed: 131 average time/residue: 0.1646 time to fit residues: 30.4155 Evaluate side-chains 128 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7437 Z= 0.184 Angle : 0.646 13.208 10176 Z= 0.306 Chirality : 0.045 0.139 1128 Planarity : 0.003 0.032 1302 Dihedral : 9.735 120.407 1173 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.48 % Allowed : 33.18 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 954 helix: 2.24 (0.48), residues: 123 sheet: -0.32 (0.28), residues: 339 loop : -0.63 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.002 0.001 HIS C 34 PHE 0.027 0.001 PHE B 38 TYR 0.015 0.001 TYR A 93 ARG 0.002 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7022 (m-70) REVERT: A 327 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: B 178 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7513 (mmm160) REVERT: C 178 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7674 (mmm160) REVERT: C 201 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7077 (m-70) REVERT: C 327 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: C 332 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6399 (tm-30) outliers start: 42 outliers final: 33 residues processed: 135 average time/residue: 0.1626 time to fit residues: 30.8438 Evaluate side-chains 134 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.7688 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7437 Z= 0.300 Angle : 0.700 13.905 10176 Z= 0.340 Chirality : 0.046 0.150 1128 Planarity : 0.003 0.035 1302 Dihedral : 9.837 118.952 1173 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 7.25 % Allowed : 32.56 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.28 (0.29), residues: 954 helix: 1.93 (0.44), residues: 141 sheet: -0.22 (0.29), residues: 324 loop : -0.74 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 258 HIS 0.003 0.001 HIS C 34 PHE 0.027 0.002 PHE B 38 TYR 0.013 0.002 TYR A 295 ARG 0.003 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 93 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7536 (mmm160) REVERT: A 201 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7059 (m-70) REVERT: A 327 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: B 178 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7645 (mmm160) REVERT: B 288 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.6569 (p90) REVERT: C 178 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7690 (mmm160) REVERT: C 201 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.7126 (m-70) REVERT: C 327 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: C 332 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6526 (tm-30) outliers start: 47 outliers final: 34 residues processed: 135 average time/residue: 0.1676 time to fit residues: 31.5243 Evaluate side-chains 130 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 87 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7437 Z= 0.150 Angle : 0.653 12.586 10176 Z= 0.309 Chirality : 0.045 0.158 1128 Planarity : 0.003 0.033 1302 Dihedral : 9.626 118.103 1173 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.17 % Allowed : 35.49 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 954 helix: 2.29 (0.49), residues: 117 sheet: -0.12 (0.29), residues: 324 loop : -0.65 (0.31), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS B 219 PHE 0.027 0.001 PHE B 38 TYR 0.015 0.001 TYR A 93 ARG 0.003 0.000 ARG B 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6793 (m-70) REVERT: A 252 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7464 (tpt) REVERT: C 178 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7634 (mmm160) REVERT: C 201 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7110 (m-70) REVERT: C 327 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (mtpp) outliers start: 27 outliers final: 20 residues processed: 126 average time/residue: 0.1489 time to fit residues: 26.9967 Evaluate side-chains 123 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084379 restraints weight = 16833.183| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.37 r_work: 0.3091 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7437 Z= 0.141 Angle : 0.634 12.880 10176 Z= 0.296 Chirality : 0.045 0.135 1128 Planarity : 0.003 0.030 1302 Dihedral : 9.333 113.971 1173 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.17 % Allowed : 36.11 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.21 (0.29), residues: 954 helix: 2.32 (0.47), residues: 126 sheet: -0.28 (0.29), residues: 327 loop : -0.63 (0.31), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.002 0.000 HIS C 34 PHE 0.027 0.001 PHE B 38 TYR 0.016 0.001 TYR C 291 ARG 0.002 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.60 seconds wall clock time: 33 minutes 31.83 seconds (2011.83 seconds total)