Starting phenix.real_space_refine on Sat Sep 12 04:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkt_25981/09_2026/7tkt_25981.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8844 2.51 5 N 2080 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNAv2': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-3': 10, 'PGW:plan-1': 11, 'PGW:plan-2': 11} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNAv2': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Restraints were copied for chains: B, C Time building chain proxies: 3.70, per 1000 atoms: 0.28 Number of scatterers: 13252 At special positions: 0 Unit cell: (105.226, 105.226, 122.763, 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 28 16.00 P 12 15.00 O 2288 8.00 N 2080 7.00 C 8844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.09 Conformation dependent library (CDL) restraints added in 550.3 milliseconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 63.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.108A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.109A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.010A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.776A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 416 " --> pdb=" O GLN D 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2088 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: 1.99 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3845 1.34 - 1.45: 1694 1.45 - 1.57: 7881 1.57 - 1.69: 16 1.69 - 1.81: 56 Bond restraints: 13492 Sorted by residual: bond pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C10 PGW D 502 " pdb=" C9 PGW D 502 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 17737 4.21 - 8.43: 387 8.43 - 12.64: 16 12.64 - 16.86: 0 16.86 - 21.07: 16 Bond angle restraints: 18156 Sorted by residual: angle pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " pdb=" C8 PGW B 513 " ideal model delta sigma weight residual 127.02 105.95 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW D 505 " pdb=" C9 PGW D 505 " pdb=" C8 PGW D 505 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 513 " pdb=" C9 PGW C 513 " pdb=" C8 PGW C 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " pdb=" C8 PGW A 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " pdb=" C8 PGW C 510 " ideal model delta sigma weight residual 127.02 106.26 20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 18151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 7924 34.68 - 69.36: 188 69.36 - 104.04: 40 104.04 - 138.71: 12 138.71 - 173.39: 12 Dihedral angle restraints: 8176 sinusoidal: 3588 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP D 507 " pdb=" O3' CMP D 507 " pdb=" P CMP D 507 " pdb=" O1P CMP D 507 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP A 501 " pdb=" O3' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1632 0.053 - 0.107: 420 0.107 - 0.160: 36 0.160 - 0.213: 8 0.213 - 0.266: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C2' CMP D 507 " pdb=" C1' CMP D 507 " pdb=" C3' CMP D 507 " pdb=" O2' CMP D 507 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2' CMP C 501 " pdb=" C1' CMP C 501 " pdb=" C3' CMP C 501 " pdb=" O2' CMP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2097 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 513 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW B 513 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PGW B 513 " -0.158 2.00e-02 2.50e+03 pdb=" C9 PGW B 513 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 505 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW D 505 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW D 505 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW D 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 513 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW C 513 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW C 513 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW C 513 " -0.156 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1950 2.76 - 3.29: 12129 3.29 - 3.83: 21391 3.83 - 4.36: 22528 4.36 - 4.90: 40837 Nonbonded interactions: 98835 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 262 " pdb=" OD2 ASP B 388 " model vdw 2.264 3.040 ... (remaining 98830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28)) or resid 510 through 511 or resid 513 through 514)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.320 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.007 0.171 13492 Z= 0.328 Angle : 1.289 21.069 18158 Z= 0.482 Chirality : 0.046 0.266 2100 Planarity : 0.008 0.159 2172 Dihedral : 18.338 173.393 5212 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1544 helix: 1.56 (0.18), residues: 936 sheet: 0.59 (0.57), residues: 84 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 311 TYR 0.009 0.001 TYR B 26 PHE 0.005 0.001 PHE D 386 TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.33 (13492) covalent geometry : angle 1.28896 / 0.48 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.12057 / 8.10 ( 728) hydrogen bonds : angle 5.41712 / 3.91 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1116 time to fit residues: 25.2425 Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.158942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125891 restraints weight = 21005.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125560 restraints weight = 16822.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126178 restraints weight = 14842.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126352 restraints weight = 12877.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128068 restraints weight = 12420.407| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13492 Z= 0.120 Angle : 0.643 9.000 18158 Z= 0.286 Chirality : 0.042 0.151 2100 Planarity : 0.004 0.042 2172 Dihedral : 16.678 166.424 2268 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.30 % Allowed : 7.69 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.23), residues: 1544 helix: 1.94 (0.18), residues: 928 sheet: -0.69 (0.41), residues: 156 loop : -1.94 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 382 TYR 0.013 0.001 TYR D 25 PHE 0.012 0.001 PHE D 40 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13492) covalent geometry : angle 0.64310 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03536 / 2.35 ( 728) hydrogen bonds : angle 4.07922 / 2.90 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.472 Fit side-chains REVERT: A 82 LEU cc_start: 0.7421 (tt) cc_final: 0.6692 (mp) REVERT: B 57 ASP cc_start: 0.5508 (t0) cc_final: 0.5183 (p0) REVERT: B 82 LEU cc_start: 0.7403 (tt) cc_final: 0.6690 (mp) REVERT: C 82 LEU cc_start: 0.7421 (tt) cc_final: 0.6687 (mp) REVERT: D 82 LEU cc_start: 0.7422 (tt) cc_final: 0.6689 (mp) REVERT: D 369 MET cc_start: 0.7611 (tpp) cc_final: 0.7400 (tpt) outliers start: 4 outliers final: 0 residues processed: 140 average time/residue: 0.0999 time to fit residues: 21.7177 Evaluate side-chains 120 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115083 restraints weight = 21475.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115470 restraints weight = 15371.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115719 restraints weight = 13269.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116781 restraints weight = 12434.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116709 restraints weight = 11175.010| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13492 Z= 0.216 Angle : 0.703 8.749 18158 Z= 0.326 Chirality : 0.044 0.145 2100 Planarity : 0.004 0.039 2172 Dihedral : 16.043 166.078 2268 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.82 % Allowed : 14.25 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1544 helix: 1.83 (0.18), residues: 928 sheet: -0.57 (0.43), residues: 128 loop : -1.79 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.017 0.001 TYR B 26 PHE 0.013 0.002 PHE C 40 TRP 0.011 0.002 TRP A 176 HIS 0.005 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (13492) covalent geometry : angle 0.70300 / 0.33 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04490 / 2.98 ( 728) hydrogen bonds : angle 4.10713 / 2.91 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7497 (tt) cc_final: 0.6805 (mp) REVERT: B 82 LEU cc_start: 0.7426 (tt) cc_final: 0.6720 (mp) REVERT: C 82 LEU cc_start: 0.7430 (tt) cc_final: 0.6730 (mp) REVERT: D 82 LEU cc_start: 0.7431 (tt) cc_final: 0.6731 (mp) REVERT: D 369 MET cc_start: 0.7851 (tpp) cc_final: 0.7629 (tpt) outliers start: 11 outliers final: 1 residues processed: 139 average time/residue: 0.1196 time to fit residues: 24.4737 Evaluate side-chains 127 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 0.0870 chunk 93 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117675 restraints weight = 21393.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120689 restraints weight = 13863.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122579 restraints weight = 10719.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123711 restraints weight = 9242.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123903 restraints weight = 8496.142| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13492 Z= 0.119 Angle : 0.633 9.631 18158 Z= 0.286 Chirality : 0.041 0.154 2100 Planarity : 0.004 0.039 2172 Dihedral : 15.133 164.693 2268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.27 % Allowed : 16.27 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1544 helix: 1.99 (0.18), residues: 928 sheet: -0.76 (0.43), residues: 128 loop : -1.73 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.006 0.001 TYR C 26 PHE 0.033 0.001 PHE A 40 TRP 0.009 0.001 TRP A 176 HIS 0.001 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13492) covalent geometry : angle 0.63344 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03454 / 2.30 ( 728) hydrogen bonds : angle 3.76871 / 2.65 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7454 (tt) cc_final: 0.6811 (mp) REVERT: A 369 MET cc_start: 0.7829 (tpp) cc_final: 0.7605 (tpt) REVERT: B 82 LEU cc_start: 0.7383 (tt) cc_final: 0.6736 (mp) REVERT: B 369 MET cc_start: 0.7833 (tpp) cc_final: 0.7614 (tpt) REVERT: C 82 LEU cc_start: 0.7403 (tt) cc_final: 0.6708 (mp) REVERT: C 369 MET cc_start: 0.7828 (tpp) cc_final: 0.7608 (tpt) REVERT: D 82 LEU cc_start: 0.7405 (tt) cc_final: 0.6707 (mp) outliers start: 17 outliers final: 0 residues processed: 148 average time/residue: 0.1270 time to fit residues: 27.0165 Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 150 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120986 restraints weight = 21248.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122009 restraints weight = 15478.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122892 restraints weight = 12712.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123357 restraints weight = 10901.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123591 restraints weight = 10051.761| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13492 Z= 0.127 Angle : 0.640 10.290 18158 Z= 0.288 Chirality : 0.042 0.153 2100 Planarity : 0.004 0.036 2172 Dihedral : 14.704 163.534 2268 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.30 % Allowed : 18.73 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1544 helix: 1.96 (0.18), residues: 928 sheet: -0.82 (0.44), residues: 128 loop : -1.77 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.006 0.001 TYR A 175 PHE 0.028 0.001 PHE A 40 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13492) covalent geometry : angle 0.64006 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03466 / 2.30 ( 728) hydrogen bonds : angle 3.68617 / 2.58 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7487 (tt) cc_final: 0.6818 (mp) REVERT: B 82 LEU cc_start: 0.7417 (tt) cc_final: 0.6742 (mp) REVERT: C 82 LEU cc_start: 0.7427 (tt) cc_final: 0.6746 (mp) REVERT: D 82 LEU cc_start: 0.7425 (tt) cc_final: 0.6746 (mp) outliers start: 4 outliers final: 4 residues processed: 150 average time/residue: 0.1264 time to fit residues: 27.3533 Evaluate side-chains 139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.155870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121564 restraints weight = 21477.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122935 restraints weight = 15781.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124016 restraints weight = 12269.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124183 restraints weight = 10325.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124437 restraints weight = 9705.210| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.114 Angle : 0.634 10.166 18158 Z= 0.284 Chirality : 0.042 0.152 2100 Planarity : 0.004 0.035 2172 Dihedral : 14.354 162.656 2268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.19 % Allowed : 21.19 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.23), residues: 1544 helix: 1.92 (0.18), residues: 924 sheet: -0.69 (0.44), residues: 128 loop : -1.70 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.006 0.001 TYR B 26 PHE 0.029 0.001 PHE A 40 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (13492) covalent geometry : angle 0.63449 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03260 / 2.17 ( 728) hydrogen bonds : angle 3.65846 / 2.55 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.421 Fit side-chains REVERT: A 82 LEU cc_start: 0.7471 (tt) cc_final: 0.6834 (mp) REVERT: B 82 LEU cc_start: 0.7389 (tt) cc_final: 0.6775 (mp) REVERT: C 82 LEU cc_start: 0.7401 (tt) cc_final: 0.6766 (mp) REVERT: D 82 LEU cc_start: 0.7402 (tt) cc_final: 0.6765 (mp) outliers start: 16 outliers final: 4 residues processed: 154 average time/residue: 0.1295 time to fit residues: 28.6052 Evaluate side-chains 136 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120424 restraints weight = 21066.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120884 restraints weight = 17646.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122234 restraints weight = 14172.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122387 restraints weight = 12865.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122518 restraints weight = 11772.426| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.129 Angle : 0.653 9.398 18158 Z= 0.296 Chirality : 0.042 0.147 2100 Planarity : 0.004 0.035 2172 Dihedral : 14.168 162.722 2268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.37 % Allowed : 22.24 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1544 helix: 1.94 (0.18), residues: 924 sheet: -0.69 (0.44), residues: 128 loop : -1.72 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.010 0.001 TYR B 26 PHE 0.025 0.001 PHE A 40 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13492) covalent geometry : angle 0.65292 / 0.30 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03413 / 2.26 ( 728) hydrogen bonds : angle 3.60405 / 2.52 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7507 (tt) cc_final: 0.6840 (mp) REVERT: B 82 LEU cc_start: 0.7420 (tt) cc_final: 0.6772 (mp) REVERT: B 327 TYR cc_start: 0.7896 (m-10) cc_final: 0.7623 (m-10) REVERT: C 82 LEU cc_start: 0.7502 (tt) cc_final: 0.6839 (mp) REVERT: C 111 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6829 (ptm160) REVERT: C 327 TYR cc_start: 0.7899 (m-10) cc_final: 0.7627 (m-10) REVERT: D 82 LEU cc_start: 0.7504 (tt) cc_final: 0.6841 (mp) outliers start: 5 outliers final: 0 residues processed: 148 average time/residue: 0.1201 time to fit residues: 25.6909 Evaluate side-chains 141 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 0.0070 chunk 125 optimal weight: 0.3980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119345 restraints weight = 21154.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122133 restraints weight = 14235.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123968 restraints weight = 11153.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124748 restraints weight = 9668.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125643 restraints weight = 8974.134| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.116 Angle : 0.645 9.318 18158 Z= 0.290 Chirality : 0.042 0.146 2100 Planarity : 0.004 0.034 2172 Dihedral : 13.855 163.063 2268 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.82 % Allowed : 22.54 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 924 sheet: -0.51 (0.53), residues: 92 loop : -1.53 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.029 0.001 TYR D 26 PHE 0.029 0.001 PHE A 40 TRP 0.005 0.001 TRP D 176 HIS 0.002 0.000 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13492) covalent geometry : angle 0.64546 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03237 / 2.14 ( 728) hydrogen bonds : angle 3.51683 / 2.46 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7558 (tt) cc_final: 0.6907 (mp) REVERT: B 82 LEU cc_start: 0.7470 (tt) cc_final: 0.6843 (mp) REVERT: B 234 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 327 TYR cc_start: 0.7918 (m-10) cc_final: 0.7640 (m-10) REVERT: B 334 MET cc_start: 0.7045 (tmm) cc_final: 0.6384 (ttt) REVERT: C 82 LEU cc_start: 0.7493 (tt) cc_final: 0.6837 (mp) REVERT: C 327 TYR cc_start: 0.7918 (m-10) cc_final: 0.7638 (m-10) REVERT: C 334 MET cc_start: 0.7047 (tmm) cc_final: 0.6405 (ttt) REVERT: D 82 LEU cc_start: 0.7494 (tt) cc_final: 0.6836 (mp) outliers start: 11 outliers final: 1 residues processed: 168 average time/residue: 0.1110 time to fit residues: 27.6497 Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119695 restraints weight = 21302.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119295 restraints weight = 18542.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119885 restraints weight = 17079.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120536 restraints weight = 13836.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121116 restraints weight = 12167.423| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.125 Angle : 0.665 9.207 18158 Z= 0.302 Chirality : 0.043 0.156 2100 Planarity : 0.004 0.034 2172 Dihedral : 13.662 162.726 2268 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.37 % Allowed : 23.58 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 924 sheet: -0.31 (0.59), residues: 84 loop : -1.56 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 111 TYR 0.018 0.001 TYR D 26 PHE 0.024 0.001 PHE A 40 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.000 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13492) covalent geometry : angle 0.66531 / 0.30 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03339 / 2.21 ( 728) hydrogen bonds : angle 3.53937 / 2.48 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7576 (tt) cc_final: 0.6849 (mp) REVERT: A 234 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 82 LEU cc_start: 0.7501 (tt) cc_final: 0.6771 (mp) REVERT: B 234 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 327 TYR cc_start: 0.7809 (m-10) cc_final: 0.7535 (m-10) REVERT: C 82 LEU cc_start: 0.7500 (tt) cc_final: 0.6770 (mp) REVERT: C 327 TYR cc_start: 0.7791 (m-10) cc_final: 0.7523 (m-10) REVERT: D 82 LEU cc_start: 0.7505 (tt) cc_final: 0.6768 (mp) REVERT: D 234 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7644 (tm-30) outliers start: 5 outliers final: 1 residues processed: 153 average time/residue: 0.1056 time to fit residues: 24.4682 Evaluate side-chains 143 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119117 restraints weight = 21244.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118856 restraints weight = 17645.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119413 restraints weight = 13965.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119820 restraints weight = 13185.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120150 restraints weight = 12346.403| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13492 Z= 0.127 Angle : 0.699 15.580 18158 Z= 0.313 Chirality : 0.043 0.187 2100 Planarity : 0.004 0.039 2172 Dihedral : 13.475 162.496 2268 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.30 % Allowed : 24.40 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1544 helix: 2.01 (0.18), residues: 924 sheet: -0.41 (0.55), residues: 92 loop : -1.46 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.014 0.001 TYR D 26 PHE 0.026 0.001 PHE A 40 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.000 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13492) covalent geometry : angle 0.69890 / 0.31 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03333 / 2.20 ( 728) hydrogen bonds : angle 3.53277 / 2.47 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7537 (tt) cc_final: 0.6809 (mp) REVERT: A 374 ARG cc_start: 0.7416 (mmm160) cc_final: 0.6916 (tpt90) REVERT: B 82 LEU cc_start: 0.7466 (tt) cc_final: 0.6728 (mp) REVERT: B 234 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 334 MET cc_start: 0.7277 (tmm) cc_final: 0.6989 (tpp) REVERT: C 82 LEU cc_start: 0.7520 (tt) cc_final: 0.6794 (mp) REVERT: C 334 MET cc_start: 0.7177 (tmm) cc_final: 0.6858 (tpp) REVERT: D 82 LEU cc_start: 0.7578 (tt) cc_final: 0.6858 (mp) outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.1096 time to fit residues: 24.0879 Evaluate side-chains 142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 110 optimal weight: 0.0000 chunk 134 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122096 restraints weight = 21063.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121002 restraints weight = 17884.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121085 restraints weight = 16497.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121363 restraints weight = 15497.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121592 restraints weight = 14774.319| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13492 Z= 0.114 Angle : 0.681 13.124 18158 Z= 0.304 Chirality : 0.043 0.159 2100 Planarity : 0.004 0.034 2172 Dihedral : 13.102 162.840 2268 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.15 % Allowed : 24.78 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1544 helix: 1.97 (0.18), residues: 932 sheet: -0.37 (0.54), residues: 92 loop : -1.37 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 311 TYR 0.010 0.001 TYR D 26 PHE 0.028 0.001 PHE A 40 TRP 0.004 0.001 TRP C 176 HIS 0.001 0.000 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13492) covalent geometry : angle 0.68068 / 0.30 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03045 / 2.01 ( 728) hydrogen bonds : angle 3.44235 / 2.40 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.69 seconds wall clock time: 33 minutes 39.82 seconds (2019.82 seconds total)