Starting phenix.real_space_refine on Thu Jul 2 22:04:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2h_16390/07_2026/8c2h_16390.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 61 5.16 5 C 6664 2.51 5 N 1558 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 10071 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1037 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 133, 1010 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 133, 1010 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1009 Chain: "B" Number of atoms: 1071 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1025 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 134, 1025 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1003 Chain: "C" Number of atoms: 1043 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1016 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 134, 1016 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1015 Chain: "D" Number of atoms: 1120 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1083 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} 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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 141, 1083 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} 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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1071 Chain: "E" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Chain: "F" Number of atoms: 1365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 bond proxies already assigned to first conformer: 1373 Chain: "G" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Chain: "H" Number of atoms: 1365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 bond proxies already assigned to first conformer: 1373 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N AGLN A 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 583 " occ=0.50 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE B 570 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.50 residue: pdb=" N AGLN B 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 583 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N AILE B 587 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 587 " occ=0.50 residue: pdb=" N AGLN C 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 583 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 ... (remaining 9 not shown) Time building chain proxies: 3.52, per 1000 atoms: 0.35 Number of scatterers: 10071 At special positions: 0 Unit cell: (99.946, 97.468, 87.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 2 15.00 O 1786 8.00 N 1558 7.00 C 6664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.02 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.05 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.01 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 730.3 milliseconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 74.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 621 removed outlier: 3.517A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 815 removed outlier: 3.621A pdb=" N VAL A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 518 through 541 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 614 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 784 through 815 removed outlier: 3.590A pdb=" N VAL B 788 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLY B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 621 Processing helix chain 'C' and resid 784 through 815 removed outlier: 3.613A pdb=" N VAL C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 543 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 614 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 784 through 815 removed outlier: 3.589A pdb=" N VAL D 788 " --> pdb=" O SER D 784 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.889A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.932A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 207 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.913A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.898A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 207 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.891A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.939A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 207 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.904A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 3.887A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 207 Processing sheet with id=AA1, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'H' and resid 77 through 79 785 hydrogen bonds defined for protein. 2309 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: 1.84 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1636 1.32 - 1.45: 3580 1.45 - 1.59: 4916 1.59 - 1.72: 4 1.72 - 1.85: 86 Bond restraints: 10222 Sorted by residual: bond pdb=" CG HIS F 60 " pdb=" CD2 HIS F 60 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.40e+00 bond pdb=" C1 POV G 401 " pdb=" O11 POV G 401 " ideal model delta sigma weight residual 1.410 1.469 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" CA SER H 144 " pdb=" CB SER H 144 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.80e+00 bond pdb=" C1 POV E 401 " pdb=" O11 POV E 401 " ideal model delta sigma weight residual 1.410 1.469 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" CG HIS H 132 " pdb=" CD2 HIS H 132 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.06e+00 ... (remaining 10217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12181 2.16 - 4.32: 1445 4.32 - 6.48: 135 6.48 - 8.65: 20 8.65 - 10.81: 4 Bond angle restraints: 13785 Sorted by residual: angle pdb=" C ARG A 541 " pdb=" CA ARG A 541 " pdb=" CB ARG A 541 " ideal model delta sigma weight residual 111.95 101.14 10.81 1.45e+00 4.76e-01 5.55e+01 angle pdb=" N LEU F 69 " pdb=" CA LEU F 69 " pdb=" CB LEU F 69 " ideal model delta sigma weight residual 110.67 101.10 9.57 1.39e+00 5.18e-01 4.74e+01 angle pdb=" CA HIS H 132 " pdb=" CB HIS H 132 " pdb=" CG HIS H 132 " ideal model delta sigma weight residual 113.80 119.45 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA ASP H 81 " pdb=" CB ASP H 81 " pdb=" CG ASP H 81 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.00e+00 1.00e+00 2.18e+01 angle pdb=" C ASP H 31 " pdb=" CA ASP H 31 " pdb=" CB ASP H 31 " ideal model delta sigma weight residual 111.45 103.46 7.99 1.72e+00 3.38e-01 2.16e+01 ... (remaining 13780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 5202 20.13 - 40.26: 441 40.26 - 60.39: 133 60.39 - 80.52: 9 80.52 - 100.65: 4 Dihedral angle restraints: 5789 sinusoidal: 2204 harmonic: 3585 Sorted by residual: dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual -86.00 -32.34 -53.66 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -32.56 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CA AASP D 586 " pdb=" C AASP D 586 " pdb=" N AILE D 587 " pdb=" CA AILE D 587 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 940 0.067 - 0.134: 473 0.134 - 0.200: 122 0.200 - 0.267: 16 0.267 - 0.334: 4 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CA ARG G 37 " pdb=" N ARG G 37 " pdb=" C ARG G 37 " pdb=" CB ARG G 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG E 37 " pdb=" N ARG E 37 " pdb=" C ARG E 37 " pdb=" CB ARG E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA PHE D 542 " pdb=" N PHE D 542 " pdb=" C PHE D 542 " pdb=" CB PHE D 542 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1552 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 602 " 0.062 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP D 602 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 602 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP D 602 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 602 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP D 602 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 602 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 602 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP D 602 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.056 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP B 602 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 583 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C GLN D 583 " 0.071 2.00e-02 2.50e+03 pdb=" O GLN D 583 " -0.026 2.00e-02 2.50e+03 pdb=" N AGLY D 584 " -0.024 2.00e-02 2.50e+03 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2940 2.84 - 3.35: 10163 3.35 - 3.87: 17740 3.87 - 4.38: 19769 4.38 - 4.90: 33587 Nonbonded interactions: 84199 Sorted by model distance: nonbonded pdb=" ND1 HIS H 82 " pdb=" O HOH H1701 " model vdw 2.319 3.120 nonbonded pdb=" NH2 ARG A 541 " pdb=" O HOH A1501 " model vdw 2.319 3.120 nonbonded pdb=" NH1 ARG D 541 " pdb=" OE1 GLU D 566 " model vdw 2.349 3.120 nonbonded pdb=" N BASP A 586 " pdb=" OD1BASP A 586 " model vdw 2.350 3.120 nonbonded pdb=" NH1 ARG B 541 " pdb=" OE1 GLU B 566 " model vdw 2.353 3.120 ... (remaining 84194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 506 through 569 or resid 571 through 582 or resid 588 thro \ ugh 1402)) selection = (chain 'B' and ((resid 506 through 507 and (name N or name CA or name C or name \ O or name CB )) or resid 508 through 542 or resid 565 through 569 or resid 571 t \ hrough 582 or resid 588 through 622 or (resid 623 through 779 and (name N or nam \ e CA or name C or name O or name CB )) or resid 780 through 815 or (resid 1401 a \ nd (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 1402 \ )) selection = (chain 'C' and (resid 506 through 542 or resid 565 through 569 or resid 571 thro \ ugh 582 or resid 588 through 1402)) selection = (chain 'D' and ((resid 506 through 507 and (name N or name CA or name C or name \ O or name CB )) or resid 508 through 542 or resid 565 through 569 or resid 571 t \ hrough 582 or resid 588 through 622 or (resid 623 and (name N or name CA or name \ C or name O or name CB )) or resid 779 through 815 or (resid 1401 and (name CA \ or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or \ name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 1402)) } ncs_group { reference = (chain 'E' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'F' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'G' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'H' and (resid 5 through 183 or resid 185 through 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.800 Find NCS groups from input model: 0.260 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.009 0.068 10230 Z= 0.591 Angle : 1.458 11.067 13801 Z= 0.996 Chirality : 0.080 0.334 1555 Planarity : 0.010 0.100 1663 Dihedral : 16.150 100.652 3471 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.15 % Allowed : 6.35 % Favored : 87.50 % Cbeta Deviations : 0.26 % 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: -1.37 (0.21), residues: 1219 helix: -0.22 (0.15), residues: 899 sheet: -2.77 (0.58), residues: 60 loop : -2.46 (0.28), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.005 ARG A 541 TYR 0.036 0.008 TYR H 156 PHE 0.040 0.007 PHE C 575 TRP 0.062 0.011 TRP D 602 HIS 0.012 0.003 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.59 (10222) covalent geometry : angle 1.44719 / 0.99 (13785) SS BOND : bond 0.01744 / 1.04 ( 8) SS BOND : angle 5.38818 / 3.68 ( 16) hydrogen bonds : bond 0.16364 / 10.66 ( 785) hydrogen bonds : angle 6.43943 / 4.74 ( 2309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.428 Fit side-chains REVERT: A 542 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5851 (p90) REVERT: A 566 GLU cc_start: 0.7086 (pp20) cc_final: 0.6842 (mm-30) REVERT: A 582 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 507 LYS cc_start: 0.6615 (ptpt) cc_final: 0.6286 (ptmm) REVERT: B 615 ASN cc_start: 0.7472 (m-40) cc_final: 0.7104 (t0) REVERT: B 803 MET cc_start: 0.8563 (mtp) cc_final: 0.8279 (mtp) REVERT: C 542 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: C 581 MET cc_start: 0.9023 (mmt) cc_final: 0.8248 (mmt) REVERT: C 590 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8263 (mpp80) REVERT: C 804 LEU cc_start: 0.8034 (tp) cc_final: 0.7769 (tt) REVERT: D 566 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: D 623 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7392 (mt-10) REVERT: D 781 SER cc_start: 0.7967 (p) cc_final: 0.7709 (t) REVERT: E 31 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: E 41 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.5033 (ptm160) REVERT: E 184 PHE cc_start: 0.7436 (m-80) cc_final: 0.7177 (m-10) REVERT: F 37 ARG cc_start: 0.7046 (mtt-85) cc_final: 0.6762 (mtp85) REVERT: F 78 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6907 (pttp) REVERT: F 99 ARG cc_start: 0.7264 (mmp80) cc_final: 0.6549 (mtt90) REVERT: F 174 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8120 (p) REVERT: F 203 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6510 (mtpt) REVERT: F 207 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4151 (pt) REVERT: G 31 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: H 24 MET cc_start: 0.8722 (tpt) cc_final: 0.7909 (tpt) REVERT: H 58 MET cc_start: 0.6513 (tpt) cc_final: 0.6043 (tmm) REVERT: H 79 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: H 99 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6792 (mmm-85) REVERT: H 132 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6522 (m-70) REVERT: H 174 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8311 (p) outliers start: 57 outliers final: 4 residues processed: 171 average time/residue: 0.5791 time to fit residues: 106.6038 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 160 ASN E 204 HIS F 132 HIS F 204 HIS G 160 ASN G 204 HIS H 132 HIS H 204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.088340 restraints weight = 51965.900| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 4.08 r_work: 0.2502 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10230 Z= 0.135 Angle : 0.500 10.233 13801 Z= 0.278 Chirality : 0.037 0.135 1555 Planarity : 0.004 0.030 1663 Dihedral : 12.865 86.293 1585 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.37 % Allowed : 10.22 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.50 (0.24), residues: 1219 helix: 2.66 (0.16), residues: 904 sheet: 0.25 (0.98), residues: 40 loop : -1.79 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 208 TYR 0.012 0.001 TYR B 793 PHE 0.018 0.002 PHE C 570 TRP 0.011 0.002 TRP D 602 HIS 0.003 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10222) covalent geometry : angle 0.49572 / 0.28 (13785) SS BOND : bond 0.00506 / 0.27 ( 8) SS BOND : angle 2.02977 / 1.34 ( 16) hydrogen bonds : bond 0.05044 / 3.32 ( 785) hydrogen bonds : angle 3.85734 / 2.81 ( 2309) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 542 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5633 (p90) REVERT: B 566 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6468 (pm20) REVERT: B 590 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8085 (mtt180) REVERT: B 615 ASN cc_start: 0.7539 (m-40) cc_final: 0.7262 (t0) REVERT: B 807 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7001 (tp) REVERT: C 581 MET cc_start: 0.9249 (mmt) cc_final: 0.8680 (mmt) REVERT: C 804 LEU cc_start: 0.8616 (tp) cc_final: 0.8321 (tt) REVERT: D 566 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: D 623 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7142 (mm-30) REVERT: D 807 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6865 (tp) REVERT: E 37 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.7094 (mtt-85) REVERT: E 58 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7092 (tpt) REVERT: E 78 LYS cc_start: 0.7269 (tttt) cc_final: 0.6989 (ttpp) REVERT: E 184 PHE cc_start: 0.7896 (m-80) cc_final: 0.7645 (m-10) REVERT: E 202 GLU cc_start: 0.7515 (pt0) cc_final: 0.7045 (mt-10) REVERT: F 99 ARG cc_start: 0.7612 (mmp80) cc_final: 0.6895 (mtt90) REVERT: F 207 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.4543 (tp) REVERT: G 31 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: G 37 ARG cc_start: 0.7918 (ptp-110) cc_final: 0.7297 (mtp85) REVERT: H 24 MET cc_start: 0.8881 (tpt) cc_final: 0.8351 (tpt) REVERT: H 37 ARG cc_start: 0.6808 (mtt-85) cc_final: 0.6569 (mtp85) REVERT: H 58 MET cc_start: 0.6667 (tpt) cc_final: 0.5976 (tmm) REVERT: H 99 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.7100 (mmm-85) REVERT: H 172 SER cc_start: 0.7274 (t) cc_final: 0.6968 (p) REVERT: H 208 ARG cc_start: 0.4909 (OUTLIER) cc_final: 0.4050 (ptm160) outliers start: 29 outliers final: 8 residues processed: 153 average time/residue: 0.5966 time to fit residues: 98.1204 Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 149 ASN E 160 ASN F 160 ASN F 204 HIS G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105670 restraints weight = 50552.174| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 6.00 r_work: 0.2556 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10230 Z= 0.127 Angle : 0.488 10.051 13801 Z= 0.262 Chirality : 0.036 0.205 1555 Planarity : 0.003 0.029 1663 Dihedral : 10.636 77.567 1551 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.37 % Allowed : 10.71 % Favored : 85.91 % 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: 3.43 (0.24), residues: 1219 helix: 3.29 (0.16), residues: 904 sheet: 0.78 (1.00), residues: 40 loop : -1.26 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 41 TYR 0.009 0.001 TYR C 612 PHE 0.017 0.001 PHE C 570 TRP 0.008 0.001 TRP D 602 HIS 0.003 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10222) covalent geometry : angle 0.47732 / 0.26 (13785) SS BOND : bond 0.00657 / 0.38 ( 8) SS BOND : angle 2.96196 / 2.05 ( 16) hydrogen bonds : bond 0.04708 / 3.10 ( 785) hydrogen bonds : angle 3.57111 / 2.60 ( 2309) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.469 Fit side-chains REVERT: A 542 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5945 (p90) REVERT: A 581 MET cc_start: 0.9260 (mmt) cc_final: 0.8654 (mmt) REVERT: B 590 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8267 (mtt180) REVERT: B 615 ASN cc_start: 0.7725 (m-40) cc_final: 0.7444 (t0) REVERT: B 807 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7073 (tp) REVERT: C 566 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 581 MET cc_start: 0.9240 (mmt) cc_final: 0.8677 (mmt) REVERT: C 804 LEU cc_start: 0.8718 (tp) cc_final: 0.8433 (tt) REVERT: C 807 LEU cc_start: 0.8088 (tp) cc_final: 0.7883 (tm) REVERT: D 566 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: D 625 MET cc_start: 0.7496 (tpp) cc_final: 0.7232 (mmt) REVERT: D 781 SER cc_start: 0.8183 (p) cc_final: 0.7900 (t) REVERT: E 37 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7374 (mtt-85) REVERT: E 58 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7180 (tpt) REVERT: E 76 VAL cc_start: 0.7647 (t) cc_final: 0.7444 (p) REVERT: E 78 LYS cc_start: 0.7418 (tttt) cc_final: 0.7104 (ttpp) REVERT: E 184 PHE cc_start: 0.8051 (m-80) cc_final: 0.7836 (m-10) REVERT: E 202 GLU cc_start: 0.7638 (pt0) cc_final: 0.7185 (mt-10) REVERT: F 99 ARG cc_start: 0.7835 (mmp80) cc_final: 0.7105 (mtt90) REVERT: F 127 PHE cc_start: 0.6300 (m-10) cc_final: 0.6039 (m-80) REVERT: G 37 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7368 (mtp85) REVERT: H 24 MET cc_start: 0.8998 (tpt) cc_final: 0.8489 (tpt) REVERT: H 37 ARG cc_start: 0.6952 (mtt-85) cc_final: 0.6565 (mtp85) REVERT: H 58 MET cc_start: 0.6720 (tpt) cc_final: 0.6186 (tmm) REVERT: H 99 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7342 (mmm-85) REVERT: H 208 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4321 (ptm160) outliers start: 30 outliers final: 15 residues processed: 143 average time/residue: 0.6057 time to fit residues: 93.0254 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 204 HIS H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108960 restraints weight = 46810.903| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 5.81 r_work: 0.2500 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 10230 Z= 0.111 Angle : 0.450 8.869 13801 Z= 0.241 Chirality : 0.036 0.198 1555 Planarity : 0.003 0.030 1663 Dihedral : 9.996 67.860 1551 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.88 % Allowed : 12.50 % Favored : 84.62 % 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: 3.66 (0.24), residues: 1219 helix: 3.41 (0.16), residues: 904 sheet: 1.49 (1.48), residues: 20 loop : -0.93 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 41 TYR 0.010 0.001 TYR H 200 PHE 0.013 0.001 PHE C 570 TRP 0.008 0.001 TRP F 177 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (10222) covalent geometry : angle 0.44099 / 0.24 (13785) SS BOND : bond 0.00354 / 0.19 ( 8) SS BOND : angle 2.71977 / 1.81 ( 16) hydrogen bonds : bond 0.04347 / 2.87 ( 785) hydrogen bonds : angle 3.45905 / 2.52 ( 2309) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.382 Fit side-chains REVERT: A 542 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5968 (p90) REVERT: A 581 MET cc_start: 0.9270 (mmt) cc_final: 0.8756 (mmt) REVERT: B 590 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8255 (mtt180) REVERT: B 615 ASN cc_start: 0.7679 (m-40) cc_final: 0.7376 (t0) REVERT: B 807 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7059 (tp) REVERT: C 566 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 581 MET cc_start: 0.9237 (mmt) cc_final: 0.8794 (mmt) REVERT: C 804 LEU cc_start: 0.8644 (tp) cc_final: 0.8364 (tt) REVERT: C 807 LEU cc_start: 0.8015 (tp) cc_final: 0.7812 (tm) REVERT: D 566 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: D 781 SER cc_start: 0.8131 (p) cc_final: 0.7841 (t) REVERT: E 58 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7230 (tpt) REVERT: E 78 LYS cc_start: 0.7472 (tttt) cc_final: 0.7121 (ttpp) REVERT: E 120 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7255 (mp) REVERT: E 184 PHE cc_start: 0.7985 (m-80) cc_final: 0.7772 (m-10) REVERT: E 202 GLU cc_start: 0.7590 (pt0) cc_final: 0.7146 (mt-10) REVERT: F 99 ARG cc_start: 0.7733 (mmp80) cc_final: 0.6958 (mtt90) REVERT: F 127 PHE cc_start: 0.6246 (m-80) cc_final: 0.5985 (m-80) REVERT: G 37 ARG cc_start: 0.7766 (ptp-110) cc_final: 0.7362 (mtp85) REVERT: G 65 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7265 (ptp90) REVERT: H 24 MET cc_start: 0.8980 (tpt) cc_final: 0.8472 (tpt) REVERT: H 37 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6707 (mtp85) REVERT: H 58 MET cc_start: 0.6715 (tpt) cc_final: 0.6186 (mmm) REVERT: H 99 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7310 (mmm-85) REVERT: H 132 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.5513 (p-80) REVERT: H 204 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.5916 (t-90) outliers start: 25 outliers final: 13 residues processed: 128 average time/residue: 0.6527 time to fit residues: 89.3618 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106826 restraints weight = 55061.385| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 6.16 r_work: 0.2446 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10230 Z= 0.148 Angle : 0.498 10.402 13801 Z= 0.268 Chirality : 0.037 0.198 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.086 74.295 1551 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.37 % Allowed : 12.50 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.23), residues: 1219 helix: 3.19 (0.16), residues: 904 sheet: 1.35 (1.43), residues: 20 loop : -0.82 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 74 TYR 0.013 0.001 TYR C 612 PHE 0.017 0.002 PHE C 570 TRP 0.009 0.002 TRP H 64 HIS 0.012 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10222) covalent geometry : angle 0.48978 / 0.26 (13785) SS BOND : bond 0.00508 / 0.30 ( 8) SS BOND : angle 2.70592 / 1.78 ( 16) hydrogen bonds : bond 0.05002 / 3.29 ( 785) hydrogen bonds : angle 3.63569 / 2.65 ( 2309) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.377 Fit side-chains REVERT: A 542 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.6140 (p90) REVERT: A 581 MET cc_start: 0.9343 (mmt) cc_final: 0.8815 (mmt) REVERT: B 615 ASN cc_start: 0.7770 (m-40) cc_final: 0.7434 (t0) REVERT: B 807 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7004 (tp) REVERT: C 566 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6567 (mt-10) REVERT: C 581 MET cc_start: 0.9274 (mmt) cc_final: 0.8769 (mmt) REVERT: C 804 LEU cc_start: 0.8619 (tp) cc_final: 0.8326 (tt) REVERT: D 566 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: D 781 SER cc_start: 0.8145 (p) cc_final: 0.7826 (t) REVERT: E 58 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7172 (tpt) REVERT: E 65 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: E 120 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7213 (mp) REVERT: E 184 PHE cc_start: 0.7988 (m-80) cc_final: 0.7732 (m-10) REVERT: E 202 GLU cc_start: 0.7505 (pt0) cc_final: 0.7099 (mt-10) REVERT: F 99 ARG cc_start: 0.7722 (mmp80) cc_final: 0.6957 (mtt90) REVERT: F 127 PHE cc_start: 0.6289 (m-80) cc_final: 0.6060 (m-80) REVERT: G 37 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: H 24 MET cc_start: 0.8952 (tpt) cc_final: 0.8436 (tpt) REVERT: H 37 ARG cc_start: 0.7009 (mtt-85) cc_final: 0.6783 (mtp85) REVERT: H 58 MET cc_start: 0.6544 (tpt) cc_final: 0.6100 (tmm) REVERT: H 99 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7256 (mmm-85) REVERT: H 204 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6085 (t-90) REVERT: H 208 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.4217 (ptm160) outliers start: 30 outliers final: 14 residues processed: 133 average time/residue: 0.6542 time to fit residues: 92.9327 Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090553 restraints weight = 63112.529| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.86 r_work: 0.2460 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10230 Z= 0.188 Angle : 0.546 12.098 13801 Z= 0.292 Chirality : 0.039 0.187 1555 Planarity : 0.004 0.032 1663 Dihedral : 10.597 78.037 1551 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.17 % Allowed : 12.80 % Favored : 84.03 % 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: 3.15 (0.23), residues: 1219 helix: 2.98 (0.16), residues: 902 sheet: 1.22 (1.42), residues: 20 loop : -0.85 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 129 TYR 0.016 0.002 TYR C 612 PHE 0.017 0.002 PHE C 570 TRP 0.011 0.002 TRP H 64 HIS 0.005 0.001 HIS E 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (10222) covalent geometry : angle 0.53855 / 0.29 (13785) SS BOND : bond 0.00425 / 0.23 ( 8) SS BOND : angle 2.77033 / 1.81 ( 16) hydrogen bonds : bond 0.05461 / 3.58 ( 785) hydrogen bonds : angle 3.80177 / 2.76 ( 2309) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.361 Fit side-chains REVERT: A 581 MET cc_start: 0.9364 (mmt) cc_final: 0.8841 (mmt) REVERT: A 590 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8231 (mtp85) REVERT: B 510 VAL cc_start: 0.8762 (m) cc_final: 0.8474 (p) REVERT: B 615 ASN cc_start: 0.7793 (m-40) cc_final: 0.7461 (t0) REVERT: B 807 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7057 (tp) REVERT: C 566 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6583 (mt-10) REVERT: C 581 MET cc_start: 0.9298 (mmt) cc_final: 0.8735 (mmt) REVERT: C 804 LEU cc_start: 0.8612 (tp) cc_final: 0.8307 (tt) REVERT: D 566 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: E 58 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7215 (tpt) REVERT: E 65 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6941 (mtm-85) REVERT: E 78 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7426 (ttpp) REVERT: E 120 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7219 (mp) REVERT: E 184 PHE cc_start: 0.8003 (m-80) cc_final: 0.7727 (m-10) REVERT: E 202 GLU cc_start: 0.7537 (pt0) cc_final: 0.7082 (mt-10) REVERT: F 99 ARG cc_start: 0.7676 (mmp80) cc_final: 0.6948 (mtt90) REVERT: G 37 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7331 (mtp85) REVERT: H 37 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6812 (mtp85) REVERT: H 58 MET cc_start: 0.6515 (tpt) cc_final: 0.6093 (tmm) REVERT: H 99 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7242 (mmm-85) REVERT: H 208 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4299 (ptm160) outliers start: 28 outliers final: 16 residues processed: 132 average time/residue: 0.6139 time to fit residues: 86.7090 Evaluate side-chains 134 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107041 restraints weight = 47671.884| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.79 r_work: 0.2478 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2449 r_free = 0.2449 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2449 r_free = 0.2449 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10230 Z= 0.119 Angle : 0.458 10.173 13801 Z= 0.244 Chirality : 0.036 0.159 1555 Planarity : 0.003 0.030 1663 Dihedral : 9.497 70.601 1549 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.88 % Allowed : 13.10 % Favored : 84.03 % 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: 3.58 (0.24), residues: 1219 helix: 3.30 (0.16), residues: 904 sheet: 1.31 (1.45), residues: 20 loop : -0.73 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 624 TYR 0.009 0.001 TYR C 519 PHE 0.012 0.001 PHE C 570 TRP 0.008 0.001 TRP E 177 HIS 0.003 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10222) covalent geometry : angle 0.45050 / 0.24 (13785) SS BOND : bond 0.00362 / 0.19 ( 8) SS BOND : angle 2.50814 / 1.61 ( 16) hydrogen bonds : bond 0.04489 / 2.96 ( 785) hydrogen bonds : angle 3.50835 / 2.55 ( 2309) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.290 Fit side-chains REVERT: A 581 MET cc_start: 0.9306 (mmt) cc_final: 0.8856 (mmt) REVERT: A 590 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8323 (mtp85) REVERT: B 510 VAL cc_start: 0.8749 (m) cc_final: 0.8464 (p) REVERT: B 615 ASN cc_start: 0.7805 (m-40) cc_final: 0.7485 (t0) REVERT: B 807 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7021 (tp) REVERT: C 566 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6641 (mt-10) REVERT: C 581 MET cc_start: 0.9279 (mmt) cc_final: 0.8793 (mmt) REVERT: C 804 LEU cc_start: 0.8613 (tp) cc_final: 0.8314 (tt) REVERT: C 807 LEU cc_start: 0.7999 (tp) cc_final: 0.7792 (tm) REVERT: D 566 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: D 625 MET cc_start: 0.7512 (tpp) cc_final: 0.7108 (mmt) REVERT: E 10 MET cc_start: 0.7787 (tpt) cc_final: 0.7578 (tpp) REVERT: E 65 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: E 78 LYS cc_start: 0.7761 (ttpp) cc_final: 0.7467 (ttpp) REVERT: E 120 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7241 (mp) REVERT: E 184 PHE cc_start: 0.8015 (m-80) cc_final: 0.7778 (m-10) REVERT: E 202 GLU cc_start: 0.7532 (pt0) cc_final: 0.7123 (mt-10) REVERT: F 99 ARG cc_start: 0.7763 (mmp80) cc_final: 0.7009 (mtt90) REVERT: G 37 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7300 (mtp85) REVERT: G 65 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7235 (ptp90) REVERT: H 37 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6799 (mtp85) REVERT: H 58 MET cc_start: 0.6563 (tpt) cc_final: 0.6159 (mmm) REVERT: H 99 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7356 (mmm-85) REVERT: H 208 ARG cc_start: 0.5204 (OUTLIER) cc_final: 0.4235 (ptm160) outliers start: 25 outliers final: 15 residues processed: 126 average time/residue: 0.6322 time to fit residues: 84.8643 Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109264 restraints weight = 49757.276| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 5.82 r_work: 0.2482 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10230 Z= 0.118 Angle : 0.456 10.045 13801 Z= 0.242 Chirality : 0.036 0.149 1555 Planarity : 0.003 0.031 1663 Dihedral : 9.213 69.361 1549 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.98 % Allowed : 13.19 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.67 (0.24), residues: 1219 helix: 3.38 (0.16), residues: 903 sheet: 1.20 (1.46), residues: 20 loop : -0.73 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 624 TYR 0.010 0.001 TYR C 519 PHE 0.012 0.001 PHE C 570 TRP 0.007 0.001 TRP H 177 HIS 0.008 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (10222) covalent geometry : angle 0.44796 / 0.24 (13785) SS BOND : bond 0.00303 / 0.16 ( 8) SS BOND : angle 2.51049 / 1.58 ( 16) hydrogen bonds : bond 0.04478 / 2.96 ( 785) hydrogen bonds : angle 3.48601 / 2.54 ( 2309) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.382 Fit side-chains REVERT: A 566 GLU cc_start: 0.7695 (pt0) cc_final: 0.7494 (pt0) REVERT: A 581 MET cc_start: 0.9294 (mmt) cc_final: 0.8814 (mmt) REVERT: A 590 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8299 (mtp85) REVERT: B 510 VAL cc_start: 0.8726 (m) cc_final: 0.8437 (p) REVERT: B 615 ASN cc_start: 0.7811 (m-40) cc_final: 0.7459 (t0) REVERT: B 807 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6990 (tp) REVERT: C 566 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6579 (mt-10) REVERT: C 581 MET cc_start: 0.9270 (mmt) cc_final: 0.8833 (mmt) REVERT: C 804 LEU cc_start: 0.8588 (tp) cc_final: 0.8299 (tt) REVERT: C 807 LEU cc_start: 0.7971 (tp) cc_final: 0.7761 (tm) REVERT: D 566 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: D 625 MET cc_start: 0.7513 (tpp) cc_final: 0.7141 (mmt) REVERT: E 10 MET cc_start: 0.7738 (tpt) cc_final: 0.7527 (tpp) REVERT: E 65 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6865 (mtm-85) REVERT: E 120 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7212 (mp) REVERT: E 184 PHE cc_start: 0.7986 (m-80) cc_final: 0.7745 (m-10) REVERT: E 202 GLU cc_start: 0.7484 (pt0) cc_final: 0.7067 (mt-10) REVERT: F 99 ARG cc_start: 0.7727 (mmp80) cc_final: 0.6961 (mtt90) REVERT: F 126 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6468 (tp30) REVERT: G 37 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: G 65 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7245 (ptp90) REVERT: G 120 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6994 (mp) REVERT: H 37 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6763 (mtp85) REVERT: H 58 MET cc_start: 0.6400 (tpt) cc_final: 0.6099 (mmm) REVERT: H 99 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.7312 (mmm-85) REVERT: H 208 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4370 (ppt-90) outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 0.6525 time to fit residues: 91.9887 Evaluate side-chains 134 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109063 restraints weight = 50364.718| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.82 r_work: 0.2500 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10230 Z= 0.114 Angle : 0.448 9.544 13801 Z= 0.238 Chirality : 0.036 0.128 1555 Planarity : 0.003 0.031 1663 Dihedral : 8.569 65.494 1547 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.88 % Allowed : 13.49 % Favored : 83.63 % 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: 3.74 (0.24), residues: 1219 helix: 3.46 (0.16), residues: 903 sheet: 1.17 (1.43), residues: 20 loop : -0.79 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 208 TYR 0.010 0.001 TYR C 519 PHE 0.012 0.001 PHE B 511 TRP 0.007 0.001 TRP G 177 HIS 0.005 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10222) covalent geometry : angle 0.44090 / 0.23 (13785) SS BOND : bond 0.00253 / 0.14 ( 8) SS BOND : angle 2.30368 / 1.45 ( 16) hydrogen bonds : bond 0.04366 / 2.88 ( 785) hydrogen bonds : angle 3.43055 / 2.49 ( 2309) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.347 Fit side-chains REVERT: A 566 GLU cc_start: 0.7669 (pt0) cc_final: 0.7453 (pt0) REVERT: A 581 MET cc_start: 0.9263 (mmt) cc_final: 0.8812 (mmt) REVERT: A 590 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8289 (mtp85) REVERT: B 510 VAL cc_start: 0.8722 (m) cc_final: 0.8410 (p) REVERT: B 615 ASN cc_start: 0.7760 (m-40) cc_final: 0.7398 (t0) REVERT: B 807 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6916 (tp) REVERT: C 566 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6541 (tt0) REVERT: C 581 MET cc_start: 0.9266 (mmt) cc_final: 0.8843 (mmt) REVERT: C 804 LEU cc_start: 0.8583 (tp) cc_final: 0.8295 (tt) REVERT: C 807 LEU cc_start: 0.7964 (tp) cc_final: 0.7763 (tm) REVERT: D 566 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: D 625 MET cc_start: 0.7519 (tpp) cc_final: 0.7115 (mmt) REVERT: E 184 PHE cc_start: 0.7975 (m-80) cc_final: 0.7736 (m-10) REVERT: E 202 GLU cc_start: 0.7481 (pt0) cc_final: 0.7093 (mt-10) REVERT: F 99 ARG cc_start: 0.7658 (mmp80) cc_final: 0.6904 (mtt90) REVERT: F 126 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6393 (tp30) REVERT: G 37 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7454 (mtp-110) REVERT: G 120 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7031 (mp) REVERT: H 37 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6725 (mtp85) REVERT: H 58 MET cc_start: 0.6444 (tpt) cc_final: 0.6134 (mmm) REVERT: H 99 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7309 (mmm-85) REVERT: H 208 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.4415 (ppt-90) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 0.5918 time to fit residues: 82.9720 Evaluate side-chains 134 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 117 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108303 restraints weight = 57289.537| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 6.16 r_work: 0.2497 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10230 Z= 0.111 Angle : 0.446 9.376 13801 Z= 0.237 Chirality : 0.035 0.127 1555 Planarity : 0.003 0.031 1663 Dihedral : 8.488 64.099 1545 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.38 % Allowed : 14.48 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.24), residues: 1219 helix: 3.48 (0.16), residues: 903 sheet: 1.14 (1.43), residues: 20 loop : -0.79 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 624 TYR 0.015 0.001 TYR E 173 PHE 0.012 0.001 PHE C 570 TRP 0.007 0.001 TRP G 177 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (10222) covalent geometry : angle 0.43938 / 0.23 (13785) SS BOND : bond 0.00221 / 0.12 ( 8) SS BOND : angle 2.31848 / 1.43 ( 16) hydrogen bonds : bond 0.04326 / 2.86 ( 785) hydrogen bonds : angle 3.41967 / 2.49 ( 2309) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.346 Fit side-chains REVERT: A 566 GLU cc_start: 0.7688 (pt0) cc_final: 0.7474 (pt0) REVERT: A 581 MET cc_start: 0.9270 (mmt) cc_final: 0.8830 (mmt) REVERT: A 590 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8336 (mtp85) REVERT: B 510 VAL cc_start: 0.8743 (m) cc_final: 0.8438 (p) REVERT: B 615 ASN cc_start: 0.7803 (m-40) cc_final: 0.7441 (t0) REVERT: B 807 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6946 (tp) REVERT: C 566 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6552 (mt-10) REVERT: C 581 MET cc_start: 0.9278 (mmt) cc_final: 0.8866 (mmt) REVERT: C 804 LEU cc_start: 0.8615 (tp) cc_final: 0.8329 (tt) REVERT: D 566 GLU cc_start: 0.7390 (pp20) cc_final: 0.7043 (pm20) REVERT: D 625 MET cc_start: 0.7463 (tpp) cc_final: 0.7058 (mmt) REVERT: E 120 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7247 (mp) REVERT: E 184 PHE cc_start: 0.8000 (m-80) cc_final: 0.7767 (m-10) REVERT: E 202 GLU cc_start: 0.7508 (pt0) cc_final: 0.7103 (mt-10) REVERT: F 99 ARG cc_start: 0.7731 (mmp80) cc_final: 0.6972 (mtt90) REVERT: F 126 GLU cc_start: 0.6689 (mm-30) cc_final: 0.6419 (tp30) REVERT: G 37 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7479 (mtp-110) REVERT: G 120 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7061 (mp) REVERT: H 37 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6747 (mtp85) REVERT: H 58 MET cc_start: 0.6476 (tpt) cc_final: 0.6167 (mmm) REVERT: H 99 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7364 (mmm-85) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 0.5580 time to fit residues: 77.2605 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 172 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 582 GLN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105811 restraints weight = 53805.524| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 6.35 r_work: 0.2478 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10230 Z= 0.120 Angle : 0.458 9.014 13801 Z= 0.242 Chirality : 0.036 0.132 1555 Planarity : 0.003 0.031 1663 Dihedral : 8.387 57.386 1542 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.58 % Allowed : 14.68 % Favored : 82.74 % 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: 3.71 (0.24), residues: 1219 helix: 3.43 (0.16), residues: 903 sheet: 1.12 (1.43), residues: 20 loop : -0.78 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 624 TYR 0.015 0.001 TYR E 173 PHE 0.012 0.001 PHE C 570 TRP 0.007 0.001 TRP A 574 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10222) covalent geometry : angle 0.45123 / 0.24 (13785) SS BOND : bond 0.00219 / 0.12 ( 8) SS BOND : angle 2.29913 / 1.43 ( 16) hydrogen bonds : bond 0.04492 / 2.97 ( 785) hydrogen bonds : angle 3.47705 / 2.53 ( 2309) =============================================================================== Job complete usr+sys time: 3549.79 seconds wall clock time: 61 minutes 18.29 seconds (3678.29 seconds total)