Starting phenix.real_space_refine on Sat Aug 23 07:29:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpg_29363/08_2025/8fpg_29363.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 S 72 5.16 5 Cl 4 4.86 5 C 6927 2.51 5 N 1657 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 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: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 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: "C" Number of atoms: 1157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1164 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1159 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 4 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 B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " 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 D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 3.24, per 1000 atoms: 0.30 Number of scatterers: 10674 At special positions: 0 Unit cell: (108.994, 105.716, 92.6035, 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) Cl 4 17.00 S 72 16.00 O 2014 8.00 N 1657 7.00 C 6927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 477.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.989A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.146A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.737A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.925A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 4.019A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.769A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.709A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.619A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.572A 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 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.711A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 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 825 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.574A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 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 825 removed outlier: 3.660A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.596A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.587A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.895A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.947A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 38 854 hydrogen bonds defined for protein. 2494 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: 2.43 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3155 1.34 - 1.46: 2703 1.46 - 1.58: 4779 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" CB MET E 200 " pdb=" CG MET E 200 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB MET G 200 " pdb=" CG MET G 200 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB MET H 200 " pdb=" CG MET H 200 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" CB MET F 200 " pdb=" CG MET F 200 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" CG MET G 200 " pdb=" SD MET G 200 " ideal model delta sigma weight residual 1.803 1.781 0.022 2.50e-02 1.60e+03 7.74e-01 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14387 1.83 - 3.66: 158 3.66 - 5.48: 17 5.48 - 7.31: 0 7.31 - 9.14: 3 Bond angle restraints: 14565 Sorted by residual: angle pdb=" C CYS H 40 " pdb=" N LYS H 41 " pdb=" CA LYS H 41 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.87e+00 angle pdb=" CA LEU A 542 " pdb=" CB LEU A 542 " pdb=" CG LEU A 542 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.82e+00 angle pdb=" CA LEU C 542 " pdb=" CB LEU C 542 " pdb=" CG LEU C 542 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU E 98 " pdb=" CB LEU E 98 " pdb=" CG LEU E 98 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" C CYS F 40 " pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.29e+00 ... (remaining 14560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5329 17.15 - 34.30: 559 34.30 - 51.45: 164 51.45 - 68.59: 39 68.59 - 85.74: 8 Dihedral angle restraints: 6099 sinusoidal: 2227 harmonic: 3872 Sorted by residual: 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 93.00 121.57 -28.57 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 590 " pdb=" CB ASP A 590 " pdb=" CG ASP A 590 " pdb=" OD1 ASP A 590 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 590 " pdb=" CB ASP C 590 " pdb=" CG ASP C 590 " pdb=" OD1 ASP C 590 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1152 0.035 - 0.071: 393 0.071 - 0.106: 89 0.106 - 0.142: 13 0.142 - 0.177: 1 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB ILE E 106 " pdb=" CA ILE E 106 " pdb=" CG1 ILE E 106 " pdb=" CG2 ILE E 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1645 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 32 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C TYR E 32 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR E 32 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP E 33 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 32 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR G 32 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR G 32 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP G 33 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 370 2.71 - 3.26: 10886 3.26 - 3.81: 18809 3.81 - 4.35: 22219 4.35 - 4.90: 37551 Nonbonded interactions: 89835 Sorted by model distance: nonbonded pdb=" OD1 ASN G 160 " pdb=" O HOH G 501 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN E 160 " pdb=" O HOH E 501 " model vdw 2.167 3.040 nonbonded pdb=" O PHE A 579 " pdb=" O HOH A 901 " model vdw 2.169 3.040 nonbonded pdb=" O HOH D 911 " pdb=" O HOH D 920 " model vdw 2.172 3.040 nonbonded pdb=" O HOH C 923 " pdb=" O HOH B1001 " model vdw 2.174 3.040 ... (remaining 89830 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 511 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 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 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 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 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 401) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 401)) selection = (chain 'G' and resid 5 through 401) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 401)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.035 10757 Z= 0.143 Angle : 0.490 9.141 14581 Z= 0.263 Chirality : 0.037 0.177 1648 Planarity : 0.003 0.031 1778 Dihedral : 16.030 85.743 3595 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 17.42 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.23), residues: 1312 helix: 3.19 (0.16), residues: 948 sheet: 0.46 (0.78), residues: 48 loop : -0.87 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 545 TYR 0.015 0.002 TYR C 523 PHE 0.017 0.002 PHE C 584 TRP 0.011 0.002 TRP F 64 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00308 (10749) covalent geometry : angle 0.48968 (14565) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.73457 ( 16) hydrogen bonds : bond 0.14449 ( 854) hydrogen bonds : angle 4.32247 ( 2494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: E 11 LEU cc_start: 0.7721 (tp) cc_final: 0.7037 (tp) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.4615 time to fit residues: 85.4200 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS C 791 ASN E 79 GLN G 9 GLN G 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134909 restraints weight = 35234.561| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.81 r_work: 0.3058 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10757 Z= 0.119 Angle : 0.449 8.385 14581 Z= 0.248 Chirality : 0.035 0.141 1648 Planarity : 0.003 0.034 1778 Dihedral : 4.132 42.244 1462 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.23 % Allowed : 16.04 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.19 (0.23), residues: 1312 helix: 3.92 (0.15), residues: 950 sheet: 0.21 (0.97), residues: 30 loop : -0.73 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.013 0.001 TYR F 181 PHE 0.014 0.001 PHE G 107 TRP 0.007 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00223 (10749) covalent geometry : angle 0.44889 (14565) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.54030 ( 16) hydrogen bonds : bond 0.05045 ( 854) hydrogen bonds : angle 3.19885 ( 2494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.400 Fit side-chains REVERT: H 78 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6549 (tmmt) REVERT: H 113 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7623 (mt) REVERT: F 113 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7600 (mt) outliers start: 35 outliers final: 7 residues processed: 176 average time/residue: 0.4061 time to fit residues: 78.0829 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 60 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.191005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133731 restraints weight = 32610.712| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.82 r_work: 0.3055 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10757 Z= 0.116 Angle : 0.434 7.178 14581 Z= 0.243 Chirality : 0.036 0.136 1648 Planarity : 0.003 0.034 1778 Dihedral : 3.331 17.350 1445 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.13 % Allowed : 15.94 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.34 (0.23), residues: 1312 helix: 4.02 (0.15), residues: 950 sheet: 1.04 (1.31), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 6 TYR 0.013 0.001 TYR H 181 PHE 0.011 0.001 PHE G 107 TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00221 (10749) covalent geometry : angle 0.43354 (14565) SS BOND : bond 0.00143 ( 8) SS BOND : angle 0.52441 ( 16) hydrogen bonds : bond 0.04919 ( 854) hydrogen bonds : angle 3.12765 ( 2494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.276 Fit side-chains REVERT: H 78 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6659 (tmmt) REVERT: H 113 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7637 (mt) REVERT: F 113 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (mt) REVERT: C 589 CYS cc_start: 0.5553 (p) cc_final: 0.4454 (m) REVERT: G 120 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6501 (tp) outliers start: 34 outliers final: 12 residues processed: 178 average time/residue: 0.4108 time to fit residues: 80.0141 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133936 restraints weight = 23527.237| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.27 r_work: 0.3084 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10757 Z= 0.112 Angle : 0.425 7.290 14581 Z= 0.238 Chirality : 0.035 0.129 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.289 16.582 1445 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.13 % Allowed : 15.94 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.43 (0.23), residues: 1312 helix: 4.09 (0.16), residues: 952 sheet: 0.89 (1.25), residues: 10 loop : -0.58 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 37 TYR 0.012 0.001 TYR H 181 PHE 0.011 0.001 PHE C 584 TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00209 (10749) covalent geometry : angle 0.42469 (14565) SS BOND : bond 0.00100 ( 8) SS BOND : angle 0.50043 ( 16) hydrogen bonds : bond 0.04678 ( 854) hydrogen bonds : angle 3.07793 ( 2494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.312 Fit side-chains REVERT: H 78 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6655 (tmmt) REVERT: H 113 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7615 (mt) REVERT: C 589 CYS cc_start: 0.5813 (p) cc_final: 0.4594 (m) REVERT: A 589 CYS cc_start: 0.5670 (p) cc_final: 0.4516 (m) REVERT: E 120 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6421 (tp) REVERT: G 12 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6680 (tp) REVERT: G 120 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6477 (tp) outliers start: 34 outliers final: 11 residues processed: 182 average time/residue: 0.4234 time to fit residues: 84.2325 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS G 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.190846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132915 restraints weight = 25963.103| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.43 r_work: 0.3073 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10757 Z= 0.113 Angle : 0.433 7.583 14581 Z= 0.242 Chirality : 0.035 0.128 1648 Planarity : 0.003 0.034 1778 Dihedral : 3.294 16.930 1445 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.04 % Allowed : 16.04 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.42 (0.23), residues: 1312 helix: 4.07 (0.16), residues: 952 sheet: 0.86 (1.17), residues: 10 loop : -0.57 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 102 TYR 0.013 0.001 TYR F 181 PHE 0.011 0.001 PHE C 584 TRP 0.008 0.001 TRP G 33 HIS 0.017 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00214 (10749) covalent geometry : angle 0.43348 (14565) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.44100 ( 16) hydrogen bonds : bond 0.04725 ( 854) hydrogen bonds : angle 3.08971 ( 2494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.398 Fit side-chains REVERT: H 78 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6666 (tmmt) REVERT: H 113 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7589 (mt) REVERT: C 589 CYS cc_start: 0.5870 (p) cc_final: 0.4548 (m) REVERT: A 589 CYS cc_start: 0.5668 (p) cc_final: 0.4500 (m) REVERT: E 120 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6479 (tp) REVERT: G 73 PHE cc_start: 0.4496 (OUTLIER) cc_final: 0.4288 (p90) outliers start: 33 outliers final: 16 residues processed: 184 average time/residue: 0.4497 time to fit residues: 89.9731 Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134563 restraints weight = 28244.679| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.55 r_work: 0.3059 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10757 Z= 0.115 Angle : 0.436 7.707 14581 Z= 0.243 Chirality : 0.035 0.130 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.275 17.014 1443 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 16.04 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.39 (0.23), residues: 1312 helix: 4.05 (0.16), residues: 952 sheet: 0.79 (1.16), residues: 10 loop : -0.58 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 209 TYR 0.013 0.001 TYR F 181 PHE 0.011 0.001 PHE A 584 TRP 0.008 0.001 TRP G 33 HIS 0.003 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00219 (10749) covalent geometry : angle 0.43660 (14565) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.29966 ( 16) hydrogen bonds : bond 0.04753 ( 854) hydrogen bonds : angle 3.09382 ( 2494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.236 Fit side-chains REVERT: H 113 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7641 (mt) REVERT: C 589 CYS cc_start: 0.5908 (p) cc_final: 0.4610 (m) REVERT: A 589 CYS cc_start: 0.5725 (p) cc_final: 0.4534 (m) REVERT: E 11 LEU cc_start: 0.7163 (tp) cc_final: 0.6553 (tp) REVERT: G 12 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6796 (tp) REVERT: G 209 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.5041 (mtp85) outliers start: 33 outliers final: 20 residues processed: 180 average time/residue: 0.4720 time to fit residues: 92.6298 Evaluate side-chains 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 HIS H 199 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134580 restraints weight = 28635.739| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.22 r_work: 0.3039 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10757 Z= 0.131 Angle : 0.467 7.837 14581 Z= 0.260 Chirality : 0.036 0.134 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.405 18.367 1443 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.86 % Allowed : 16.31 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.24 (0.23), residues: 1312 helix: 3.93 (0.16), residues: 950 sheet: 0.92 (1.17), residues: 10 loop : -0.57 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 209 TYR 0.015 0.001 TYR H 181 PHE 0.014 0.001 PHE A 584 TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00262 (10749) covalent geometry : angle 0.46705 (14565) SS BOND : bond 0.00229 ( 8) SS BOND : angle 0.39234 ( 16) hydrogen bonds : bond 0.05201 ( 854) hydrogen bonds : angle 3.18938 ( 2494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.365 Fit side-chains REVERT: H 24 MET cc_start: 0.8529 (tpt) cc_final: 0.8180 (tpt) REVERT: H 113 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7621 (mt) REVERT: F 113 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7546 (mt) REVERT: C 589 CYS cc_start: 0.5998 (p) cc_final: 0.4700 (m) REVERT: A 589 CYS cc_start: 0.5915 (p) cc_final: 0.4666 (m) REVERT: E 11 LEU cc_start: 0.7161 (tp) cc_final: 0.6575 (tp) REVERT: E 95 GLU cc_start: 0.5347 (tt0) cc_final: 0.4930 (mp0) REVERT: G 120 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6536 (tp) REVERT: G 209 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.5049 (mtp85) outliers start: 31 outliers final: 19 residues processed: 178 average time/residue: 0.4776 time to fit residues: 92.2336 Evaluate side-chains 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS H 205 HIS F 199 HIS E 60 HIS E 132 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137123 restraints weight = 31238.772| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.41 r_work: 0.3050 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10757 Z= 0.116 Angle : 0.442 8.133 14581 Z= 0.246 Chirality : 0.036 0.127 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.319 18.320 1443 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 16.13 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.35 (0.23), residues: 1312 helix: 4.03 (0.16), residues: 950 sheet: 0.83 (1.14), residues: 10 loop : -0.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 102 TYR 0.014 0.001 TYR F 181 PHE 0.011 0.001 PHE A 584 TRP 0.009 0.001 TRP G 33 HIS 0.017 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00223 (10749) covalent geometry : angle 0.44234 (14565) SS BOND : bond 0.00195 ( 8) SS BOND : angle 0.32400 ( 16) hydrogen bonds : bond 0.04761 ( 854) hydrogen bonds : angle 3.10580 ( 2494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.352 Fit side-chains REVERT: H 113 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7662 (mt) REVERT: C 589 CYS cc_start: 0.5901 (p) cc_final: 0.4624 (m) REVERT: A 589 CYS cc_start: 0.5719 (p) cc_final: 0.4547 (m) REVERT: E 11 LEU cc_start: 0.7148 (tp) cc_final: 0.6551 (tp) REVERT: E 95 GLU cc_start: 0.5240 (tt0) cc_final: 0.4848 (mp0) REVERT: G 11 LEU cc_start: 0.7136 (tp) cc_final: 0.6473 (tp) REVERT: G 120 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6564 (tp) REVERT: G 209 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.5051 (mtp85) outliers start: 35 outliers final: 19 residues processed: 176 average time/residue: 0.4528 time to fit residues: 86.7021 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 60 HIS E 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135063 restraints weight = 26008.074| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.21 r_work: 0.3071 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10757 Z= 0.114 Angle : 0.441 8.845 14581 Z= 0.245 Chirality : 0.035 0.125 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.299 17.861 1443 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.76 % Allowed : 16.41 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.36 (0.23), residues: 1312 helix: 4.03 (0.15), residues: 950 sheet: 0.83 (1.14), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 102 TYR 0.013 0.001 TYR F 181 PHE 0.018 0.001 PHE A 531 TRP 0.009 0.001 TRP G 33 HIS 0.014 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00219 (10749) covalent geometry : angle 0.44083 (14565) SS BOND : bond 0.00171 ( 8) SS BOND : angle 0.28436 ( 16) hydrogen bonds : bond 0.04707 ( 854) hydrogen bonds : angle 3.09191 ( 2494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.395 Fit side-chains REVERT: H 113 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7640 (mt) REVERT: C 589 CYS cc_start: 0.5860 (p) cc_final: 0.4579 (m) REVERT: A 589 CYS cc_start: 0.5747 (p) cc_final: 0.4456 (m) REVERT: E 11 LEU cc_start: 0.7220 (tp) cc_final: 0.6648 (tp) REVERT: E 95 GLU cc_start: 0.5200 (tt0) cc_final: 0.4823 (mp0) REVERT: G 11 LEU cc_start: 0.7126 (tp) cc_final: 0.6491 (tp) REVERT: G 120 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6524 (tp) outliers start: 30 outliers final: 21 residues processed: 174 average time/residue: 0.4553 time to fit residues: 86.1852 Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133439 restraints weight = 29287.565| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.33 r_work: 0.3004 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10757 Z= 0.175 Angle : 0.542 8.257 14581 Z= 0.300 Chirality : 0.039 0.145 1648 Planarity : 0.004 0.037 1778 Dihedral : 3.656 20.042 1443 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.58 % Allowed : 16.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.86 (0.23), residues: 1312 helix: 3.60 (0.15), residues: 950 sheet: 1.17 (1.12), residues: 10 loop : -0.55 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 545 TYR 0.016 0.002 TYR F 181 PHE 0.019 0.002 PHE A 584 TRP 0.011 0.002 TRP E 33 HIS 0.007 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00381 (10749) covalent geometry : angle 0.54190 (14565) SS BOND : bond 0.00317 ( 8) SS BOND : angle 0.61368 ( 16) hydrogen bonds : bond 0.05993 ( 854) hydrogen bonds : angle 3.36902 ( 2494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.432 Fit side-chains REVERT: H 24 MET cc_start: 0.8532 (tpt) cc_final: 0.8204 (tpt) REVERT: H 113 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7709 (mt) REVERT: F 113 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7522 (mt) REVERT: E 11 LEU cc_start: 0.7193 (tp) cc_final: 0.6643 (tp) REVERT: G 11 LEU cc_start: 0.7140 (tp) cc_final: 0.6452 (tp) REVERT: G 120 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6519 (tp) outliers start: 28 outliers final: 16 residues processed: 172 average time/residue: 0.4667 time to fit residues: 87.0222 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130136 restraints weight = 25218.010| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.41 r_work: 0.3028 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10757 Z= 0.160 Angle : 0.519 8.287 14581 Z= 0.288 Chirality : 0.038 0.136 1648 Planarity : 0.003 0.037 1778 Dihedral : 3.618 19.704 1443 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.03 % Allowed : 17.24 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.23), residues: 1312 helix: 3.59 (0.15), residues: 950 sheet: 1.19 (1.08), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.017 0.002 TYR H 181 PHE 0.017 0.002 PHE A 584 TRP 0.011 0.002 TRP H 64 HIS 0.006 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00341 (10749) covalent geometry : angle 0.51867 (14565) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.51305 ( 16) hydrogen bonds : bond 0.05696 ( 854) hydrogen bonds : angle 3.32505 ( 2494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4281.94 seconds wall clock time: 73 minutes 22.55 seconds (4402.55 seconds total)