Starting phenix.real_space_refine on Sun Aug 24 13:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l3u_0826/08_2025/6l3u_0826.map" } resolution = 2.53 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= 0.007 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 66 5.16 5 C 6540 2.51 5 N 1638 2.21 5 O 1860 1.98 5 H 9588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19698 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {' CA': 1, 'LMN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 3.88, per 1000 atoms: 0.20 Number of scatterers: 19698 At special positions: 0 Unit cell: (119.121, 120.467, 92.874, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 66 16.00 O 1860 8.00 N 1638 7.00 C 6540 6.00 H 9588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " 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: 1.67 Conformation dependent library (CDL) restraints added in 552.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 78.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.043A pdb=" N LEU A 6 " --> pdb=" O CYS A 2 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 45 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix removed outlier: 3.531A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 45 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix removed outlier: 3.531A pdb=" N HIS B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 214 removed outlier: 3.592A pdb=" N LEU B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 45 Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix removed outlier: 3.531A pdb=" N HIS C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.592A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 45 Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix removed outlier: 3.532A pdb=" N HIS D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 105 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 8 " --> pdb=" O ARG E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 45 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix removed outlier: 3.532A pdb=" N HIS E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'F' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 45 Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix removed outlier: 3.531A pdb=" N HIS F 102 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG F 132 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 53 690 hydrogen bonds defined for protein. 2052 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: 4.95 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9576 1.03 - 1.23: 12 1.23 - 1.42: 4380 1.42 - 1.62: 5760 1.62 - 1.82: 84 Bond restraints: 19812 Sorted by residual: bond pdb=" CBS LMN C 301 " pdb=" CCM LMN C 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN A 303 " pdb=" CCM LMN A 303 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN E 301 " pdb=" CCM LMN E 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CBS LMN D 301 " pdb=" CCM LMN D 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" CBS LMN A 301 " pdb=" CCM LMN A 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 33931 1.77 - 3.55: 1382 3.55 - 5.32: 208 5.32 - 7.10: 23 7.10 - 8.87: 6 Bond angle restraints: 35550 Sorted by residual: angle pdb=" N GLY E 45 " pdb=" CA GLY E 45 " pdb=" C GLY E 45 " ideal model delta sigma weight residual 112.73 117.03 -4.30 1.20e+00 6.94e-01 1.28e+01 angle pdb=" N GLY D 45 " pdb=" CA GLY D 45 " pdb=" C GLY D 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N GLY B 45 " pdb=" CA GLY B 45 " pdb=" C GLY B 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY C 45 " pdb=" CA GLY C 45 " pdb=" C GLY C 45 " ideal model delta sigma weight residual 112.73 116.99 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY F 45 " pdb=" CA GLY F 45 " pdb=" C GLY F 45 " ideal model delta sigma weight residual 112.73 116.95 -4.22 1.20e+00 6.94e-01 1.23e+01 ... (remaining 35545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 8670 17.20 - 34.41: 750 34.41 - 51.61: 284 51.61 - 68.81: 142 68.81 - 86.01: 48 Dihedral angle restraints: 9894 sinusoidal: 5592 harmonic: 4302 Sorted by residual: dihedral pdb=" CAZ LMN A 303 " pdb=" CBB LMN A 303 " pdb=" CBD LMN A 303 " pdb=" CBF LMN A 303 " ideal model delta sinusoidal sigma weight residual 180.29 94.28 86.01 1 3.00e+01 1.11e-03 9.93e+00 dihedral pdb=" CAZ LMN E 301 " pdb=" CBB LMN E 301 " pdb=" CBD LMN E 301 " pdb=" CBF LMN E 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.29 86.00 1 3.00e+01 1.11e-03 9.92e+00 dihedral pdb=" CAZ LMN A 301 " pdb=" CBB LMN A 301 " pdb=" CBD LMN A 301 " pdb=" CBF LMN A 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.31 85.98 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1132 0.045 - 0.089: 352 0.089 - 0.134: 82 0.134 - 0.178: 6 0.178 - 0.223: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CCV LMN D 301 " pdb=" CCR LMN D 301 " pdb=" CCT LMN D 301 " pdb=" OAU LMN D 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CCV LMN E 301 " pdb=" CCR LMN E 301 " pdb=" CCT LMN E 301 " pdb=" OAU LMN E 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CCV LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCT LMN A 301 " pdb=" OAU LMN A 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1575 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 26 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 26 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 26 " -0.023 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 2775 2.28 - 2.86: 40450 2.86 - 3.44: 45782 3.44 - 4.02: 64892 4.02 - 4.60: 99365 Nonbonded interactions: 253264 Sorted by model distance: nonbonded pdb="HH11 ARG F 75 " pdb=" O HOH F 405 " model vdw 1.706 2.450 nonbonded pdb="HH11 ARG C 75 " pdb=" O HOH C 405 " model vdw 1.706 2.450 nonbonded pdb=" O CYS B 202 " pdb=" HG1 THR B 206 " model vdw 1.707 2.450 nonbonded pdb=" O CYS E 202 " pdb=" HG1 THR E 206 " model vdw 1.708 2.450 nonbonded pdb=" O CYS A 202 " pdb=" HG1 THR A 206 " model vdw 1.708 2.450 ... (remaining 253259 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 2 through 221) selection = (chain 'B' and resid 2 through 221) selection = (chain 'C' and resid 2 through 221) selection = (chain 'D' and resid 2 through 221) selection = (chain 'E' and resid 2 through 221) selection = (chain 'F' and resid 2 through 221) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.085 10242 Z= 0.444 Angle : 0.962 8.874 13908 Z= 0.425 Chirality : 0.047 0.223 1578 Planarity : 0.006 0.041 1650 Dihedral : 17.458 86.014 4194 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.01 % Allowed : 6.63 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: -2.86 (0.20), residues: 1182 helix: -1.90 (0.13), residues: 822 sheet: 0.71 (0.65), residues: 60 loop : -1.82 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 7 TYR 0.006 0.002 TYR D 156 PHE 0.013 0.002 PHE F 51 TRP 0.016 0.002 TRP D 103 HIS 0.004 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.01029 (10224) covalent geometry : angle 0.96220 (13872) SS BOND : bond 0.00316 ( 18) SS BOND : angle 0.98129 ( 36) hydrogen bonds : bond 0.27944 ( 690) hydrogen bonds : angle 7.90224 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: A 50 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 132 ARG cc_start: 0.7174 (ptp-170) cc_final: 0.6151 (tpm170) REVERT: B 16 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: B 50 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 102 HIS cc_start: 0.7959 (m-70) cc_final: 0.7734 (m-70) REVERT: B 132 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6258 (tpm170) REVERT: B 135 TRP cc_start: 0.7514 (m-10) cc_final: 0.7122 (m100) REVERT: C 16 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: C 132 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6328 (tmt170) REVERT: C 135 TRP cc_start: 0.7492 (m-10) cc_final: 0.7177 (m100) REVERT: D 16 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7005 (mtt-85) REVERT: D 50 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 132 ARG cc_start: 0.7149 (ptp-170) cc_final: 0.6125 (tpm170) REVERT: D 135 TRP cc_start: 0.7529 (m-10) cc_final: 0.7228 (m100) REVERT: E 16 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6919 (mtt-85) REVERT: E 50 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 102 HIS cc_start: 0.7969 (m-70) cc_final: 0.7744 (m-70) REVERT: E 132 ARG cc_start: 0.7199 (ptp-170) cc_final: 0.6250 (tpm170) REVERT: E 135 TRP cc_start: 0.7530 (m-10) cc_final: 0.7157 (m100) REVERT: F 16 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: F 132 ARG cc_start: 0.7161 (ptp-170) cc_final: 0.6312 (tmt170) REVERT: F 135 TRP cc_start: 0.7503 (m-10) cc_final: 0.7191 (m100) outliers start: 30 outliers final: 6 residues processed: 178 average time/residue: 1.5049 time to fit residues: 283.2492 Evaluate side-chains 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN C 80 GLN D 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126316 restraints weight = 26414.960| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.27 r_work: 0.3113 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10242 Z= 0.161 Angle : 0.597 4.371 13908 Z= 0.311 Chirality : 0.037 0.158 1578 Planarity : 0.006 0.029 1650 Dihedral : 12.533 84.592 2106 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.11 % Allowed : 11.95 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.95 (0.24), residues: 1182 helix: 1.24 (0.17), residues: 864 sheet: 0.47 (0.58), residues: 60 loop : -1.28 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 7 TYR 0.006 0.001 TYR B 91 PHE 0.012 0.001 PHE E 94 TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00282 (10224) covalent geometry : angle 0.59685 (13872) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.48530 ( 36) hydrogen bonds : bond 0.08547 ( 690) hydrogen bonds : angle 4.55534 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.531 Fit side-chains REVERT: A 16 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7079 (mtt-85) REVERT: A 135 TRP cc_start: 0.8056 (m-10) cc_final: 0.7561 (m100) REVERT: B 16 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7060 (mtt-85) REVERT: B 135 TRP cc_start: 0.7988 (m-10) cc_final: 0.7379 (m100) REVERT: C 16 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7054 (mtt-85) REVERT: C 135 TRP cc_start: 0.7993 (m-10) cc_final: 0.7482 (m100) REVERT: D 16 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: D 135 TRP cc_start: 0.8001 (m-10) cc_final: 0.7498 (m100) REVERT: E 16 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7074 (mtt-85) REVERT: E 135 TRP cc_start: 0.8000 (m-10) cc_final: 0.7386 (m100) REVERT: F 16 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7049 (mtt-85) REVERT: F 135 TRP cc_start: 0.7973 (m-10) cc_final: 0.7458 (m100) outliers start: 21 outliers final: 13 residues processed: 123 average time/residue: 1.5281 time to fit residues: 197.5531 Evaluate side-chains 127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN E 80 GLN F 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117813 restraints weight = 26196.333| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.34 r_work: 0.3010 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10242 Z= 0.197 Angle : 0.653 4.709 13908 Z= 0.328 Chirality : 0.039 0.117 1578 Planarity : 0.006 0.032 1650 Dihedral : 12.616 86.918 2106 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.91 % Allowed : 11.14 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 1.78 (0.24), residues: 1182 helix: 1.95 (0.17), residues: 864 sheet: 0.77 (0.56), residues: 60 loop : -1.42 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 132 TYR 0.011 0.003 TYR B 159 PHE 0.015 0.002 PHE C 51 TRP 0.007 0.001 TRP E 101 HIS 0.003 0.001 HIS E 98 Details of bonding type rmsd covalent geometry : bond 0.00443 (10224) covalent geometry : angle 0.65133 (13872) SS BOND : bond 0.00617 ( 18) SS BOND : angle 1.01436 ( 36) hydrogen bonds : bond 0.08623 ( 690) hydrogen bonds : angle 4.19396 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.472 Fit side-chains REVERT: A 16 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7126 (mtt-85) REVERT: A 135 TRP cc_start: 0.8021 (m-10) cc_final: 0.7534 (m100) REVERT: A 220 ARG cc_start: 0.1905 (OUTLIER) cc_final: 0.1534 (tpm170) REVERT: B 16 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7098 (mtt-85) REVERT: B 102 HIS cc_start: 0.7814 (m-70) cc_final: 0.7512 (m-70) REVERT: B 135 TRP cc_start: 0.7988 (m-10) cc_final: 0.7493 (m100) REVERT: B 220 ARG cc_start: 0.2004 (OUTLIER) cc_final: 0.1535 (tpm170) REVERT: C 16 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: C 102 HIS cc_start: 0.7863 (m-70) cc_final: 0.7630 (m-70) REVERT: C 135 TRP cc_start: 0.8071 (m-10) cc_final: 0.7549 (m100) REVERT: C 220 ARG cc_start: 0.2056 (OUTLIER) cc_final: 0.1568 (tpm170) REVERT: D 16 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7136 (mtt-85) REVERT: D 135 TRP cc_start: 0.8004 (m-10) cc_final: 0.7524 (m100) REVERT: D 220 ARG cc_start: 0.1882 (OUTLIER) cc_final: 0.1468 (tpm170) REVERT: E 16 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7096 (mtt-85) REVERT: E 102 HIS cc_start: 0.7838 (m-70) cc_final: 0.7534 (m-70) REVERT: E 135 TRP cc_start: 0.7990 (m-10) cc_final: 0.7489 (m100) REVERT: E 220 ARG cc_start: 0.1928 (OUTLIER) cc_final: 0.1462 (tpm170) REVERT: F 16 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7114 (mtt-85) REVERT: F 135 TRP cc_start: 0.8073 (m-10) cc_final: 0.7551 (m100) REVERT: F 220 ARG cc_start: 0.2040 (OUTLIER) cc_final: 0.1561 (tpm170) outliers start: 29 outliers final: 10 residues processed: 141 average time/residue: 1.7995 time to fit residues: 266.3989 Evaluate side-chains 134 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121408 restraints weight = 26082.652| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.33 r_work: 0.3048 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10242 Z= 0.125 Angle : 0.505 4.447 13908 Z= 0.261 Chirality : 0.034 0.115 1578 Planarity : 0.004 0.028 1650 Dihedral : 11.615 89.753 2106 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.71 % Allowed : 13.25 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.37 (0.25), residues: 1182 helix: 2.40 (0.17), residues: 864 sheet: 1.17 (0.58), residues: 60 loop : -1.37 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 184 TYR 0.008 0.002 TYR D 97 PHE 0.010 0.001 PHE A 51 TRP 0.007 0.001 TRP F 103 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00247 (10224) covalent geometry : angle 0.50479 (13872) SS BOND : bond 0.00324 ( 18) SS BOND : angle 0.62804 ( 36) hydrogen bonds : bond 0.06767 ( 690) hydrogen bonds : angle 3.99812 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.505 Fit side-chains REVERT: A 16 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7194 (mtt-85) REVERT: A 135 TRP cc_start: 0.7996 (m-10) cc_final: 0.7502 (m100) REVERT: B 16 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7140 (mtt-85) REVERT: B 102 HIS cc_start: 0.7733 (m-70) cc_final: 0.7464 (m-70) REVERT: B 135 TRP cc_start: 0.7946 (m-10) cc_final: 0.7446 (m100) REVERT: C 102 HIS cc_start: 0.7773 (m-70) cc_final: 0.7538 (m-70) REVERT: C 135 TRP cc_start: 0.8027 (m-10) cc_final: 0.7529 (m100) REVERT: D 16 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7206 (mtt-85) REVERT: D 135 TRP cc_start: 0.7980 (m-10) cc_final: 0.7482 (m100) REVERT: E 16 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7189 (mtt-85) REVERT: E 102 HIS cc_start: 0.7743 (m-70) cc_final: 0.7473 (m-70) REVERT: E 135 TRP cc_start: 0.7937 (m-10) cc_final: 0.7442 (m100) REVERT: F 135 TRP cc_start: 0.8030 (m-10) cc_final: 0.7529 (m100) outliers start: 17 outliers final: 6 residues processed: 134 average time/residue: 1.9158 time to fit residues: 269.8812 Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 178 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118916 restraints weight = 26020.304| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.35 r_work: 0.3023 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10242 Z= 0.150 Angle : 0.559 4.612 13908 Z= 0.281 Chirality : 0.036 0.114 1578 Planarity : 0.005 0.029 1650 Dihedral : 11.115 89.452 2092 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.20 % Allowed : 13.55 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.52 (0.25), residues: 1182 helix: 2.53 (0.17), residues: 864 sheet: 1.45 (0.60), residues: 60 loop : -1.45 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 15 TYR 0.010 0.002 TYR D 97 PHE 0.013 0.002 PHE C 51 TRP 0.007 0.001 TRP F 103 HIS 0.002 0.001 HIS F 98 Details of bonding type rmsd covalent geometry : bond 0.00323 (10224) covalent geometry : angle 0.55805 (13872) SS BOND : bond 0.00475 ( 18) SS BOND : angle 0.80211 ( 36) hydrogen bonds : bond 0.07292 ( 690) hydrogen bonds : angle 3.94041 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.553 Fit side-chains REVERT: A 16 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7263 (mtt-85) REVERT: A 135 TRP cc_start: 0.8028 (m-10) cc_final: 0.7510 (m100) REVERT: B 16 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7306 (mtt-85) REVERT: B 102 HIS cc_start: 0.7721 (m-70) cc_final: 0.7457 (m-70) REVERT: B 135 TRP cc_start: 0.7968 (m-10) cc_final: 0.7469 (m100) REVERT: C 102 HIS cc_start: 0.7783 (m-70) cc_final: 0.7556 (m-70) REVERT: C 135 TRP cc_start: 0.8068 (m-10) cc_final: 0.7562 (m100) REVERT: D 135 TRP cc_start: 0.8016 (m-10) cc_final: 0.7509 (m100) REVERT: E 16 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7353 (mtt-85) REVERT: E 102 HIS cc_start: 0.7723 (m-70) cc_final: 0.7448 (m-70) REVERT: E 135 TRP cc_start: 0.7979 (m-10) cc_final: 0.7478 (m100) REVERT: F 135 TRP cc_start: 0.8072 (m-10) cc_final: 0.7556 (m100) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 1.5857 time to fit residues: 205.1609 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116424 restraints weight = 25313.104| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.36 r_work: 0.3050 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10242 Z= 0.126 Angle : 0.503 4.558 13908 Z= 0.257 Chirality : 0.034 0.133 1578 Planarity : 0.004 0.028 1650 Dihedral : 9.321 85.957 2088 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.90 % Allowed : 14.16 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.70 (0.25), residues: 1182 helix: 2.66 (0.17), residues: 864 sheet: 1.63 (0.62), residues: 60 loop : -1.43 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 8 TYR 0.009 0.002 TYR D 156 PHE 0.011 0.001 PHE C 51 TRP 0.006 0.001 TRP B 101 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00261 (10224) covalent geometry : angle 0.50241 (13872) SS BOND : bond 0.00383 ( 18) SS BOND : angle 0.65954 ( 36) hydrogen bonds : bond 0.06480 ( 690) hydrogen bonds : angle 3.85725 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7970 (m-10) cc_final: 0.7491 (m100) REVERT: B 16 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7321 (mtt-85) REVERT: B 135 TRP cc_start: 0.7965 (m-10) cc_final: 0.7464 (m100) REVERT: C 135 TRP cc_start: 0.8050 (m-10) cc_final: 0.7542 (m100) REVERT: D 135 TRP cc_start: 0.7998 (m-10) cc_final: 0.7483 (m100) REVERT: E 16 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7313 (mtt-85) REVERT: E 102 HIS cc_start: 0.7656 (m-70) cc_final: 0.7408 (m-70) REVERT: E 135 TRP cc_start: 0.7961 (m-10) cc_final: 0.7463 (m100) REVERT: F 135 TRP cc_start: 0.8060 (m-10) cc_final: 0.7549 (m100) outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 1.5460 time to fit residues: 196.9166 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118099 restraints weight = 25419.297| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.37 r_work: 0.3070 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10242 Z= 0.108 Angle : 0.470 4.255 13908 Z= 0.240 Chirality : 0.033 0.141 1578 Planarity : 0.004 0.030 1650 Dihedral : 8.467 88.712 2084 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.10 % Allowed : 14.16 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.94 (0.25), residues: 1182 helix: 2.87 (0.17), residues: 864 sheet: 1.82 (0.66), residues: 60 loop : -1.49 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.007 0.001 TYR B 156 PHE 0.008 0.001 PHE C 51 TRP 0.006 0.001 TRP B 101 HIS 0.003 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00214 (10224) covalent geometry : angle 0.47007 (13872) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.53334 ( 36) hydrogen bonds : bond 0.05736 ( 690) hydrogen bonds : angle 3.74342 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7970 (m-10) cc_final: 0.7479 (m100) REVERT: B 16 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7796 (mtt90) REVERT: B 102 HIS cc_start: 0.7649 (m-70) cc_final: 0.7364 (m-70) REVERT: B 135 TRP cc_start: 0.7949 (m-10) cc_final: 0.7448 (m100) REVERT: C 135 TRP cc_start: 0.8028 (m-10) cc_final: 0.7516 (m100) REVERT: D 132 ARG cc_start: 0.7001 (ptm160) cc_final: 0.6652 (ptm160) REVERT: D 135 TRP cc_start: 0.7947 (m-10) cc_final: 0.7466 (m100) REVERT: E 16 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7802 (mtt90) REVERT: E 135 TRP cc_start: 0.7936 (m-10) cc_final: 0.7438 (m100) REVERT: F 135 TRP cc_start: 0.8032 (m-10) cc_final: 0.7520 (m100) outliers start: 11 outliers final: 8 residues processed: 123 average time/residue: 1.8783 time to fit residues: 242.6544 Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 140 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114122 restraints weight = 25392.399| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.37 r_work: 0.3032 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10242 Z= 0.166 Angle : 0.570 4.753 13908 Z= 0.287 Chirality : 0.037 0.135 1578 Planarity : 0.005 0.052 1650 Dihedral : 9.008 85.996 2084 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.90 % Allowed : 14.56 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.70 (0.25), residues: 1182 helix: 2.62 (0.17), residues: 870 sheet: 1.77 (0.64), residues: 60 loop : -1.38 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.011 0.003 TYR E 159 PHE 0.015 0.002 PHE C 51 TRP 0.009 0.001 TRP B 103 HIS 0.003 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00369 (10224) covalent geometry : angle 0.56838 (13872) SS BOND : bond 0.00549 ( 18) SS BOND : angle 0.91486 ( 36) hydrogen bonds : bond 0.07272 ( 690) hydrogen bonds : angle 3.83458 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7140 (ptm160) cc_final: 0.6777 (ptm160) REVERT: A 135 TRP cc_start: 0.8013 (m-10) cc_final: 0.7490 (m100) REVERT: B 16 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7819 (mtt90) REVERT: B 135 TRP cc_start: 0.7967 (m-10) cc_final: 0.7472 (m100) REVERT: C 135 TRP cc_start: 0.8065 (m-10) cc_final: 0.7549 (m100) REVERT: D 132 ARG cc_start: 0.7154 (ptm160) cc_final: 0.6806 (ptm160) REVERT: D 135 TRP cc_start: 0.8002 (m-10) cc_final: 0.7513 (m100) REVERT: E 16 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: E 135 TRP cc_start: 0.7978 (m-10) cc_final: 0.7483 (m100) REVERT: F 135 TRP cc_start: 0.8077 (m-10) cc_final: 0.7552 (m100) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 2.0116 time to fit residues: 252.9655 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115133 restraints weight = 25238.078| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.35 r_work: 0.3029 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10242 Z= 0.144 Angle : 0.532 4.756 13908 Z= 0.271 Chirality : 0.036 0.138 1578 Planarity : 0.005 0.035 1650 Dihedral : 8.645 81.731 2084 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.80 % Allowed : 14.56 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.70 (0.25), residues: 1182 helix: 2.62 (0.17), residues: 870 sheet: 1.79 (0.65), residues: 60 loop : -1.38 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 8 TYR 0.010 0.002 TYR A 97 PHE 0.012 0.002 PHE C 51 TRP 0.007 0.001 TRP E 103 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00313 (10224) covalent geometry : angle 0.53076 (13872) SS BOND : bond 0.00441 ( 18) SS BOND : angle 0.81728 ( 36) hydrogen bonds : bond 0.06882 ( 690) hydrogen bonds : angle 3.82853 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6796 (ptm160) REVERT: A 135 TRP cc_start: 0.8000 (m-10) cc_final: 0.7514 (m100) REVERT: B 16 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: B 135 TRP cc_start: 0.7979 (m-10) cc_final: 0.7380 (m100) REVERT: C 135 TRP cc_start: 0.8058 (m-10) cc_final: 0.7551 (m100) REVERT: D 135 TRP cc_start: 0.7989 (m-10) cc_final: 0.7509 (m100) REVERT: E 16 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7815 (mtt90) REVERT: E 135 TRP cc_start: 0.7976 (m-10) cc_final: 0.7379 (m100) REVERT: F 135 TRP cc_start: 0.8057 (m-10) cc_final: 0.7538 (m100) outliers start: 8 outliers final: 6 residues processed: 119 average time/residue: 2.0156 time to fit residues: 251.5075 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117364 restraints weight = 25513.198| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.36 r_work: 0.3061 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10242 Z= 0.111 Angle : 0.479 4.362 13908 Z= 0.244 Chirality : 0.034 0.143 1578 Planarity : 0.004 0.040 1650 Dihedral : 7.969 73.854 2084 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.70 % Allowed : 14.86 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 2.90 (0.25), residues: 1182 helix: 2.80 (0.17), residues: 870 sheet: 1.82 (0.65), residues: 60 loop : -1.43 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 15 TYR 0.008 0.002 TYR D 156 PHE 0.008 0.001 PHE C 51 TRP 0.007 0.001 TRP B 103 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00221 (10224) covalent geometry : angle 0.47821 (13872) SS BOND : bond 0.00290 ( 18) SS BOND : angle 0.60081 ( 36) hydrogen bonds : bond 0.05888 ( 690) hydrogen bonds : angle 3.74139 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6704 (ptm160) REVERT: A 135 TRP cc_start: 0.7988 (m-10) cc_final: 0.7507 (m100) REVERT: B 16 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7768 (mtt90) REVERT: B 135 TRP cc_start: 0.7976 (m-10) cc_final: 0.7374 (m100) REVERT: C 135 TRP cc_start: 0.8036 (m-10) cc_final: 0.7505 (m100) REVERT: D 132 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6694 (ptm160) REVERT: D 135 TRP cc_start: 0.7975 (m-10) cc_final: 0.7493 (m100) REVERT: E 135 TRP cc_start: 0.7972 (m-10) cc_final: 0.7372 (m100) REVERT: F 135 TRP cc_start: 0.8051 (m-10) cc_final: 0.7517 (m100) outliers start: 7 outliers final: 6 residues processed: 120 average time/residue: 1.7195 time to fit residues: 216.8305 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.158016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119051 restraints weight = 25629.288| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.37 r_work: 0.3087 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10242 Z= 0.101 Angle : 0.455 4.130 13908 Z= 0.230 Chirality : 0.033 0.145 1578 Planarity : 0.004 0.056 1650 Dihedral : 7.267 59.146 2080 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.60 % Allowed : 14.86 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 3.13 (0.25), residues: 1182 helix: 3.06 (0.17), residues: 864 sheet: 1.87 (0.66), residues: 60 loop : -1.62 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 8 TYR 0.008 0.001 TYR A 156 PHE 0.008 0.001 PHE A 51 TRP 0.006 0.001 TRP F 103 HIS 0.002 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00199 (10224) covalent geometry : angle 0.45460 (13872) SS BOND : bond 0.00233 ( 18) SS BOND : angle 0.51779 ( 36) hydrogen bonds : bond 0.05222 ( 690) hydrogen bonds : angle 3.62530 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7549.48 seconds wall clock time: 128 minutes 20.21 seconds (7700.21 seconds total)