Starting phenix.real_space_refine on Thu Jul 2 22:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpg_29363/07_2026/8fpg_29363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpg_29363/07_2026/8fpg_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_29363/07_2026/8fpg_29363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpg_29363/07_2026/8fpg_29363.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpg_29363/07_2026/8fpg_29363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpg_29363/07_2026/8fpg_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 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: 3.43, per 1000 atoms: 0.32 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: 0.76 Conformation dependent library (CDL) restraints added in 482.4 milliseconds 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: 0.29 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: 1.67 Time building geometry restraints manager: 1.05 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: 3.220 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 are 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/Z covalent geometry : bond 0.00308 / 0.14 (10749) covalent geometry : angle 0.48968 / 0.26 (14565) SS BOND : bond 0.00257 / 0.15 ( 8) SS BOND : angle 0.73457 / 0.42 ( 16) hydrogen bonds : bond 0.14449 / 9.82 ( 854) hydrogen bonds : angle 4.32247 / 3.09 ( 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 : 0.268 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: 0.4712 time to fit residues: 87.5494 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 : 0.398 ------------------------------------------------------------------------------- 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... H 199 HIS F 199 HIS C 791 ASN E 79 GLN G 9 GLN G 79 GLN G 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.191749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135863 restraints weight = 35219.074| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.60 r_work: 0.3064 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 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 = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10757 Z= 0.118 Angle : 0.446 8.368 14581 Z= 0.247 Chirality : 0.035 0.142 1648 Planarity : 0.003 0.034 1778 Dihedral : 4.135 42.768 1462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 are not related in a simple way. whole: 4.22 (0.23), residues: 1312 helix: 3.92 (0.15), residues: 950 sheet: 1.03 (1.32), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.013 0.001 TYR H 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/Z covalent geometry : bond 0.00221 / 0.12 (10749) covalent geometry : angle 0.44616 / 0.25 (14565) SS BOND : bond 0.00134 / 0.08 ( 8) SS BOND : angle 0.52536 / 0.31 ( 16) hydrogen bonds : bond 0.05015 / 3.35 ( 854) hydrogen bonds : angle 3.18593 / 2.27 ( 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 : 0.370 Fit side-chains REVERT: H 78 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6557 (tmmt) REVERT: H 113 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7639 (mt) REVERT: F 113 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7624 (mt) outliers start: 35 outliers final: 7 residues processed: 176 average time/residue: 0.4327 time to fit residues: 83.5780 Evaluate side-chains 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 60 HIS F 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132839 restraints weight = 31921.256| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.56 r_work: 0.3023 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0923 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= 0.141 Angle : 0.477 7.078 14581 Z= 0.267 Chirality : 0.037 0.141 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.525 18.531 1445 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.32 % Allowed : 15.48 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.23), residues: 1312 helix: 3.85 (0.16), residues: 950 sheet: 1.35 (1.31), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 6 TYR 0.015 0.001 TYR H 181 PHE 0.014 0.002 PHE A 584 TRP 0.010 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (10749) covalent geometry : angle 0.47672 / 0.27 (14565) SS BOND : bond 0.00206 / 0.12 ( 8) SS BOND : angle 0.66217 / 0.39 ( 16) hydrogen bonds : bond 0.05525 / 3.68 ( 854) hydrogen bonds : angle 3.26212 / 2.32 ( 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 192 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.425 Fit side-chains REVERT: H 78 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6574 (tmmt) REVERT: H 113 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7631 (mt) REVERT: F 78 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6649 (tmmt) REVERT: F 113 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7611 (mt) outliers start: 36 outliers final: 13 residues processed: 182 average time/residue: 0.4436 time to fit residues: 88.0937 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 78 LYS 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 106 ILE 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 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.190993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133608 restraints weight = 23621.333| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.27 r_work: 0.3084 rms_B_bonded: 3.81 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1184 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= 0.115 Angle : 0.433 7.230 14581 Z= 0.243 Chirality : 0.035 0.126 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.359 16.865 1445 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.04 % Allowed : 15.58 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.36 (0.23), residues: 1312 helix: 4.04 (0.16), residues: 950 sheet: 0.80 (1.14), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 102 TYR 0.013 0.001 TYR H 181 PHE 0.011 0.001 PHE A 584 TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (10749) covalent geometry : angle 0.43308 / 0.24 (14565) SS BOND : bond 0.00216 / 0.12 ( 8) SS BOND : angle 0.47292 / 0.27 ( 16) hydrogen bonds : bond 0.04776 / 3.19 ( 854) hydrogen bonds : angle 3.12258 / 2.23 ( 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 196 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.297 Fit side-chains REVERT: H 78 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6651 (tmmt) REVERT: H 113 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7589 (mt) REVERT: F 113 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7591 (mt) REVERT: E 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7119 (mp) outliers start: 33 outliers final: 13 residues processed: 187 average time/residue: 0.4363 time to fit residues: 88.8689 Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 12 LEU 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 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 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: 2.9990 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 132 HIS G 60 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134982 restraints weight = 25686.182| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.16 r_work: 0.3068 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1224 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= 0.117 Angle : 0.441 7.521 14581 Z= 0.246 Chirality : 0.035 0.123 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.360 17.334 1445 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 16.59 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.23), residues: 1312 helix: 4.03 (0.15), residues: 950 sheet: 0.87 (1.18), residues: 10 loop : -0.59 (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 0.012 0.001 PHE C 584 TRP 0.008 0.001 TRP E 33 HIS 0.017 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (10749) covalent geometry : angle 0.44092 / 0.25 (14565) SS BOND : bond 0.00239 / 0.15 ( 8) SS BOND : angle 0.35773 / 0.19 ( 16) hydrogen bonds : bond 0.04846 / 3.23 ( 854) hydrogen bonds : angle 3.11834 / 2.23 ( 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 184 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.392 Fit side-chains REVERT: H 78 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6739 (tmmt) REVERT: H 113 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7672 (mt) REVERT: F 113 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7663 (mt) REVERT: E 12 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7109 (mp) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 0.3940 time to fit residues: 76.4531 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 8 VAL Chi-restraints excluded: chain E residue 12 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.0270 chunk 31 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 132 HIS G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133416 restraints weight = 28024.670| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.36 r_work: 0.3051 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1222 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= 0.122 Angle : 0.452 7.664 14581 Z= 0.252 Chirality : 0.036 0.125 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.365 17.544 1443 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.04 % Allowed : 16.22 % 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 are not related in a simple way. whole: 4.28 (0.23), residues: 1312 helix: 3.97 (0.16), residues: 950 sheet: 0.88 (1.18), residues: 10 loop : -0.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 6 TYR 0.014 0.001 TYR H 181 PHE 0.012 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/Z covalent geometry : bond 0.00240 / 0.12 (10749) covalent geometry : angle 0.45211 / 0.25 (14565) SS BOND : bond 0.00205 / 0.13 ( 8) SS BOND : angle 0.33855 / 0.17 ( 16) hydrogen bonds : bond 0.04989 / 3.33 ( 854) hydrogen bonds : angle 3.15119 / 2.25 ( 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 185 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.400 Fit side-chains REVERT: H 78 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6659 (tmmt) REVERT: H 113 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7579 (mt) REVERT: F 113 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7579 (mt) REVERT: E 11 LEU cc_start: 0.7099 (tp) cc_final: 0.6466 (tp) REVERT: G 209 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.5041 (mtp85) outliers start: 33 outliers final: 17 residues processed: 175 average time/residue: 0.4546 time to fit residues: 86.7178 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE 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 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: 0.9990 chunk 78 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4148 r_free = 0.4148 target = 0.190711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135595 restraints weight = 28820.509| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.20 r_work: 0.3059 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1304 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= 0.117 Angle : 0.442 7.863 14581 Z= 0.247 Chirality : 0.036 0.124 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.332 17.134 1443 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.32 % Allowed : 15.76 % 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 are not related in a simple way. whole: 4.32 (0.23), residues: 1312 helix: 4.01 (0.15), residues: 950 sheet: 0.90 (1.16), residues: 10 loop : -0.61 (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 0.003 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (10749) covalent geometry : angle 0.44248 / 0.25 (14565) SS BOND : bond 0.00176 / 0.11 ( 8) SS BOND : angle 0.30690 / 0.16 ( 16) hydrogen bonds : bond 0.04813 / 3.21 ( 854) hydrogen bonds : angle 3.11194 / 2.22 ( 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 191 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.387 Fit side-chains REVERT: H 113 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7654 (mt) REVERT: F 113 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 589 CYS cc_start: 0.5785 (p) cc_final: 0.4568 (m) REVERT: A 589 CYS cc_start: 0.5788 (p) cc_final: 0.4572 (m) REVERT: E 11 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6506 (tp) REVERT: G 12 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6843 (tp) REVERT: G 209 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.5039 (mtp85) outliers start: 36 outliers final: 17 residues processed: 180 average time/residue: 0.4311 time to fit residues: 84.9406 Evaluate side-chains 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE 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 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS H 205 HIS F 199 HIS E 60 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.190832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137286 restraints weight = 31294.207| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.36 r_work: 0.3049 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.025 10757 Z= 0.117 Angle : 0.444 8.548 14581 Z= 0.247 Chirality : 0.036 0.125 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.336 18.458 1443 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 15.94 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.31 (0.23), residues: 1312 helix: 4.00 (0.15), residues: 950 sheet: 0.88 (1.15), residues: 10 loop : -0.60 (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 H 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/Z covalent geometry : bond 0.00224 / 0.12 (10749) covalent geometry : angle 0.44430 / 0.25 (14565) SS BOND : bond 0.00170 / 0.10 ( 8) SS BOND : angle 0.33874 / 0.19 ( 16) hydrogen bonds : bond 0.04793 / 3.20 ( 854) hydrogen bonds : angle 3.11305 / 2.23 ( 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 187 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.385 Fit side-chains REVERT: H 113 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7669 (mt) REVERT: F 113 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 589 CYS cc_start: 0.5772 (p) cc_final: 0.4551 (m) REVERT: A 589 CYS cc_start: 0.5763 (p) cc_final: 0.4537 (m) REVERT: E 11 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6575 (tp) REVERT: E 12 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7104 (mp) REVERT: E 95 GLU cc_start: 0.5269 (tt0) cc_final: 0.4875 (mp0) REVERT: G 141 PHE cc_start: 0.7429 (m-80) cc_final: 0.7204 (m-80) REVERT: G 209 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5047 (mtp85) outliers start: 33 outliers final: 17 residues processed: 177 average time/residue: 0.4619 time to fit residues: 89.1007 Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 LEU 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 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 60 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133889 restraints weight = 25795.384| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.34 r_work: 0.3054 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 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 = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10757 Z= 0.123 Angle : 0.458 8.371 14581 Z= 0.254 Chirality : 0.036 0.127 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.385 18.788 1443 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.76 % Allowed : 16.22 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.23), residues: 1312 helix: 3.94 (0.16), residues: 950 sheet: 0.91 (1.17), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 545 TYR 0.014 0.001 TYR H 181 PHE 0.019 0.001 PHE A 531 TRP 0.008 0.001 TRP G 33 HIS 0.016 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10749) covalent geometry : angle 0.45786 / 0.25 (14565) SS BOND : bond 0.00189 / 0.11 ( 8) SS BOND : angle 0.32731 / 0.17 ( 16) hydrogen bonds : bond 0.04963 / 3.31 ( 854) hydrogen bonds : angle 3.15269 / 2.26 ( 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 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.398 Fit side-chains REVERT: H 113 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7577 (mt) REVERT: F 113 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7567 (mt) REVERT: C 589 CYS cc_start: 0.5780 (p) cc_final: 0.4567 (m) REVERT: A 589 CYS cc_start: 0.5731 (p) cc_final: 0.4491 (m) REVERT: E 11 LEU cc_start: 0.7023 (tp) cc_final: 0.6409 (tp) REVERT: E 12 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7104 (mp) REVERT: E 95 GLU cc_start: 0.5218 (tt0) cc_final: 0.4852 (mp0) REVERT: G 11 LEU cc_start: 0.7104 (tp) cc_final: 0.6549 (tp) outliers start: 30 outliers final: 20 residues processed: 168 average time/residue: 0.4237 time to fit residues: 77.6368 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 12 LEU 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 10 MET 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 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 82 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135070 restraints weight = 29446.363| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.23 r_work: 0.3045 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10757 Z= 0.126 Angle : 0.466 8.381 14581 Z= 0.258 Chirality : 0.036 0.127 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.408 18.836 1443 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 16.59 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.23), residues: 1312 helix: 3.91 (0.15), residues: 950 sheet: 0.90 (1.16), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 545 TYR 0.014 0.001 TYR H 181 PHE 0.013 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/Z covalent geometry : bond 0.00251 / 0.13 (10749) covalent geometry : angle 0.46604 / 0.26 (14565) SS BOND : bond 0.00204 / 0.12 ( 8) SS BOND : angle 0.34913 / 0.19 ( 16) hydrogen bonds : bond 0.05009 / 3.34 ( 854) hydrogen bonds : angle 3.16026 / 2.26 ( 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 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.389 Fit side-chains REVERT: H 113 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (mt) REVERT: F 113 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7608 (mt) REVERT: C 589 CYS cc_start: 0.5751 (p) cc_final: 0.4534 (m) REVERT: A 589 CYS cc_start: 0.5726 (p) cc_final: 0.4498 (m) REVERT: E 11 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6528 (tp) REVERT: E 12 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7110 (mp) REVERT: E 95 GLU cc_start: 0.5231 (tt0) cc_final: 0.4858 (mp0) REVERT: G 11 LEU cc_start: 0.7099 (tp) cc_final: 0.6559 (tp) REVERT: G 102 ARG cc_start: 0.7817 (tpt90) cc_final: 0.7438 (tpt90) outliers start: 25 outliers final: 18 residues processed: 161 average time/residue: 0.4594 time to fit residues: 80.6578 Evaluate side-chains 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 11 LEU Chi-restraints excluded: chain E residue 12 LEU 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 10 MET 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 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.190762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133721 restraints weight = 25881.593| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.43 r_work: 0.3058 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10757 Z= 0.122 Angle : 0.459 8.340 14581 Z= 0.255 Chirality : 0.036 0.136 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.391 18.570 1443 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.30 % Allowed : 16.77 % 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 are not related in a simple way. whole: 4.25 (0.23), residues: 1312 helix: 3.95 (0.15), residues: 950 sheet: 0.87 (1.16), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 545 TYR 0.014 0.001 TYR H 181 PHE 0.018 0.001 PHE G 141 TRP 0.009 0.001 TRP G 33 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10749) covalent geometry : angle 0.45936 / 0.25 (14565) SS BOND : bond 0.00185 / 0.11 ( 8) SS BOND : angle 0.30977 / 0.17 ( 16) hydrogen bonds : bond 0.04889 / 3.26 ( 854) hydrogen bonds : angle 3.14224 / 2.25 ( 2494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.28 seconds wall clock time: 71 minutes 13.91 seconds (4273.91 seconds total)