Starting phenix.real_space_refine on Sat Aug 23 09:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1s_16382/08_2025/8c1s_16382_neut.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 72 5.16 5 C 7136 2.51 5 N 1638 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s 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: 10668 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1173 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 151, 1173 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1180 Chain: "B" Number of atoms: 1204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1182 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 154, 1182 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1189 Chain: "C" Number of atoms: 1169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1147 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 149, 1147 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1152 Chain: "D" Number of atoms: 1217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1195 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 155, 1195 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1202 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1381 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1379 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'PLM': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'PLM': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE B 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 574 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE C 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 574 " occ=0.50 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 3.30, per 1000 atoms: 0.31 Number of scatterers: 10668 At special positions: 0 Unit cell: (96.642, 97.468, 96.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 4 15.00 O 1818 8.00 N 1638 7.00 C 7136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.05 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.07 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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: 0.79 Conformation dependent library (CDL) restraints added in 568.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 69.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.693A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.550A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.667A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 removed outlier: 3.587A pdb=" N TRP B 551 " --> pdb=" O PRO B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.560A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.648A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.708A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.582A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.549A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.735A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.639A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.899A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 208 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.937A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.083A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.541A pdb=" N GLY G 139 " --> pdb=" O ILE G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 208 removed outlier: 3.623A pdb=" N LEU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 removed outlier: 4.049A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 removed outlier: 3.554A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 3.996A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG H 209 " --> pdb=" O HIS H 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA2, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.887A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AA6, first strand: chain 'H' and resid 65 through 67 770 hydrogen bonds defined for protein. 2266 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: 1.74 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1578 1.31 - 1.44: 3310 1.44 - 1.58: 5908 1.58 - 1.71: 9 1.71 - 1.84: 111 Bond restraints: 10916 Sorted by residual: bond pdb=" CA SER B 544 " pdb=" CB SER B 544 " ideal model delta sigma weight residual 1.533 1.441 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CG MET B 585 " pdb=" SD MET B 585 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.48e+01 bond pdb=" CA SER D 592 " pdb=" CB SER D 592 " ideal model delta sigma weight residual 1.536 1.460 0.076 1.83e-02 2.99e+03 1.74e+01 bond pdb=" C LEU D 581 " pdb=" N GLY D 582 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" C GLN G 207 " pdb=" O GLN G 207 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.17e-02 7.31e+03 1.57e+01 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 13810 2.45 - 4.90: 818 4.90 - 7.35: 57 7.35 - 9.80: 4 9.80 - 12.26: 5 Bond angle restraints: 14694 Sorted by residual: angle pdb=" N ASN B 575 " pdb=" CA ASN B 575 " pdb=" C ASN B 575 " ideal model delta sigma weight residual 113.50 103.41 10.09 1.23e+00 6.61e-01 6.73e+01 angle pdb=" O GLN C 587 " pdb=" C GLN C 587 " pdb=" N GLY C 588 " ideal model delta sigma weight residual 120.83 125.68 -4.85 7.40e-01 1.83e+00 4.30e+01 angle pdb=" O GLN G 207 " pdb=" C GLN G 207 " pdb=" N LEU G 208 " ideal model delta sigma weight residual 122.12 115.54 6.58 1.06e+00 8.90e-01 3.85e+01 angle pdb=" N PRO A 548 " pdb=" CA PRO A 548 " pdb=" CB PRO A 548 " ideal model delta sigma weight residual 103.25 96.78 6.47 1.05e+00 9.07e-01 3.80e+01 angle pdb=" C GLN C 587 " pdb=" CA GLN C 587 " pdb=" CB GLN C 587 " ideal model delta sigma weight residual 115.27 103.01 12.26 2.00e+00 2.50e-01 3.75e+01 ... (remaining 14689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 5954 29.36 - 58.72: 302 58.72 - 88.07: 38 88.07 - 117.43: 8 117.43 - 146.79: 2 Dihedral angle restraints: 6304 sinusoidal: 2514 harmonic: 3790 Sorted by residual: dihedral pdb=" CD ARG G 204 " pdb=" NE ARG G 204 " pdb=" CZ ARG G 204 " pdb=" NH1 ARG G 204 " ideal model delta sinusoidal sigma weight residual 0.00 82.28 -82.28 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 28.27 64.73 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 42.48 50.52 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 980 0.067 - 0.135: 477 0.135 - 0.202: 140 0.202 - 0.270: 26 0.270 - 0.337: 5 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CB ILE F 157 " pdb=" CA ILE F 157 " pdb=" CG1 ILE F 157 " pdb=" CG2 ILE F 157 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA SER D 615 " pdb=" N SER D 615 " pdb=" C SER D 615 " pdb=" CB SER D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PHE F 107 " pdb=" N PHE F 107 " pdb=" C PHE F 107 " pdb=" CB PHE F 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1625 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 204 " 1.040 9.50e-02 1.11e+02 4.67e-01 1.39e+02 pdb=" NE ARG G 204 " -0.080 2.00e-02 2.50e+03 pdb=" CZ ARG G 204 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG G 204 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 204 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 209 " -0.916 9.50e-02 1.11e+02 4.12e-01 1.13e+02 pdb=" NE ARG H 209 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG H 209 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG H 209 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG H 209 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 586 " -0.833 9.50e-02 1.11e+02 3.75e-01 9.49e+01 pdb=" NE ARG C 586 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 586 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 586 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 586 " -0.042 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1903 2.77 - 3.30: 10912 3.30 - 3.83: 17815 3.83 - 4.37: 20332 4.37 - 4.90: 35968 Nonbonded interactions: 86930 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.234 3.040 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.249 3.040 nonbonded pdb=" O ASP E 31 " pdb=" O SER E 61 " model vdw 2.313 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.338 3.120 nonbonded pdb=" N MET E 58 " pdb=" OE2 GLU E 70 " model vdw 2.339 3.120 ... (remaining 86925 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 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 549 or resid 571 t \ hrough 573 or resid 575 through 622 or resid 624 through 626 or (resid 627 and ( \ name N or name CA or name C or name O or name CB )) or resid 628 through 633 or \ (resid 634 through 784 and (name N or name CA or name C or name O or name CB )) \ or resid 785 through 812 or (resid 813 and (name N or name CA or name C or name \ O or name CB )) or resid 814 through 818 or (resid 819 through 823 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 549 or resid 5 \ 71 through 573 or resid 575 or (resid 576 and (name N or name CA or name C or na \ me O or name CB )) or resid 577 through 622 or resid 624 through 634 or (resid 7 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 785 through \ 823)) selection = (chain 'C' and (resid 506 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 622 or resid 624 \ through 626 or (resid 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 633 or (resid 634 through 784 and (name N or name CA or \ name C or name O or name CB )) or resid 785 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 818 or (resi \ d 819 through 823 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 549 or resid 5 \ 71 through 573 or resid 575 or (resid 576 and (name N or name CA or name C or na \ me O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 6 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 628 through \ 634 or (resid 784 and (name N or name CA or name C or name O or name CB )) or r \ esid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 208 or (resid 209 through \ 210 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.012 0.125 10924 Z= 0.714 Angle : 1.291 12.255 14710 Z= 0.812 Chirality : 0.084 0.337 1628 Planarity : 0.025 0.467 1760 Dihedral : 17.433 146.791 3852 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 1.87 % Allowed : 3.82 % Favored : 94.31 % 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 aren not related in a simple way. whole: 1.35 (0.23), residues: 1286 helix: 2.11 (0.16), residues: 921 sheet: -0.09 (1.96), residues: 10 loop : -2.53 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.005 ARG H 209 TYR 0.058 0.010 TYR H 35 PHE 0.078 0.011 PHE A 571 TRP 0.050 0.013 TRP B 578 HIS 0.016 0.005 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.01157 (10916) covalent geometry : angle 1.28520 (14694) SS BOND : bond 0.01952 ( 8) SS BOND : angle 3.77354 ( 16) hydrogen bonds : bond 0.13788 ( 770) hydrogen bonds : angle 5.06635 ( 2266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 LYS cc_start: 0.7861 (tttm) cc_final: 0.7546 (tmmt) REVERT: B 594 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8061 (mtm-85) REVERT: C 594 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8383 (mtp-110) REVERT: C 807 MET cc_start: 0.8925 (mtm) cc_final: 0.8538 (mtm) REVERT: D 594 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8587 (mtm110) REVERT: E 122 ILE cc_start: 0.7947 (mm) cc_final: 0.7703 (tt) REVERT: E 199 HIS cc_start: 0.7571 (t-90) cc_final: 0.7331 (t-90) REVERT: F 61 SER cc_start: 0.8883 (t) cc_final: 0.8644 (m) REVERT: F 65 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7391 (mtp85) REVERT: F 204 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7717 (mpt-90) REVERT: F 207 GLN cc_start: 0.7437 (tt0) cc_final: 0.7185 (tm-30) REVERT: H 56 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7086 (mm-30) REVERT: H 65 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7245 (mtm-85) REVERT: H 99 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7529 (mtt180) outliers start: 20 outliers final: 5 residues processed: 214 average time/residue: 0.6172 time to fit residues: 140.7440 Evaluate side-chains 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 204 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS G 133 ASN H 79 GLN H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090365 restraints weight = 43509.933| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 5.40 r_work: 0.2588 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10924 Z= 0.138 Angle : 0.549 7.637 14710 Z= 0.298 Chirality : 0.039 0.211 1628 Planarity : 0.004 0.038 1760 Dihedral : 13.840 111.856 1725 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.24 % Allowed : 11.29 % Favored : 86.47 % 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 aren not related in a simple way. whole: 2.63 (0.25), residues: 1286 helix: 3.08 (0.17), residues: 925 sheet: -0.32 (1.82), residues: 10 loop : -2.16 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 586 TYR 0.014 0.001 TYR H 174 PHE 0.018 0.001 PHE G 73 TRP 0.011 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00295 (10916) covalent geometry : angle 0.54581 (14694) SS BOND : bond 0.00419 ( 8) SS BOND : angle 1.98002 ( 16) hydrogen bonds : bond 0.04725 ( 770) hydrogen bonds : angle 3.53339 ( 2266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 586 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8635 (mmm-85) REVERT: B 594 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8029 (mtm-85) REVERT: B 818 SER cc_start: 0.7689 (t) cc_final: 0.7376 (m) REVERT: C 586 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8136 (mmm-85) REVERT: C 594 ARG cc_start: 0.8674 (mtt180) cc_final: 0.8406 (mtp-110) REVERT: D 594 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8580 (mtm110) REVERT: E 58 MET cc_start: 0.7056 (mmt) cc_final: 0.6840 (tpp) REVERT: E 73 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6358 (p90) REVERT: E 199 HIS cc_start: 0.8291 (t-90) cc_final: 0.8050 (t-90) REVERT: F 11 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8391 (tm) REVERT: F 65 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7629 (mtp85) REVERT: F 98 LEU cc_start: 0.7866 (tt) cc_final: 0.7521 (tp) REVERT: F 128 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6517 (t80) REVERT: F 174 TYR cc_start: 0.8993 (p90) cc_final: 0.8731 (p90) REVERT: F 208 LEU cc_start: 0.8467 (tt) cc_final: 0.8242 (tp) REVERT: G 79 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8220 (tp40) REVERT: G 131 ARG cc_start: 0.7350 (tpp80) cc_final: 0.7061 (tpp80) REVERT: G 205 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7334 (t-90) REVERT: H 99 ARG cc_start: 0.7809 (mmt180) cc_final: 0.7340 (tpp80) outliers start: 24 outliers final: 9 residues processed: 185 average time/residue: 0.6061 time to fit residues: 119.4451 Evaluate side-chains 177 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.088402 restraints weight = 44644.062| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 5.46 r_work: 0.2559 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10924 Z= 0.155 Angle : 0.540 7.871 14710 Z= 0.290 Chirality : 0.039 0.191 1628 Planarity : 0.004 0.038 1760 Dihedral : 12.424 98.578 1713 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.43 % Allowed : 13.34 % Favored : 84.24 % 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 aren not related in a simple way. whole: 2.79 (0.25), residues: 1286 helix: 3.18 (0.17), residues: 926 sheet: -1.77 (1.52), residues: 12 loop : -2.03 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 586 TYR 0.013 0.001 TYR B 523 PHE 0.024 0.002 PHE E 127 TRP 0.007 0.001 TRP E 178 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00352 (10916) covalent geometry : angle 0.53690 (14694) SS BOND : bond 0.01032 ( 8) SS BOND : angle 1.88957 ( 16) hydrogen bonds : bond 0.04624 ( 770) hydrogen bonds : angle 3.38764 ( 2266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.448 Fit side-chains REVERT: B 509 LYS cc_start: 0.7743 (tmmt) cc_final: 0.7448 (tttp) REVERT: B 594 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: C 594 ARG cc_start: 0.8691 (mtt180) cc_final: 0.8431 (mtp-110) REVERT: D 594 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8573 (mtm110) REVERT: D 626 VAL cc_start: 0.8884 (p) cc_final: 0.8462 (m) REVERT: E 58 MET cc_start: 0.7224 (mmt) cc_final: 0.6997 (tpt) REVERT: F 11 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8306 (tm) REVERT: F 65 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7632 (mtp85) REVERT: F 98 LEU cc_start: 0.7923 (tt) cc_final: 0.7707 (tp) REVERT: F 174 TYR cc_start: 0.8990 (p90) cc_final: 0.8776 (p90) REVERT: G 79 GLN cc_start: 0.8439 (mt0) cc_final: 0.8235 (tp40) REVERT: G 131 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7187 (tpp80) REVERT: G 205 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: H 37 ARG cc_start: 0.8115 (ttt-90) cc_final: 0.7732 (mtp85) REVERT: H 65 ARG cc_start: 0.8136 (ptt-90) cc_final: 0.7827 (ptt-90) REVERT: H 99 ARG cc_start: 0.7853 (mmt180) cc_final: 0.7366 (tpp80) outliers start: 26 outliers final: 12 residues processed: 186 average time/residue: 0.6187 time to fit residues: 122.8791 Evaluate side-chains 172 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN E 205 HIS H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.085395 restraints weight = 46489.555| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 5.69 r_work: 0.2478 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10924 Z= 0.195 Angle : 0.569 7.271 14710 Z= 0.306 Chirality : 0.041 0.247 1628 Planarity : 0.004 0.039 1760 Dihedral : 12.259 89.119 1712 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.73 % Allowed : 14.37 % Favored : 81.90 % 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 aren not related in a simple way. whole: 2.66 (0.24), residues: 1286 helix: 3.05 (0.17), residues: 925 sheet: -1.31 (1.56), residues: 12 loop : -1.95 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 586 TYR 0.016 0.001 TYR B 523 PHE 0.020 0.002 PHE G 73 TRP 0.007 0.001 TRP B 578 HIS 0.005 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00462 (10916) covalent geometry : angle 0.56606 (14694) SS BOND : bond 0.00895 ( 8) SS BOND : angle 1.82973 ( 16) hydrogen bonds : bond 0.04966 ( 770) hydrogen bonds : angle 3.44011 ( 2266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 509 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7467 (tttp) REVERT: B 594 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8298 (mtt180) REVERT: C 587 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8384 (tp40) REVERT: C 594 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8351 (mtp-110) REVERT: C 807 MET cc_start: 0.9250 (mtm) cc_final: 0.8977 (mtm) REVERT: D 594 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8553 (mtm110) REVERT: D 626 VAL cc_start: 0.8914 (p) cc_final: 0.8497 (m) REVERT: E 37 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7979 (ttt90) REVERT: E 58 MET cc_start: 0.7347 (mmt) cc_final: 0.7137 (tpt) REVERT: E 122 ILE cc_start: 0.8360 (mm) cc_final: 0.7868 (tt) REVERT: E 131 ARG cc_start: 0.6361 (mmm160) cc_final: 0.5898 (mmt180) REVERT: E 199 HIS cc_start: 0.8423 (t-90) cc_final: 0.8204 (t-90) REVERT: F 11 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8356 (tm) REVERT: F 65 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7803 (mtp85) REVERT: F 98 LEU cc_start: 0.7981 (tt) cc_final: 0.7773 (tp) REVERT: F 204 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7814 (ttm170) REVERT: F 207 GLN cc_start: 0.7758 (tt0) cc_final: 0.7422 (tm-30) REVERT: G 79 GLN cc_start: 0.8478 (mt0) cc_final: 0.8201 (tp40) REVERT: G 131 ARG cc_start: 0.7506 (tpp80) cc_final: 0.7186 (tpp80) REVERT: G 205 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7196 (t-90) REVERT: H 11 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8083 (tp) REVERT: H 65 ARG cc_start: 0.8132 (ptt-90) cc_final: 0.7856 (ptt-90) REVERT: H 99 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7483 (tpp80) outliers start: 40 outliers final: 13 residues processed: 191 average time/residue: 0.5696 time to fit residues: 115.8415 Evaluate side-chains 179 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN E 205 HIS H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.089546 restraints weight = 45264.053| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.91 r_work: 0.2640 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.126 Angle : 0.513 7.841 14710 Z= 0.274 Chirality : 0.038 0.199 1628 Planarity : 0.004 0.037 1760 Dihedral : 11.561 87.781 1712 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.71 % Allowed : 16.14 % Favored : 81.16 % 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 aren not related in a simple way. whole: 3.02 (0.24), residues: 1286 helix: 3.35 (0.17), residues: 925 sheet: -1.26 (1.49), residues: 12 loop : -1.93 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 586 TYR 0.017 0.001 TYR B 523 PHE 0.017 0.001 PHE B 584 TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00274 (10916) covalent geometry : angle 0.50794 (14694) SS BOND : bond 0.00797 ( 8) SS BOND : angle 2.13101 ( 16) hydrogen bonds : bond 0.04250 ( 770) hydrogen bonds : angle 3.23340 ( 2266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 509 LYS cc_start: 0.7619 (tmmt) cc_final: 0.7383 (tttp) REVERT: B 594 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8267 (mtt180) REVERT: C 594 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8328 (mtp-110) REVERT: D 594 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8511 (mtm110) REVERT: D 626 VAL cc_start: 0.8717 (p) cc_final: 0.8318 (m) REVERT: E 58 MET cc_start: 0.7184 (mmt) cc_final: 0.6965 (tpt) REVERT: E 73 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6691 (p90) REVERT: E 122 ILE cc_start: 0.8126 (mm) cc_final: 0.7803 (tt) REVERT: E 131 ARG cc_start: 0.6249 (mmm160) cc_final: 0.5822 (mtt90) REVERT: F 11 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8315 (tm) REVERT: F 65 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7612 (mtp85) REVERT: F 204 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7511 (ttm170) REVERT: F 207 GLN cc_start: 0.7605 (tt0) cc_final: 0.7250 (tm-30) REVERT: G 79 GLN cc_start: 0.8343 (mt0) cc_final: 0.8133 (tp40) REVERT: G 131 ARG cc_start: 0.7491 (tpp80) cc_final: 0.6285 (mtp180) REVERT: G 205 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7154 (t-90) REVERT: H 65 ARG cc_start: 0.7989 (ptt-90) cc_final: 0.7659 (ptt-90) REVERT: H 99 ARG cc_start: 0.7798 (mmt180) cc_final: 0.7366 (ttp80) outliers start: 29 outliers final: 16 residues processed: 189 average time/residue: 0.5830 time to fit residues: 117.0917 Evaluate side-chains 181 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN E 205 HIS F 149 ASN H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090127 restraints weight = 47438.267| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.42 r_work: 0.2587 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.133 Angle : 0.514 7.264 14710 Z= 0.274 Chirality : 0.038 0.205 1628 Planarity : 0.003 0.036 1760 Dihedral : 11.209 86.661 1712 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.43 % Allowed : 16.60 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.24), residues: 1286 helix: 3.43 (0.16), residues: 925 sheet: -1.07 (1.56), residues: 12 loop : -1.82 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.017 0.001 TYR B 523 PHE 0.013 0.001 PHE G 127 TRP 0.007 0.001 TRP E 178 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00294 (10916) covalent geometry : angle 0.51002 (14694) SS BOND : bond 0.00910 ( 8) SS BOND : angle 1.98064 ( 16) hydrogen bonds : bond 0.04257 ( 770) hydrogen bonds : angle 3.18366 ( 2266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 509 LYS cc_start: 0.7612 (tmmt) cc_final: 0.7384 (tttp) REVERT: B 594 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8421 (mtt180) REVERT: C 594 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8477 (mpp80) REVERT: D 594 ARG cc_start: 0.8960 (mtt180) cc_final: 0.8535 (mtm110) REVERT: E 73 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6751 (p90) REVERT: E 122 ILE cc_start: 0.8185 (mm) cc_final: 0.7845 (tt) REVERT: E 131 ARG cc_start: 0.6298 (mmm160) cc_final: 0.5814 (mmt180) REVERT: E 208 LEU cc_start: 0.7609 (tt) cc_final: 0.7363 (mp) REVERT: F 11 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8336 (tm) REVERT: F 65 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7685 (mtp85) REVERT: G 131 ARG cc_start: 0.7520 (tpp80) cc_final: 0.6322 (mtp180) REVERT: G 205 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: H 65 ARG cc_start: 0.8071 (ptt-90) cc_final: 0.7747 (ptt-90) REVERT: H 99 ARG cc_start: 0.7781 (mmt180) cc_final: 0.7406 (tpp80) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.5778 time to fit residues: 113.0522 Evaluate side-chains 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS H 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090911 restraints weight = 44477.737| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.97 r_work: 0.2646 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10924 Z= 0.116 Angle : 0.492 7.626 14710 Z= 0.261 Chirality : 0.037 0.181 1628 Planarity : 0.003 0.034 1760 Dihedral : 10.729 85.093 1712 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.89 % Allowed : 16.42 % Favored : 80.69 % 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 aren not related in a simple way. whole: 3.37 (0.24), residues: 1286 helix: 3.56 (0.16), residues: 926 sheet: 0.19 (1.68), residues: 10 loop : -1.70 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 586 TYR 0.018 0.001 TYR B 523 PHE 0.013 0.001 PHE E 127 TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00249 (10916) covalent geometry : angle 0.48828 (14694) SS BOND : bond 0.00583 ( 8) SS BOND : angle 1.77713 ( 16) hydrogen bonds : bond 0.03984 ( 770) hydrogen bonds : angle 3.07394 ( 2266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7996 (mp0) REVERT: B 509 LYS cc_start: 0.7571 (tmmt) cc_final: 0.7321 (tttp) REVERT: B 594 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8306 (mtt180) REVERT: C 594 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8463 (mpp80) REVERT: D 594 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8509 (mtm110) REVERT: E 58 MET cc_start: 0.7515 (tpp) cc_final: 0.7225 (tpp) REVERT: E 73 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6777 (p90) REVERT: E 122 ILE cc_start: 0.8154 (mm) cc_final: 0.7819 (tt) REVERT: E 131 ARG cc_start: 0.6177 (mmm160) cc_final: 0.5741 (mmt180) REVERT: E 208 LEU cc_start: 0.7625 (tt) cc_final: 0.7376 (mp) REVERT: F 11 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8349 (tm) REVERT: F 65 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7705 (mtp85) REVERT: F 73 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6450 (p90) REVERT: G 131 ARG cc_start: 0.7587 (tpp80) cc_final: 0.6395 (mtp180) REVERT: G 205 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7162 (t-90) REVERT: H 99 ARG cc_start: 0.7743 (mmt180) cc_final: 0.7378 (tpp80) outliers start: 31 outliers final: 16 residues processed: 195 average time/residue: 0.6335 time to fit residues: 131.3667 Evaluate side-chains 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 160 ASN H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088098 restraints weight = 42811.710| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.79 r_work: 0.2602 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10924 Z= 0.157 Angle : 0.550 11.537 14710 Z= 0.287 Chirality : 0.039 0.170 1628 Planarity : 0.003 0.036 1760 Dihedral : 10.936 81.588 1712 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.61 % Allowed : 17.26 % Favored : 80.13 % 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 aren not related in a simple way. whole: 3.21 (0.24), residues: 1286 helix: 3.41 (0.16), residues: 926 sheet: -1.05 (1.63), residues: 12 loop : -1.64 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.018 0.001 TYR B 523 PHE 0.016 0.001 PHE G 127 TRP 0.009 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00363 (10916) covalent geometry : angle 0.54655 (14694) SS BOND : bond 0.00640 ( 8) SS BOND : angle 1.83286 ( 16) hydrogen bonds : bond 0.04529 ( 770) hydrogen bonds : angle 3.22727 ( 2266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8432 (mtm-85) REVERT: C 594 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8445 (mpp80) REVERT: D 586 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8472 (mmt90) REVERT: D 594 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8475 (mtm110) REVERT: E 58 MET cc_start: 0.7383 (tpp) cc_final: 0.7127 (tpt) REVERT: E 122 ILE cc_start: 0.8123 (mm) cc_final: 0.7803 (tt) REVERT: E 208 LEU cc_start: 0.7589 (tt) cc_final: 0.7334 (mp) REVERT: F 11 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8301 (tm) REVERT: F 65 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7664 (mtp85) REVERT: F 73 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6354 (p90) REVERT: F 128 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6396 (t80) REVERT: F 131 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7331 (mmt180) REVERT: F 207 GLN cc_start: 0.7595 (tt0) cc_final: 0.7375 (tm-30) REVERT: G 131 ARG cc_start: 0.7518 (tpp80) cc_final: 0.6304 (mtp180) REVERT: G 205 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: H 99 ARG cc_start: 0.7724 (mmt180) cc_final: 0.7352 (tpp80) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 0.6906 time to fit residues: 136.9030 Evaluate side-chains 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 55 optimal weight: 0.0030 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 160 ASN H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.090682 restraints weight = 44448.953| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.89 r_work: 0.2632 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10924 Z= 0.113 Angle : 0.500 8.722 14710 Z= 0.265 Chirality : 0.037 0.163 1628 Planarity : 0.003 0.034 1760 Dihedral : 10.537 81.358 1712 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.43 % Allowed : 17.35 % Favored : 80.22 % 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 aren not related in a simple way. whole: 3.43 (0.24), residues: 1286 helix: 3.57 (0.16), residues: 926 sheet: 0.06 (1.73), residues: 10 loop : -1.57 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.019 0.001 TYR B 523 PHE 0.015 0.001 PHE E 127 TRP 0.016 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00235 (10916) covalent geometry : angle 0.49746 (14694) SS BOND : bond 0.00796 ( 8) SS BOND : angle 1.61719 ( 16) hydrogen bonds : bond 0.03992 ( 770) hydrogen bonds : angle 3.07241 ( 2266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8448 (mtm-85) REVERT: C 594 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8421 (mpp80) REVERT: D 586 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8409 (mmt90) REVERT: D 594 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8483 (mtm110) REVERT: E 58 MET cc_start: 0.7450 (tpp) cc_final: 0.7168 (tpp) REVERT: E 73 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6897 (p90) REVERT: E 122 ILE cc_start: 0.8169 (mm) cc_final: 0.7846 (tt) REVERT: E 131 ARG cc_start: 0.6157 (mmm160) cc_final: 0.5711 (mmt180) REVERT: F 11 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8366 (tm) REVERT: F 65 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7694 (mtp85) REVERT: F 73 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6291 (p90) REVERT: F 207 GLN cc_start: 0.7576 (tt0) cc_final: 0.7374 (tm-30) REVERT: G 131 ARG cc_start: 0.7560 (tpp80) cc_final: 0.6394 (mtp180) REVERT: G 205 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7066 (t-90) REVERT: H 99 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7359 (tpp80) outliers start: 26 outliers final: 15 residues processed: 188 average time/residue: 0.6053 time to fit residues: 121.0358 Evaluate side-chains 184 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS F 149 ASN G 160 ASN H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089441 restraints weight = 58584.803| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 6.73 r_work: 0.2493 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10924 Z= 0.147 Angle : 0.528 8.903 14710 Z= 0.281 Chirality : 0.038 0.164 1628 Planarity : 0.003 0.035 1760 Dihedral : 10.575 80.183 1712 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.05 % Allowed : 18.00 % Favored : 79.94 % 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 aren not related in a simple way. whole: 3.33 (0.24), residues: 1286 helix: 3.48 (0.16), residues: 926 sheet: 0.10 (1.70), residues: 10 loop : -1.55 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.020 0.001 TYR B 523 PHE 0.019 0.001 PHE G 127 TRP 0.019 0.001 TRP D 551 HIS 0.006 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00337 (10916) covalent geometry : angle 0.52563 (14694) SS BOND : bond 0.00596 ( 8) SS BOND : angle 1.68564 ( 16) hydrogen bonds : bond 0.04335 ( 770) hydrogen bonds : angle 3.15245 ( 2266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8064 (mp0) cc_final: 0.7592 (mp0) REVERT: B 594 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8535 (mtm-85) REVERT: C 594 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8509 (mpp80) REVERT: D 594 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8558 (mtm110) REVERT: E 58 MET cc_start: 0.7654 (tpp) cc_final: 0.7434 (tpt) REVERT: E 73 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6955 (p90) REVERT: E 122 ILE cc_start: 0.8312 (mm) cc_final: 0.7934 (tt) REVERT: F 11 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8414 (tm) REVERT: F 65 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7831 (mtp85) REVERT: F 73 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6316 (p90) REVERT: F 128 TYR cc_start: 0.7017 (t80) cc_final: 0.6684 (t80) REVERT: F 131 ARG cc_start: 0.7404 (mmm160) cc_final: 0.7195 (mmm160) REVERT: G 131 ARG cc_start: 0.7642 (tpp80) cc_final: 0.6440 (mtp180) REVERT: G 205 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: H 99 ARG cc_start: 0.7908 (mmt180) cc_final: 0.7522 (tpp80) outliers start: 22 outliers final: 15 residues processed: 181 average time/residue: 0.6580 time to fit residues: 126.4609 Evaluate side-chains 185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS H 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.089897 restraints weight = 47888.273| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.63 r_work: 0.2556 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10924 Z= 0.122 Angle : 0.506 9.621 14710 Z= 0.268 Chirality : 0.037 0.161 1628 Planarity : 0.003 0.034 1760 Dihedral : 10.271 79.821 1712 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.05 % Allowed : 17.91 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.24), residues: 1286 helix: 3.56 (0.16), residues: 926 sheet: -0.10 (1.65), residues: 10 loop : -1.51 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.018 0.001 TYR B 523 PHE 0.016 0.001 PHE E 127 TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00265 (10916) covalent geometry : angle 0.50348 (14694) SS BOND : bond 0.00577 ( 8) SS BOND : angle 1.59249 ( 16) hydrogen bonds : bond 0.04063 ( 770) hydrogen bonds : angle 3.07009 ( 2266) =============================================================================== Job complete usr+sys time: 3458.65 seconds wall clock time: 59 minutes 34.59 seconds (3574.59 seconds total)