Starting phenix.real_space_refine on Tue Jun 10 00:58:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1s_16382/06_2025/8c1s_16382_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1s_16382/06_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_16382/06_2025/8c1s_16382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1s_16382/06_2025/8c1s_16382.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1s_16382/06_2025/8c1s_16382_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1s_16382/06_2025/8c1s_16382_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.79, per 1000 atoms: 0.92 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: 3.19 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 0.92 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: 3.21 Time building geometry restraints manager: 3.32 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: 0.010 Normalize map: mean=0, sd=1: 3.290 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (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 TRP 0.050 0.013 TRP B 578 HIS 0.016 0.005 HIS F 205 PHE 0.078 0.011 PHE A 571 TYR 0.058 0.010 TYR H 35 ARG 0.058 0.005 ARG H 209 Details of bonding type rmsd hydrogen bonds : bond 0.13788 ( 770) hydrogen bonds : angle 5.06635 ( 2266) SS BOND : bond 0.01952 ( 8) SS BOND : angle 3.77354 ( 16) covalent geometry : bond 0.01157 (10916) covalent geometry : angle 1.28520 (14694) *********************** 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 : 1.143 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: 1.4021 time to fit residues: 321.1993 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 : 1.140 ------------------------------------------------------------------------------- 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 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.090342 restraints weight = 44702.598| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.39 r_work: 0.2591 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 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 = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1888 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= 0.138 Angle : 0.548 7.532 14710 Z= 0.299 Chirality : 0.039 0.210 1628 Planarity : 0.004 0.039 1760 Dihedral : 13.756 110.361 1725 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.24 % Allowed : 11.10 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1286 helix: 3.11 (0.17), residues: 925 sheet: -0.21 (1.88), residues: 10 loop : -2.15 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 PHE 0.019 0.001 PHE G 73 TYR 0.013 0.001 TYR H 174 ARG 0.010 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 770) hydrogen bonds : angle 3.52933 ( 2266) SS BOND : bond 0.00927 ( 8) SS BOND : angle 2.00131 ( 16) covalent geometry : bond 0.00285 (10916) covalent geometry : angle 0.54432 (14694) *********************** 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 196 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: B 818 SER cc_start: 0.7701 (t) cc_final: 0.7381 (m) REVERT: C 594 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8403 (mtp-110) REVERT: D 594 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8591 (mtm110) REVERT: E 73 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6426 (p90) REVERT: E 78 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7644 (pttp) REVERT: E 99 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8188 (mtt180) REVERT: E 199 HIS cc_start: 0.8290 (t-90) cc_final: 0.8049 (t-90) REVERT: F 11 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8400 (tm) REVERT: F 65 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7624 (mtp85) REVERT: F 98 LEU cc_start: 0.7876 (tt) cc_final: 0.7533 (tp) REVERT: F 174 TYR cc_start: 0.8996 (p90) cc_final: 0.8732 (p90) REVERT: F 208 LEU cc_start: 0.8442 (tt) cc_final: 0.8230 (tp) REVERT: G 79 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8217 (tp40) REVERT: G 131 ARG cc_start: 0.7353 (tpp80) cc_final: 0.7053 (tpp80) REVERT: G 205 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7398 (t-90) REVERT: H 99 ARG cc_start: 0.7794 (mmt180) cc_final: 0.7329 (tpp80) outliers start: 24 outliers final: 8 residues processed: 185 average time/residue: 1.3580 time to fit residues: 269.0399 Evaluate side-chains 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.129261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.090023 restraints weight = 47913.138| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 6.09 r_work: 0.2524 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2355 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= 0.129 Angle : 0.515 7.695 14710 Z= 0.276 Chirality : 0.038 0.181 1628 Planarity : 0.004 0.037 1760 Dihedral : 12.181 99.475 1713 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 13.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.25), residues: 1286 helix: 3.31 (0.17), residues: 926 sheet: -0.60 (1.68), residues: 10 loop : -1.96 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.003 0.001 HIS E 132 PHE 0.024 0.001 PHE E 127 TYR 0.013 0.001 TYR B 523 ARG 0.010 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 770) hydrogen bonds : angle 3.29677 ( 2266) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.94688 ( 16) covalent geometry : bond 0.00279 (10916) covalent geometry : angle 0.51096 (14694) *********************** 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 192 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.019 Fit side-chains REVERT: B 509 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7437 (tttp) REVERT: B 594 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8037 (mtm-85) REVERT: C 594 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8364 (mtp-110) REVERT: D 594 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8540 (mtm110) REVERT: D 626 VAL cc_start: 0.8851 (p) cc_final: 0.8413 (m) REVERT: E 73 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6482 (p90) REVERT: F 11 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8332 (tm) REVERT: F 65 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7571 (mtp85) REVERT: F 98 LEU cc_start: 0.7864 (tt) cc_final: 0.7645 (tp) REVERT: F 174 TYR cc_start: 0.9024 (p90) cc_final: 0.8791 (p90) REVERT: F 204 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7822 (ttm170) REVERT: G 79 GLN cc_start: 0.8423 (mt0) cc_final: 0.8219 (tp40) REVERT: G 131 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7259 (tpp80) REVERT: G 205 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7181 (t-90) REVERT: H 99 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7387 (tpp80) outliers start: 25 outliers final: 11 residues processed: 183 average time/residue: 1.4489 time to fit residues: 283.5954 Evaluate side-chains 170 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 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 107 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** 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 = 0.3573 r_free = 0.3573 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091707 restraints weight = 50327.585| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 5.75 r_work: 0.2590 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.2590 ------------------------------------------------------------------------------- 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10924 Z= 0.121 Angle : 0.541 14.159 14710 Z= 0.288 Chirality : 0.039 0.323 1628 Planarity : 0.003 0.037 1760 Dihedral : 11.536 93.012 1712 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.71 % Allowed : 14.83 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.25), residues: 1286 helix: 3.42 (0.17), residues: 926 sheet: -0.34 (1.70), residues: 10 loop : -1.89 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.003 0.001 HIS E 132 PHE 0.015 0.001 PHE G 73 TYR 0.016 0.001 TYR B 523 ARG 0.008 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 770) hydrogen bonds : angle 3.18117 ( 2266) SS BOND : bond 0.00897 ( 8) SS BOND : angle 3.53705 ( 16) covalent geometry : bond 0.00258 (10916) covalent geometry : angle 0.52817 (14694) *********************** 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 197 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.077 Fit side-chains REVERT: B 509 LYS cc_start: 0.7636 (tmmt) cc_final: 0.7342 (tttp) REVERT: B 594 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8430 (mtt180) REVERT: C 594 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8428 (mtp-110) REVERT: D 594 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8575 (mtm110) REVERT: E 58 MET cc_start: 0.7551 (tpt) cc_final: 0.7291 (tpp) REVERT: E 73 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6436 (p90) REVERT: E 122 ILE cc_start: 0.8201 (mm) cc_final: 0.7732 (tt) REVERT: E 131 ARG cc_start: 0.6187 (mmm160) cc_final: 0.5808 (mmt180) REVERT: F 11 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8349 (tm) REVERT: F 65 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7692 (mtp85) REVERT: F 66 THR cc_start: 0.8857 (t) cc_final: 0.8627 (t) REVERT: F 98 LEU cc_start: 0.7929 (tt) cc_final: 0.7710 (tp) REVERT: F 128 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6477 (t80) REVERT: F 174 TYR cc_start: 0.9005 (p90) cc_final: 0.8794 (p90) REVERT: F 204 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7809 (ttm170) REVERT: G 131 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7103 (tpp80) REVERT: G 205 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7213 (t-90) REVERT: H 99 ARG cc_start: 0.7794 (mmt180) cc_final: 0.7330 (ttp80) outliers start: 29 outliers final: 12 residues processed: 186 average time/residue: 1.4019 time to fit residues: 278.7744 Evaluate side-chains 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER 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 F residue 77 CYS Chi-restraints excluded: chain F residue 122 ILE 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 61 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** 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 = 0.3566 r_free = 0.3566 target = 0.132155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091801 restraints weight = 49567.825| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 6.01 r_work: 0.2580 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 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 = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10924 Z= 0.118 Angle : 0.517 10.789 14710 Z= 0.275 Chirality : 0.038 0.252 1628 Planarity : 0.003 0.036 1760 Dihedral : 11.155 90.708 1712 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.80 % Allowed : 15.86 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.25), residues: 1286 helix: 3.51 (0.17), residues: 925 sheet: -0.55 (1.55), residues: 10 loop : -1.85 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.005 0.001 HIS F 199 PHE 0.020 0.001 PHE F 127 TYR 0.018 0.001 TYR B 523 ARG 0.007 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 770) hydrogen bonds : angle 3.10746 ( 2266) SS BOND : bond 0.00610 ( 8) SS BOND : angle 3.19004 ( 16) covalent geometry : bond 0.00251 (10916) covalent geometry : angle 0.50666 (14694) *********************** 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 196 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.210 Fit side-chains REVERT: B 594 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8400 (mtt180) REVERT: B 629 MET cc_start: 0.7541 (mpp) cc_final: 0.7329 (mmm) REVERT: C 594 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8419 (mtp-110) REVERT: D 586 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8200 (mtp85) REVERT: D 594 ARG cc_start: 0.8985 (mtt180) cc_final: 0.8586 (mtm110) REVERT: E 58 MET cc_start: 0.7537 (tpt) cc_final: 0.7291 (tpp) REVERT: E 73 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6527 (p90) REVERT: E 122 ILE cc_start: 0.8212 (mm) cc_final: 0.7835 (tt) REVERT: E 131 ARG cc_start: 0.6246 (mmm160) cc_final: 0.5852 (mmt180) REVERT: F 11 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8352 (tm) REVERT: F 65 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: F 98 LEU cc_start: 0.7893 (tt) cc_final: 0.7678 (tp) REVERT: F 128 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6482 (t80) REVERT: F 174 TYR cc_start: 0.8970 (p90) cc_final: 0.8764 (p90) REVERT: G 131 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7020 (tpp-160) REVERT: G 205 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: H 65 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7868 (ptt-90) REVERT: H 99 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7329 (ttp80) outliers start: 30 outliers final: 16 residues processed: 186 average time/residue: 1.4493 time to fit residues: 287.3235 Evaluate side-chains 182 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 F residue 11 LEU Chi-restraints excluded: chain F residue 128 TYR 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 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 205 HIS 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 43 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** E 205 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088142 restraints weight = 44197.332| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.76 r_work: 0.2621 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 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 = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2815 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= 0.172 Angle : 0.568 11.031 14710 Z= 0.301 Chirality : 0.040 0.271 1628 Planarity : 0.004 0.036 1760 Dihedral : 11.416 88.057 1712 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.24 % Allowed : 16.60 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.24), residues: 1286 helix: 3.33 (0.17), residues: 925 sheet: -0.63 (1.47), residues: 10 loop : -1.82 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 PHE 0.015 0.001 PHE A 584 TYR 0.018 0.001 TYR B 523 ARG 0.005 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 770) hydrogen bonds : angle 3.28619 ( 2266) SS BOND : bond 0.00638 ( 8) SS BOND : angle 3.60423 ( 16) covalent geometry : bond 0.00403 (10916) covalent geometry : angle 0.55523 (14694) *********************** 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 192 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8379 (mtm-85) REVERT: C 594 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8426 (mpp80) REVERT: D 586 ARG cc_start: 0.8485 (mmt90) cc_final: 0.8143 (mtp85) REVERT: D 594 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8515 (mtm110) REVERT: E 122 ILE cc_start: 0.8135 (mm) cc_final: 0.7774 (tt) REVERT: E 131 ARG cc_start: 0.6352 (mmm160) cc_final: 0.5888 (mmt180) REVERT: F 11 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8275 (tm) REVERT: F 65 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7638 (mtp85) REVERT: F 128 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6634 (t80) REVERT: F 204 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7515 (ttm170) REVERT: F 207 GLN cc_start: 0.7642 (tt0) cc_final: 0.7277 (tm-30) REVERT: G 131 ARG cc_start: 0.7498 (tpp80) cc_final: 0.6936 (tpp-160) REVERT: G 205 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7077 (t-90) REVERT: H 99 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7267 (ttp80) outliers start: 24 outliers final: 16 residues processed: 184 average time/residue: 1.5592 time to fit residues: 306.0729 Evaluate side-chains 182 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 F residue 77 CYS 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 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 61 SER 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 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3566 r_free = 0.3566 target = 0.132398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089477 restraints weight = 45350.465| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 5.06 r_work: 0.2623 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 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 = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10924 Z= 0.148 Angle : 0.542 8.519 14710 Z= 0.287 Chirality : 0.039 0.208 1628 Planarity : 0.003 0.037 1760 Dihedral : 11.239 89.485 1712 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.80 % Allowed : 16.60 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.24), residues: 1286 helix: 3.41 (0.16), residues: 925 sheet: -0.45 (1.50), residues: 10 loop : -1.79 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 PHE 0.014 0.001 PHE G 127 TYR 0.018 0.001 TYR B 523 ARG 0.006 0.001 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 770) hydrogen bonds : angle 3.20715 ( 2266) SS BOND : bond 0.00694 ( 8) SS BOND : angle 3.22989 ( 16) covalent geometry : bond 0.00337 (10916) covalent geometry : angle 0.53180 (14694) *********************** 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 193 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8395 (mtm-85) REVERT: C 594 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8454 (mpp80) REVERT: D 586 ARG cc_start: 0.8516 (mmt90) cc_final: 0.8108 (mtp85) REVERT: D 594 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8487 (mtm110) REVERT: E 58 MET cc_start: 0.7405 (tpt) cc_final: 0.7174 (tpp) REVERT: E 73 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6737 (p90) REVERT: E 122 ILE cc_start: 0.8111 (mm) cc_final: 0.7779 (tt) REVERT: E 131 ARG cc_start: 0.6205 (mmm160) cc_final: 0.5755 (mmt180) REVERT: F 11 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8311 (tm) REVERT: F 65 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7594 (mtp85) REVERT: F 131 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7451 (mmt180) REVERT: G 131 ARG cc_start: 0.7482 (tpp80) cc_final: 0.6908 (tpp-160) REVERT: G 205 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: H 11 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8029 (tp) REVERT: H 65 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7942 (ptt-90) REVERT: H 99 ARG cc_start: 0.7729 (mmt180) cc_final: 0.7349 (tpp80) outliers start: 30 outliers final: 17 residues processed: 185 average time/residue: 1.4669 time to fit residues: 288.9379 Evaluate side-chains 185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 817 LYS 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 E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 77 CYS 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 11 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU 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 116 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** 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 = 0.3582 r_free = 0.3582 target = 0.133663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.091018 restraints weight = 56625.421| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.89 r_work: 0.2608 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3151 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= 0.126 Angle : 0.523 9.031 14710 Z= 0.275 Chirality : 0.038 0.200 1628 Planarity : 0.003 0.035 1760 Dihedral : 10.761 82.682 1712 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.89 % Allowed : 16.51 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.24), residues: 1286 helix: 3.52 (0.16), residues: 925 sheet: -0.19 (1.51), residues: 10 loop : -1.72 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 PHE 0.014 0.001 PHE G 127 TYR 0.018 0.001 TYR B 523 ARG 0.005 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 770) hydrogen bonds : angle 3.11145 ( 2266) SS BOND : bond 0.00456 ( 8) SS BOND : angle 2.91057 ( 16) covalent geometry : bond 0.00278 (10916) covalent geometry : angle 0.51397 (14694) *********************** 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 203 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8047 (mp0) REVERT: B 594 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: C 594 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8500 (mpp80) REVERT: D 586 ARG cc_start: 0.8523 (mmt90) cc_final: 0.8144 (mtp85) REVERT: D 594 ARG cc_start: 0.8939 (mtt180) cc_final: 0.8526 (mtm110) REVERT: E 58 MET cc_start: 0.7527 (tpt) cc_final: 0.7279 (tpp) REVERT: E 73 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6808 (p90) REVERT: E 122 ILE cc_start: 0.8108 (mm) cc_final: 0.7773 (tt) REVERT: F 11 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8340 (tm) REVERT: F 65 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7618 (mtp85) REVERT: F 128 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6375 (t80) REVERT: F 131 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7420 (mmm160) REVERT: G 131 ARG cc_start: 0.7538 (tpp80) cc_final: 0.6344 (mtp180) REVERT: G 205 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7165 (t-90) REVERT: H 65 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.8002 (ptt-90) REVERT: H 99 ARG cc_start: 0.7721 (mmt180) cc_final: 0.7339 (tpp80) outliers start: 31 outliers final: 20 residues processed: 193 average time/residue: 1.6964 time to fit residues: 350.5015 Evaluate side-chains 189 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 C residue 817 LYS 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 77 CYS 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 61 SER 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 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU 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 2 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** E 205 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3576 r_free = 0.3576 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090421 restraints weight = 40206.505| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.68 r_work: 0.2646 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 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 = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10924 Z= 0.130 Angle : 0.540 11.422 14710 Z= 0.282 Chirality : 0.038 0.169 1628 Planarity : 0.003 0.035 1760 Dihedral : 10.627 81.154 1712 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.80 % Allowed : 16.79 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.24), residues: 1286 helix: 3.49 (0.16), residues: 926 sheet: -0.11 (1.59), residues: 10 loop : -1.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.004 0.001 HIS F 199 PHE 0.021 0.001 PHE G 127 TYR 0.019 0.001 TYR B 523 ARG 0.007 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 770) hydrogen bonds : angle 3.12289 ( 2266) SS BOND : bond 0.00472 ( 8) SS BOND : angle 2.90422 ( 16) covalent geometry : bond 0.00289 (10916) covalent geometry : angle 0.53181 (14694) *********************** 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: 30 poor density : 165 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7988 (mp0) REVERT: B 594 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8397 (mtm-85) REVERT: C 594 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8430 (mpp80) REVERT: D 586 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8090 (mtp85) REVERT: D 594 ARG cc_start: 0.8888 (mtt180) cc_final: 0.8465 (mtm110) REVERT: E 58 MET cc_start: 0.7400 (tpt) cc_final: 0.7161 (tpp) REVERT: E 73 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6729 (p90) REVERT: E 122 ILE cc_start: 0.8088 (mm) cc_final: 0.7761 (tt) REVERT: E 208 LEU cc_start: 0.7667 (tt) cc_final: 0.7394 (mp) REVERT: F 11 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8318 (tm) REVERT: F 65 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7550 (mtp85) REVERT: F 131 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7383 (mmm160) REVERT: F 204 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7274 (ttm170) REVERT: F 207 GLN cc_start: 0.7585 (tt0) cc_final: 0.7378 (tm-30) REVERT: G 131 ARG cc_start: 0.7528 (tpp80) cc_final: 0.6357 (mtp180) REVERT: G 205 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7086 (t-90) REVERT: H 65 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7985 (ptt-90) REVERT: H 99 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7315 (tpp80) outliers start: 30 outliers final: 19 residues processed: 186 average time/residue: 1.7581 time to fit residues: 348.0356 Evaluate side-chains 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 C residue 817 LYS 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 F residue 77 CYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 61 SER 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 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU 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 48 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN E 205 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3528 r_free = 0.3528 target = 0.129014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089289 restraints weight = 54214.339| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 6.26 r_work: 0.2526 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10924 Z= 0.147 Angle : 0.544 8.686 14710 Z= 0.286 Chirality : 0.039 0.188 1628 Planarity : 0.003 0.036 1760 Dihedral : 10.696 80.460 1712 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 16.98 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.24), residues: 1286 helix: 3.44 (0.16), residues: 926 sheet: -1.30 (1.57), residues: 12 loop : -1.66 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 PHE 0.014 0.001 PHE E 127 TYR 0.018 0.001 TYR B 523 ARG 0.007 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 770) hydrogen bonds : angle 3.16258 ( 2266) SS BOND : bond 0.00469 ( 8) SS BOND : angle 3.02801 ( 16) covalent geometry : bond 0.00335 (10916) covalent geometry : angle 0.53455 (14694) ********************** 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 191 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8578 (mtm-85) REVERT: C 594 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8512 (mpp80) REVERT: D 586 ARG cc_start: 0.8586 (mmt90) cc_final: 0.8234 (mtp85) REVERT: D 594 ARG cc_start: 0.9009 (mtt180) cc_final: 0.8601 (mtm110) REVERT: E 73 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6906 (p90) REVERT: E 122 ILE cc_start: 0.8262 (mm) cc_final: 0.7897 (tt) REVERT: F 11 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8393 (tm) REVERT: F 65 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7753 (mtp85) REVERT: F 204 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7396 (ttm170) REVERT: F 207 GLN cc_start: 0.7658 (tt0) cc_final: 0.7412 (tm-30) REVERT: G 131 ARG cc_start: 0.7609 (tpp80) cc_final: 0.6422 (mtp180) REVERT: G 205 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: H 99 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7464 (tpp80) outliers start: 26 outliers final: 17 residues processed: 181 average time/residue: 1.4837 time to fit residues: 285.7358 Evaluate side-chains 185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 C residue 817 LYS 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 F residue 77 CYS 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 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU 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 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3518 r_free = 0.3518 target = 0.128259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088830 restraints weight = 54912.369| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 6.37 r_work: 0.2503 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3209 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= 0.168 Angle : 0.559 9.254 14710 Z= 0.295 Chirality : 0.040 0.181 1628 Planarity : 0.003 0.035 1760 Dihedral : 10.782 79.692 1712 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 16.79 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.24), residues: 1286 helix: 3.36 (0.16), residues: 926 sheet: -1.38 (1.56), residues: 12 loop : -1.66 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 551 HIS 0.004 0.001 HIS F 199 PHE 0.018 0.001 PHE G 127 TYR 0.018 0.001 TYR B 523 ARG 0.006 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 770) hydrogen bonds : angle 3.22832 ( 2266) SS BOND : bond 0.00478 ( 8) SS BOND : angle 2.99828 ( 16) covalent geometry : bond 0.00392 (10916) covalent geometry : angle 0.55055 (14694) =============================================================================== Job complete usr+sys time: 8286.46 seconds wall clock time: 144 minutes 55.18 seconds (8695.18 seconds total)