Starting phenix.real_space_refine on Fri Sep 11 17:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.map" model { file = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xev_22154/09_2026/6xev_22154.cif" } resolution = 3.5 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= 0.002 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: 7 Type Number sf(0) Gaussians K 13 8.98 5 P 12 5.49 5 S 60 5.16 5 Na 4 4.78 5 C 6848 2.51 5 N 1704 2.21 5 O 1904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 10545 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "E" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "I" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "M" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 78 Unusual residues: {' K': 11, ' NA': 1, 'PIO': 1, 'Y01': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {' NA': 1, 'PIO': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' K': 1, ' NA': 1, 'PIO': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' K': 1, ' NA': 1, 'PIO': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.64, per 1000 atoms: 0.25 Number of scatterers: 10545 At special positions: 0 Unit cell: (90.95, 90.95, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 13 19.00 S 60 16.00 P 12 15.00 Na 4 11.00 O 1904 8.00 N 1704 7.00 C 6848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 166 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 166 " distance=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 374.2 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 36.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.611A pdb=" N THR A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 121 removed outlier: 3.693A pdb=" N LEU A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.122A pdb=" N ILE A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.566A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 196 removed outlier: 3.571A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.788A pdb=" N LEU A 205 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.611A pdb=" N THR E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 89 " --> pdb=" O THR E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 121 removed outlier: 3.693A pdb=" N LEU E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.122A pdb=" N ILE E 126 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 153 removed outlier: 3.566A pdb=" N ALA E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 196 removed outlier: 3.571A pdb=" N ILE E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 186 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.788A pdb=" N LEU E 205 " --> pdb=" O ALA E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 382 Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'I' and resid 81 through 89 removed outlier: 3.611A pdb=" N THR I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 121 removed outlier: 3.693A pdb=" N LEU I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG I 120 " --> pdb=" O ILE I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 4.122A pdb=" N ILE I 126 " --> pdb=" O MET I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 153 removed outlier: 3.566A pdb=" N ALA I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 196 removed outlier: 3.571A pdb=" N ILE I 175 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 185 " --> pdb=" O SER I 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE I 186 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 205 removed outlier: 3.788A pdb=" N LEU I 205 " --> pdb=" O ALA I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 382 Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'M' and resid 81 through 89 removed outlier: 3.611A pdb=" N THR M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU M 89 " --> pdb=" O THR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 121 removed outlier: 3.693A pdb=" N LEU M 96 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 removed outlier: 4.122A pdb=" N ILE M 126 " --> pdb=" O MET M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 153 removed outlier: 3.566A pdb=" N ALA M 144 " --> pdb=" O GLY M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 196 removed outlier: 3.571A pdb=" N ILE M 175 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE M 186 " --> pdb=" O ILE M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 205 removed outlier: 3.787A pdb=" N LEU M 205 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 382 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.612A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 248 removed outlier: 3.764A pdb=" N LYS A 247 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 removed outlier: 6.615A pdb=" N TYR A 349 " --> pdb=" O HIS M 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AA8, first strand: chain 'E' and resid 279 through 284 Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 5.612A pdb=" N GLU E 236 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET E 313 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 247 through 248 removed outlier: 3.764A pdb=" N LYS E 247 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=AB3, first strand: chain 'I' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'I' and resid 279 through 284 Processing sheet with id=AB5, first strand: chain 'I' and resid 259 through 261 removed outlier: 5.612A pdb=" N GLU I 236 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET I 313 " --> pdb=" O GLU I 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 247 through 248 removed outlier: 3.764A pdb=" N LYS I 247 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'M' and resid 279 through 284 Processing sheet with id=AB9, first strand: chain 'M' and resid 259 through 261 removed outlier: 5.612A pdb=" N GLU M 236 " --> pdb=" O MET M 313 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET M 313 " --> pdb=" O GLU M 236 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 247 through 248 removed outlier: 3.765A pdb=" N LYS M 247 " --> pdb=" O ILE M 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 336 through 338 474 hydrogen bonds defined for protein. 1266 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: 1.55 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1592 1.31 - 1.44: 3044 1.44 - 1.56: 6008 1.56 - 1.68: 48 1.68 - 1.81: 96 Bond restraints: 10788 Sorted by residual: bond pdb=" C1B PIO M 402 " pdb=" O3C PIO M 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C1B PIO A 401 " pdb=" O3C PIO A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C1B PIO I 402 " pdb=" O3C PIO I 402 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C1B PIO E 401 " pdb=" O3C PIO E 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4 PIO E 401 " pdb=" P4 PIO E 401 " ideal model delta sigma weight residual 1.710 1.610 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 10783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 14588 3.34 - 6.68: 112 6.68 - 10.02: 8 10.02 - 13.36: 4 13.36 - 16.70: 8 Bond angle restraints: 14720 Sorted by residual: angle pdb=" C2C PIO M 402 " pdb=" C3C PIO M 402 " pdb=" O3C PIO M 402 " ideal model delta sigma weight residual 107.31 124.01 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C2C PIO E 401 " pdb=" C3C PIO E 401 " pdb=" O3C PIO E 401 " ideal model delta sigma weight residual 107.31 124.01 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C2C PIO I 402 " pdb=" C3C PIO I 402 " pdb=" O3C PIO I 402 " ideal model delta sigma weight residual 107.31 124.01 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C2C PIO A 401 " pdb=" C3C PIO A 401 " pdb=" O3C PIO A 401 " ideal model delta sigma weight residual 107.31 124.01 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C1B PIO M 402 " pdb=" O3C PIO M 402 " pdb=" C3C PIO M 402 " ideal model delta sigma weight residual 117.85 133.55 -15.70 3.00e+00 1.11e-01 2.74e+01 ... (remaining 14715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 5367 15.31 - 30.62: 553 30.62 - 45.93: 240 45.93 - 61.24: 60 61.24 - 76.55: 8 Dihedral angle restraints: 6228 sinusoidal: 2392 harmonic: 3836 Sorted by residual: dihedral pdb=" CG ARG M 57 " pdb=" CD ARG M 57 " pdb=" NE ARG M 57 " pdb=" CZ ARG M 57 " ideal model delta sinusoidal sigma weight residual 180.00 135.35 44.65 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 57 " pdb=" CD ARG A 57 " pdb=" NE ARG A 57 " pdb=" CZ ARG A 57 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG E 57 " pdb=" CD ARG E 57 " pdb=" NE ARG E 57 " pdb=" CZ ARG E 57 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1542 0.076 - 0.152: 166 0.152 - 0.228: 12 0.228 - 0.304: 8 0.304 - 0.380: 4 Chirality restraints: 1732 Sorted by residual: chirality pdb=" CBG Y01 E 402 " pdb=" CAQ Y01 E 402 " pdb=" CBD Y01 E 402 " pdb=" CBI Y01 E 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CBG Y01 I 403 " pdb=" CAQ Y01 I 403 " pdb=" CBD Y01 I 403 " pdb=" CBI Y01 I 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CBG Y01 M 403 " pdb=" CAQ Y01 M 403 " pdb=" CBD Y01 M 403 " pdb=" CBI Y01 M 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1729 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 168 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU A 168 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A 168 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 169 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 168 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU M 168 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU M 168 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY M 169 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 168 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU I 168 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU I 168 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY I 169 " 0.009 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 4223 2.88 - 3.44: 10697 3.44 - 4.01: 16800 4.01 - 4.57: 23143 4.57 - 5.14: 36271 Nonbonded interactions: 91134 Sorted by model distance: nonbonded pdb=" O3 PIO M 402 " pdb=" O43 PIO M 402 " model vdw 2.310 3.040 nonbonded pdb=" O3 PIO A 401 " pdb=" O43 PIO A 401 " model vdw 2.310 3.040 nonbonded pdb=" O3 PIO E 401 " pdb=" O43 PIO E 401 " model vdw 2.310 3.040 nonbonded pdb=" O3 PIO I 402 " pdb=" O43 PIO I 402 " model vdw 2.310 3.040 nonbonded pdb=" O SER E 366 " pdb=" OG SER E 366 " model vdw 2.343 3.040 ... (remaining 91129 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 382) selection = (chain 'E' and resid 55 through 382) selection = (chain 'I' and resid 55 through 382) selection = (chain 'M' and resid 55 through 382) } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.124 10792 Z= 0.352 Angle : 0.858 16.698 14728 Z= 0.450 Chirality : 0.051 0.380 1732 Planarity : 0.003 0.027 1768 Dihedral : 15.586 76.551 3744 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.13 % Allowed : 12.09 % Favored : 82.78 % 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: -2.90 (0.21), residues: 1304 helix: -1.69 (0.21), residues: 432 sheet: 0.45 (0.36), residues: 208 loop : -2.99 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 201 TYR 0.005 0.001 TYR A 360 PHE 0.010 0.001 PHE M 98 TRP 0.004 0.001 TRP M 91 HIS 0.001 0.000 HIS M 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.35 (10788) covalent geometry : angle 0.85834 / 0.45 (14720) SS BOND : bond 0.00142 / 0.07 ( 4) SS BOND : angle 0.29650 / 0.17 ( 8) hydrogen bonds : bond 0.15406 / 10.27 ( 474) hydrogen bonds : angle 5.87688 / 4.17 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 0.356 Fit side-chains REVERT: A 352 ASP cc_start: 0.8258 (t0) cc_final: 0.7958 (t0) REVERT: E 352 ASP cc_start: 0.8258 (t0) cc_final: 0.7958 (t0) REVERT: I 352 ASP cc_start: 0.8261 (t0) cc_final: 0.7961 (t0) REVERT: M 352 ASP cc_start: 0.8263 (t0) cc_final: 0.7958 (t0) outliers start: 56 outliers final: 28 residues processed: 184 average time/residue: 0.0742 time to fit residues: 21.7858 Evaluate side-chains 124 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 119 ILE Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 372 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 354 ASN I 354 ASN M 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.065586 restraints weight = 24776.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067870 restraints weight = 11559.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.069304 restraints weight = 7402.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.070352 restraints weight = 5727.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070799 restraints weight = 4840.129| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10792 Z= 0.112 Angle : 0.530 5.744 14728 Z= 0.280 Chirality : 0.042 0.131 1732 Planarity : 0.003 0.025 1768 Dihedral : 8.345 52.309 1552 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.93 % Allowed : 14.65 % Favored : 82.42 % 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: -0.88 (0.24), residues: 1304 helix: 1.12 (0.26), residues: 444 sheet: 0.85 (0.34), residues: 248 loop : -2.67 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 230 TYR 0.006 0.001 TYR M 360 PHE 0.017 0.001 PHE I 98 TRP 0.006 0.001 TRP A 106 HIS 0.002 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10788) covalent geometry : angle 0.53011 / 0.28 (14720) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.29409 / 0.16 ( 8) hydrogen bonds : bond 0.04915 / 3.17 ( 474) hydrogen bonds : angle 3.78291 / 2.66 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.437 Fit side-chains REVERT: A 273 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9194 (pp) REVERT: A 304 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8935 (pp) REVERT: E 273 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9193 (pp) REVERT: E 304 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8933 (pp) REVERT: I 273 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9190 (pp) REVERT: I 304 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8933 (pp) REVERT: M 273 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9192 (pp) REVERT: M 304 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8933 (pp) outliers start: 32 outliers final: 16 residues processed: 116 average time/residue: 0.0728 time to fit residues: 13.8287 Evaluate side-chains 92 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 7.9990 chunk 71 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.080346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.063547 restraints weight = 25126.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.065831 restraints weight = 11805.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067320 restraints weight = 7566.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.068328 restraints weight = 5845.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.068661 restraints weight = 4959.558| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10792 Z= 0.139 Angle : 0.521 5.151 14728 Z= 0.276 Chirality : 0.042 0.130 1732 Planarity : 0.003 0.025 1768 Dihedral : 6.799 52.786 1520 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.93 % Allowed : 14.56 % Favored : 82.51 % 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: 0.00 (0.25), residues: 1304 helix: 2.06 (0.26), residues: 424 sheet: 1.25 (0.35), residues: 248 loop : -2.14 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 324 TYR 0.008 0.001 TYR M 360 PHE 0.021 0.001 PHE M 186 TRP 0.004 0.001 TRP M 114 HIS 0.002 0.001 HIS E 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10788) covalent geometry : angle 0.52138 / 0.28 (14720) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 0.18710 / 0.11 ( 8) hydrogen bonds : bond 0.05389 / 3.47 ( 474) hydrogen bonds : angle 3.77408 / 2.66 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.455 Fit side-chains REVERT: A 139 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9125 (p0) REVERT: A 273 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9209 (pp) REVERT: A 304 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9026 (pp) REVERT: E 139 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.9122 (p0) REVERT: E 273 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9208 (pp) REVERT: E 304 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9024 (pp) REVERT: I 139 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9124 (p0) REVERT: I 273 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9209 (pp) REVERT: I 304 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9025 (pp) REVERT: M 139 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.9122 (p0) REVERT: M 273 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9214 (pp) REVERT: M 304 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9028 (pp) outliers start: 32 outliers final: 12 residues processed: 100 average time/residue: 0.0711 time to fit residues: 11.9468 Evaluate side-chains 84 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.077270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.060217 restraints weight = 25681.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.062486 restraints weight = 11960.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.063735 restraints weight = 7695.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064874 restraints weight = 6103.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.065257 restraints weight = 5175.810| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 10792 Z= 0.226 Angle : 0.604 7.692 14728 Z= 0.319 Chirality : 0.043 0.130 1732 Planarity : 0.003 0.026 1768 Dihedral : 6.750 51.794 1504 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.57 % Allowed : 16.12 % Favored : 80.31 % 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: -0.26 (0.24), residues: 1304 helix: 1.64 (0.26), residues: 448 sheet: 1.26 (0.35), residues: 248 loop : -2.37 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.011 0.001 TYR A 360 PHE 0.017 0.002 PHE M 186 TRP 0.007 0.001 TRP I 114 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (10788) covalent geometry : angle 0.60416 / 0.32 (14720) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.31986 / 0.19 ( 8) hydrogen bonds : bond 0.06774 / 4.38 ( 474) hydrogen bonds : angle 4.13469 / 2.91 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.423 Fit side-chains REVERT: A 139 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9099 (p0) REVERT: A 273 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9244 (pp) REVERT: A 304 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9200 (pp) REVERT: E 139 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9096 (p0) REVERT: E 273 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9245 (pp) REVERT: E 304 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9196 (pp) REVERT: I 139 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9098 (p0) REVERT: I 273 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9246 (pp) REVERT: I 304 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9197 (pp) REVERT: M 139 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.9100 (p0) REVERT: M 273 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9247 (pp) REVERT: M 304 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9200 (pp) outliers start: 39 outliers final: 20 residues processed: 95 average time/residue: 0.0695 time to fit residues: 11.0411 Evaluate side-chains 84 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 359 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN A 354 ASN M 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.060155 restraints weight = 25437.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062439 restraints weight = 11826.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.063924 restraints weight = 7636.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.064773 restraints weight = 5925.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065296 restraints weight = 5139.524| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10792 Z= 0.226 Angle : 0.598 8.579 14728 Z= 0.314 Chirality : 0.043 0.130 1732 Planarity : 0.003 0.026 1768 Dihedral : 6.844 52.764 1504 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.66 % Allowed : 17.58 % Favored : 78.75 % 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: -0.24 (0.24), residues: 1304 helix: 1.65 (0.26), residues: 448 sheet: 1.33 (0.35), residues: 248 loop : -2.37 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 201 TYR 0.010 0.001 TYR M 360 PHE 0.016 0.001 PHE M 186 TRP 0.005 0.001 TRP M 114 HIS 0.003 0.001 HIS M 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (10788) covalent geometry : angle 0.59765 / 0.31 (14720) SS BOND : bond 0.00144 / 0.07 ( 4) SS BOND : angle 0.24536 / 0.15 ( 8) hydrogen bonds : bond 0.06626 / 4.28 ( 474) hydrogen bonds : angle 4.11600 / 2.88 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.422 Fit side-chains REVERT: A 139 ASN cc_start: 0.9344 (OUTLIER) cc_final: 0.9108 (p0) REVERT: A 273 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9229 (pp) REVERT: A 304 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9185 (pp) REVERT: E 139 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9106 (p0) REVERT: E 273 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9230 (pp) REVERT: E 304 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9183 (pp) REVERT: I 139 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9107 (p0) REVERT: I 273 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9230 (pp) REVERT: I 304 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9182 (pp) REVERT: M 139 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9110 (p0) REVERT: M 273 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9232 (pp) REVERT: M 304 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9180 (pp) outliers start: 40 outliers final: 20 residues processed: 100 average time/residue: 0.0691 time to fit residues: 11.6191 Evaluate side-chains 88 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 359 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 0.0770 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.078797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.061814 restraints weight = 25326.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.064110 restraints weight = 11835.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.065677 restraints weight = 7597.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066555 restraints weight = 5841.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066880 restraints weight = 5030.892| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10792 Z= 0.151 Angle : 0.534 7.325 14728 Z= 0.283 Chirality : 0.042 0.133 1732 Planarity : 0.003 0.026 1768 Dihedral : 6.687 54.674 1504 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.38 % Allowed : 20.15 % Favored : 77.47 % 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: 0.30 (0.24), residues: 1304 helix: 2.27 (0.26), residues: 424 sheet: 2.03 (0.37), residues: 208 loop : -1.94 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 57 TYR 0.008 0.001 TYR M 360 PHE 0.017 0.001 PHE A 186 TRP 0.004 0.001 TRP A 292 HIS 0.002 0.001 HIS M 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10788) covalent geometry : angle 0.53366 / 0.28 (14720) SS BOND : bond 0.00001 / 0.00 ( 4) SS BOND : angle 0.15986 / 0.09 ( 8) hydrogen bonds : bond 0.05713 / 3.68 ( 474) hydrogen bonds : angle 3.76507 / 2.64 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.433 Fit side-chains REVERT: A 139 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9086 (p0) REVERT: A 273 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9216 (pp) REVERT: A 304 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9118 (pp) REVERT: E 139 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.9084 (p0) REVERT: E 273 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9216 (pp) REVERT: E 304 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9113 (pp) REVERT: I 139 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.9085 (p0) REVERT: I 273 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9218 (pp) REVERT: I 304 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9116 (pp) REVERT: M 139 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9087 (p0) REVERT: M 273 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9219 (pp) REVERT: M 304 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9113 (pp) outliers start: 26 outliers final: 10 residues processed: 86 average time/residue: 0.0659 time to fit residues: 9.5688 Evaluate side-chains 82 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 79 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 354 ASN I 354 ASN M 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.060824 restraints weight = 25236.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.063115 restraints weight = 11740.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.064654 restraints weight = 7572.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.065511 restraints weight = 5837.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.066156 restraints weight = 5042.934| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 10792 Z= 0.192 Angle : 0.561 6.962 14728 Z= 0.298 Chirality : 0.042 0.131 1732 Planarity : 0.003 0.027 1768 Dihedral : 6.768 54.616 1504 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.67 % Allowed : 19.14 % Favored : 76.19 % 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: 0.22 (0.24), residues: 1304 helix: 2.31 (0.26), residues: 424 sheet: 0.96 (0.32), residues: 292 loop : -2.06 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 201 TYR 0.009 0.001 TYR A 360 PHE 0.016 0.001 PHE M 186 TRP 0.004 0.001 TRP M 114 HIS 0.002 0.001 HIS I 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (10788) covalent geometry : angle 0.56138 / 0.30 (14720) SS BOND : bond 0.00071 / 0.03 ( 4) SS BOND : angle 0.19525 / 0.12 ( 8) hydrogen bonds : bond 0.06226 / 4.01 ( 474) hydrogen bonds : angle 3.86406 / 2.70 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 60 time to evaluate : 0.421 Fit side-chains REVERT: A 139 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9092 (p0) REVERT: A 273 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9227 (pp) REVERT: A 304 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9156 (pp) REVERT: E 139 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9091 (p0) REVERT: E 273 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9228 (pp) REVERT: E 304 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9152 (pp) REVERT: I 139 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9092 (p0) REVERT: I 273 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9229 (pp) REVERT: I 304 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9154 (pp) REVERT: M 139 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9093 (p0) REVERT: M 273 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9228 (pp) REVERT: M 304 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9150 (pp) outliers start: 51 outliers final: 24 residues processed: 111 average time/residue: 0.0701 time to fit residues: 12.8949 Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.077564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.060623 restraints weight = 25092.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.062905 restraints weight = 11701.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.064440 restraints weight = 7557.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.065302 restraints weight = 5829.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.065964 restraints weight = 5039.231| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 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 : 0.005 0.026 10792 Z= 0.201 Angle : 0.564 7.509 14728 Z= 0.301 Chirality : 0.042 0.128 1732 Planarity : 0.003 0.027 1768 Dihedral : 6.825 55.054 1504 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.66 % Allowed : 20.15 % Favored : 76.19 % 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: 0.31 (0.24), residues: 1304 helix: 2.29 (0.25), residues: 424 sheet: 1.63 (0.37), residues: 228 loop : -1.91 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 60 TYR 0.009 0.001 TYR I 360 PHE 0.016 0.001 PHE E 186 TRP 0.004 0.001 TRP M 131 HIS 0.003 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (10788) covalent geometry : angle 0.56372 / 0.30 (14720) SS BOND : bond 0.00080 / 0.04 ( 4) SS BOND : angle 0.19644 / 0.12 ( 8) hydrogen bonds : bond 0.06292 / 4.06 ( 474) hydrogen bonds : angle 3.87612 / 2.71 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.419 Fit side-chains REVERT: A 139 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9088 (p0) REVERT: A 273 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9236 (pp) REVERT: A 304 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9169 (pp) REVERT: E 139 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9086 (p0) REVERT: E 273 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9235 (pp) REVERT: E 304 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9166 (pp) REVERT: I 139 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9086 (p0) REVERT: I 273 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9235 (pp) REVERT: I 304 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9167 (pp) REVERT: M 139 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9088 (p0) REVERT: M 273 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9235 (pp) REVERT: M 304 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9165 (pp) outliers start: 40 outliers final: 28 residues processed: 100 average time/residue: 0.0701 time to fit residues: 11.7762 Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 359 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.078872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.061967 restraints weight = 25147.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.064254 restraints weight = 11675.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.065858 restraints weight = 7554.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.066726 restraints weight = 5805.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067231 restraints weight = 4998.907| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 10792 Z= 0.159 Angle : 0.546 7.683 14728 Z= 0.290 Chirality : 0.042 0.132 1732 Planarity : 0.003 0.027 1768 Dihedral : 6.705 55.883 1504 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.66 % Allowed : 20.51 % Favored : 75.82 % 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: 0.41 (0.24), residues: 1304 helix: 2.38 (0.26), residues: 424 sheet: 1.69 (0.36), residues: 228 loop : -1.85 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 57 TYR 0.008 0.001 TYR I 360 PHE 0.018 0.001 PHE A 186 TRP 0.005 0.001 TRP A 91 HIS 0.002 0.001 HIS I 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10788) covalent geometry : angle 0.54572 / 0.29 (14720) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 0.15665 / 0.09 ( 8) hydrogen bonds : bond 0.05788 / 3.71 ( 474) hydrogen bonds : angle 3.76887 / 2.64 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9072 (p0) REVERT: A 273 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9219 (pp) REVERT: A 304 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9109 (pp) REVERT: E 139 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9070 (p0) REVERT: E 273 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9218 (pp) REVERT: E 304 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9104 (pp) REVERT: I 139 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9071 (p0) REVERT: I 273 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9217 (pp) REVERT: I 304 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9107 (pp) REVERT: M 139 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.9073 (p0) REVERT: M 273 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9218 (pp) REVERT: M 304 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9106 (pp) outliers start: 40 outliers final: 28 residues processed: 111 average time/residue: 0.0705 time to fit residues: 13.1059 Evaluate side-chains 112 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 359 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.078952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.062094 restraints weight = 25097.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.064405 restraints weight = 11711.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.065967 restraints weight = 7524.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066768 restraints weight = 5798.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067422 restraints weight = 5024.675| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10792 Z= 0.159 Angle : 0.547 9.139 14728 Z= 0.289 Chirality : 0.042 0.130 1732 Planarity : 0.003 0.027 1768 Dihedral : 6.643 56.363 1504 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.03 % Allowed : 20.15 % Favored : 75.82 % 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: 0.46 (0.24), residues: 1304 helix: 2.40 (0.26), residues: 424 sheet: 1.71 (0.36), residues: 228 loop : -1.80 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 57 TYR 0.008 0.001 TYR I 360 PHE 0.017 0.001 PHE M 186 TRP 0.005 0.001 TRP M 131 HIS 0.002 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10788) covalent geometry : angle 0.54685 / 0.29 (14720) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.17878 / 0.11 ( 8) hydrogen bonds : bond 0.05676 / 3.64 ( 474) hydrogen bonds : angle 3.73845 / 2.62 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: A 111 MET cc_start: 0.8228 (mtt) cc_final: 0.8022 (mtp) REVERT: A 139 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9070 (p0) REVERT: A 273 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9215 (pp) REVERT: A 304 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9108 (pp) REVERT: E 98 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: E 111 MET cc_start: 0.8222 (mtt) cc_final: 0.8018 (mtp) REVERT: E 139 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.9071 (p0) REVERT: E 273 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9213 (pp) REVERT: E 304 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9103 (pp) REVERT: I 98 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: I 111 MET cc_start: 0.8227 (mtt) cc_final: 0.8019 (mtp) REVERT: I 139 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9071 (p0) REVERT: I 273 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9214 (pp) REVERT: I 304 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9106 (pp) REVERT: M 98 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: M 111 MET cc_start: 0.8232 (mtt) cc_final: 0.8028 (mtp) REVERT: M 139 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.9073 (p0) REVERT: M 273 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9214 (pp) REVERT: M 304 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9109 (pp) outliers start: 44 outliers final: 28 residues processed: 108 average time/residue: 0.0695 time to fit residues: 12.5816 Evaluate side-chains 112 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 139 ASN Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain M residue 359 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.079160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.062251 restraints weight = 25160.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.064565 restraints weight = 11713.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.066098 restraints weight = 7504.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.066979 restraints weight = 5789.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067472 restraints weight = 4986.424| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10792 Z= 0.155 Angle : 0.538 8.667 14728 Z= 0.285 Chirality : 0.042 0.131 1732 Planarity : 0.003 0.027 1768 Dihedral : 6.582 56.943 1504 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.30 % Allowed : 20.88 % Favored : 75.82 % 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: 0.51 (0.24), residues: 1304 helix: 2.46 (0.26), residues: 424 sheet: 1.72 (0.36), residues: 228 loop : -1.78 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 57 TYR 0.008 0.001 TYR E 360 PHE 0.016 0.001 PHE M 186 TRP 0.004 0.001 TRP M 131 HIS 0.002 0.001 HIS I 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10788) covalent geometry : angle 0.53802 / 0.29 (14720) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.14797 / 0.09 ( 8) hydrogen bonds : bond 0.05548 / 3.56 ( 474) hydrogen bonds : angle 3.70131 / 2.59 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1532.83 seconds wall clock time: 27 minutes 20.15 seconds (1640.15 seconds total)