Starting phenix.real_space_refine on Tue May 13 12:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_16390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_16390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_16390.map" model { file = "/net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_16390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2h_16390/05_2025/8c2h_16390.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.62, per 1000 atoms: 0.96 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: 2.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 0.92 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: 2.85 Time building geometry restraints manager: 2.97 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 - 30.43: 5524 30.43 - 60.86: 273 60.86 - 91.29: 16 91.29 - 121.72: 10 121.72 - 152.15: 2 Dihedral angle restraints: 5825 sinusoidal: 2240 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 5822 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 815 or resid 1401 through 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 815 or resid 1401 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 28.900 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 17.608 152.149 3507 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (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 TRP 0.062 0.011 TRP D 602 HIS 0.012 0.003 HIS F 132 PHE 0.040 0.007 PHE C 575 TYR 0.036 0.008 TYR H 156 ARG 0.051 0.005 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.16364 ( 785) hydrogen bonds : angle 6.43943 ( 2309) SS BOND : bond 0.01744 ( 8) SS BOND : angle 5.38818 ( 16) covalent geometry : bond 0.00910 (10222) covalent geometry : angle 1.44719 (13785) *********************** 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 : 1.013 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: 0.7242 (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: 0.8642 (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: 1.1627 time to fit residues: 214.1520 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 : 1.055 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN F 132 HIS F 204 HIS G 160 ASN H 132 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 = 0.3596 r_free = 0.3596 target = 0.142851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108699 restraints weight = 41938.227| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 5.48 r_work: 0.2442 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10230 Z= 0.139 Angle : 0.512 10.021 13801 Z= 0.284 Chirality : 0.037 0.139 1555 Planarity : 0.004 0.030 1663 Dihedral : 14.580 150.078 1621 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.17 % Allowed : 10.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1219 helix: 2.61 (0.16), residues: 904 sheet: 0.11 (0.97), residues: 40 loop : -1.80 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 602 HIS 0.003 0.001 HIS F 82 PHE 0.019 0.002 PHE C 570 TYR 0.011 0.001 TYR B 793 ARG 0.003 0.000 ARG F 6 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 785) hydrogen bonds : angle 3.88840 ( 2309) SS BOND : bond 0.00504 ( 8) SS BOND : angle 2.12502 ( 16) covalent geometry : bond 0.00287 (10222) covalent geometry : angle 0.50709 (13785) *********************** 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 158 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 3.171 Fit side-chains REVERT: A 542 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.5698 (p90) REVERT: B 566 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6511 (pm20) REVERT: B 590 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8189 (mtt180) REVERT: B 615 ASN cc_start: 0.7658 (m-40) cc_final: 0.7357 (t0) REVERT: B 807 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7025 (tp) REVERT: C 566 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7476 (mm-30) REVERT: C 581 MET cc_start: 0.9274 (mmt) cc_final: 0.8715 (mmt) REVERT: C 804 LEU cc_start: 0.8689 (tp) cc_final: 0.8402 (tt) REVERT: D 566 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: D 623 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7182 (mm-30) REVERT: E 58 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7117 (tpt) REVERT: E 78 LYS cc_start: 0.7313 (tttt) cc_final: 0.6965 (ttpp) REVERT: E 184 PHE cc_start: 0.7985 (m-80) cc_final: 0.7748 (m-10) REVERT: E 202 GLU cc_start: 0.7558 (pt0) cc_final: 0.7125 (mt-10) REVERT: F 67 CYS cc_start: 0.7079 (m) cc_final: 0.6842 (m) REVERT: F 99 ARG cc_start: 0.7738 (mmp80) cc_final: 0.7020 (mtt90) REVERT: F 207 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4543 (tp) REVERT: G 31 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: G 37 ARG cc_start: 0.7974 (ptp-110) cc_final: 0.7370 (mtp85) REVERT: H 24 MET cc_start: 0.8939 (tpt) cc_final: 0.8413 (tpt) REVERT: H 37 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6578 (mtp85) REVERT: H 58 MET cc_start: 0.6754 (tpt) cc_final: 0.6065 (tmm) REVERT: H 99 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7230 (mmm-85) REVERT: H 172 SER cc_start: 0.7313 (t) cc_final: 0.7001 (p) REVERT: H 208 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4120 (ptm160) outliers start: 27 outliers final: 8 residues processed: 151 average time/residue: 1.2631 time to fit residues: 205.2501 Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN E 160 ASN F 160 ASN F 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 = 0.3556 r_free = 0.3556 target = 0.139608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104668 restraints weight = 50328.211| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 5.98 r_work: 0.2422 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10230 Z= 0.156 Angle : 0.531 9.960 13801 Z= 0.286 Chirality : 0.038 0.192 1555 Planarity : 0.003 0.031 1663 Dihedral : 12.939 137.771 1587 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.87 % Allowed : 10.42 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.24), residues: 1219 helix: 3.04 (0.16), residues: 904 sheet: 0.69 (0.98), residues: 40 loop : -1.27 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 574 HIS 0.004 0.001 HIS H 132 PHE 0.020 0.002 PHE C 570 TYR 0.013 0.002 TYR C 612 ARG 0.003 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 785) hydrogen bonds : angle 3.74395 ( 2309) SS BOND : bond 0.00374 ( 8) SS BOND : angle 2.92869 ( 16) covalent geometry : bond 0.00348 (10222) covalent geometry : angle 0.52185 (13785) *********************** 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: 34 poor density : 116 time to evaluate : 1.120 Fit side-chains REVERT: A 542 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5981 (p90) REVERT: B 590 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8179 (mtt180) REVERT: B 615 ASN cc_start: 0.7690 (m-40) cc_final: 0.7362 (t0) REVERT: B 807 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7057 (tp) REVERT: C 581 MET cc_start: 0.9282 (mmt) cc_final: 0.8710 (mmt) REVERT: C 804 LEU cc_start: 0.8641 (tp) cc_final: 0.8359 (tt) REVERT: D 566 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: D 781 SER cc_start: 0.8130 (p) cc_final: 0.7829 (t) REVERT: D 807 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6841 (tp) REVERT: E 58 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7201 (tpt) REVERT: E 65 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: E 78 LYS cc_start: 0.7352 (tttt) cc_final: 0.7043 (ttpp) REVERT: E 184 PHE cc_start: 0.8012 (m-80) cc_final: 0.7742 (m-10) REVERT: E 202 GLU cc_start: 0.7481 (pt0) cc_final: 0.7084 (mt-10) REVERT: F 99 ARG cc_start: 0.7725 (mmp80) cc_final: 0.6939 (mtt90) REVERT: G 37 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7342 (mtp85) REVERT: H 24 MET cc_start: 0.8920 (tpt) cc_final: 0.8368 (tpt) REVERT: H 37 ARG cc_start: 0.6876 (mtt-85) cc_final: 0.6646 (mtp85) REVERT: H 58 MET cc_start: 0.6758 (tpt) cc_final: 0.6155 (tmm) REVERT: H 99 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7220 (mmm-85) REVERT: H 208 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.4457 (ppt-90) outliers start: 34 outliers final: 14 residues processed: 141 average time/residue: 1.3334 time to fit residues: 201.2561 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 132 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 66 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN F 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107990 restraints weight = 56475.162| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 6.21 r_work: 0.2457 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10230 Z= 0.134 Angle : 0.488 9.602 13801 Z= 0.262 Chirality : 0.037 0.195 1555 Planarity : 0.003 0.031 1663 Dihedral : 12.067 123.154 1587 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.78 % Allowed : 12.00 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.24), residues: 1219 helix: 3.18 (0.16), residues: 904 sheet: 1.45 (1.44), residues: 20 loop : -0.99 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.004 0.001 HIS F 204 PHE 0.016 0.001 PHE C 570 TYR 0.011 0.001 TYR C 612 ARG 0.002 0.000 ARG F 6 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 785) hydrogen bonds : angle 3.63314 ( 2309) SS BOND : bond 0.00319 ( 8) SS BOND : angle 2.84312 ( 16) covalent geometry : bond 0.00292 (10222) covalent geometry : angle 0.47867 (13785) *********************** 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 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.174 Fit side-chains REVERT: A 542 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.6171 (p90) REVERT: A 581 MET cc_start: 0.9327 (mmt) cc_final: 0.8813 (mmt) REVERT: B 590 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8239 (mtt180) REVERT: B 615 ASN cc_start: 0.7699 (m-40) cc_final: 0.7409 (t0) REVERT: B 807 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7055 (tp) REVERT: C 581 MET cc_start: 0.9266 (mmt) cc_final: 0.8762 (mmt) REVERT: C 804 LEU cc_start: 0.8663 (tp) cc_final: 0.8378 (tt) REVERT: D 566 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: D 781 SER cc_start: 0.8161 (p) cc_final: 0.7850 (t) REVERT: E 58 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7232 (tpt) REVERT: E 65 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6977 (mtm-85) REVERT: E 78 LYS cc_start: 0.7469 (tttt) cc_final: 0.7150 (ttpp) REVERT: E 184 PHE cc_start: 0.8008 (m-80) cc_final: 0.7773 (m-10) REVERT: E 202 GLU cc_start: 0.7581 (pt0) cc_final: 0.7127 (mt-10) REVERT: F 99 ARG cc_start: 0.7759 (mmp80) cc_final: 0.6989 (mtt90) REVERT: F 127 PHE cc_start: 0.6328 (m-80) cc_final: 0.6064 (m-80) REVERT: G 37 ARG cc_start: 0.7803 (ptp-110) cc_final: 0.7468 (mtp-110) REVERT: H 24 MET cc_start: 0.8961 (tpt) cc_final: 0.8446 (tpt) REVERT: H 37 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6653 (mtp85) REVERT: H 58 MET cc_start: 0.6551 (tpt) cc_final: 0.6128 (tmm) REVERT: H 99 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7331 (mmm-85) REVERT: H 132 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5652 (OUTLIER) REVERT: H 208 ARG cc_start: 0.4970 (OUTLIER) cc_final: 0.4239 (ptm160) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 1.4124 time to fit residues: 192.7377 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain G residue 8 ILE 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 Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN F 204 HIS G 204 HIS H 132 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107004 restraints weight = 44753.817| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.83 r_work: 0.2517 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2867 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= 0.120 Angle : 0.458 10.591 13801 Z= 0.245 Chirality : 0.036 0.193 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.837 111.926 1587 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.27 % Allowed : 12.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.24), residues: 1219 helix: 3.35 (0.16), residues: 903 sheet: 1.49 (1.47), residues: 20 loop : -0.83 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 177 HIS 0.005 0.001 HIS H 132 PHE 0.014 0.001 PHE C 570 TYR 0.009 0.001 TYR C 612 ARG 0.003 0.000 ARG F 6 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 785) hydrogen bonds : angle 3.48936 ( 2309) SS BOND : bond 0.00265 ( 8) SS BOND : angle 2.57509 ( 16) covalent geometry : bond 0.00254 (10222) covalent geometry : angle 0.44935 (13785) *********************** 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 143 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.998 Fit side-chains REVERT: A 581 MET cc_start: 0.9303 (mmt) cc_final: 0.8813 (mmt) REVERT: A 590 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8328 (mtp85) REVERT: B 507 LYS cc_start: 0.6700 (ptmt) cc_final: 0.6366 (mptt) REVERT: B 590 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8261 (mtt180) REVERT: B 615 ASN cc_start: 0.7823 (m-40) cc_final: 0.7499 (t0) REVERT: B 807 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7040 (tp) REVERT: C 581 MET cc_start: 0.9258 (mmt) cc_final: 0.8770 (mmt) REVERT: C 804 LEU cc_start: 0.8628 (tp) cc_final: 0.8337 (tt) REVERT: C 807 LEU cc_start: 0.7995 (tp) cc_final: 0.7791 (tm) REVERT: D 566 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: D 781 SER cc_start: 0.8184 (p) cc_final: 0.7863 (t) REVERT: E 58 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7237 (tpt) REVERT: E 78 LYS cc_start: 0.7474 (tttt) cc_final: 0.7255 (ttpp) REVERT: E 184 PHE cc_start: 0.8011 (m-80) cc_final: 0.7788 (m-10) REVERT: E 202 GLU cc_start: 0.7563 (pt0) cc_final: 0.7130 (mt-10) REVERT: F 99 ARG cc_start: 0.7772 (mmp80) cc_final: 0.7034 (mtt90) REVERT: F 127 PHE cc_start: 0.6250 (m-80) cc_final: 0.6023 (m-80) REVERT: G 37 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7368 (mtp85) REVERT: G 65 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.7277 (ptp90) REVERT: H 24 MET cc_start: 0.8977 (tpt) cc_final: 0.8484 (tpt) REVERT: H 37 ARG cc_start: 0.7025 (mtt-85) cc_final: 0.6787 (mtp85) REVERT: H 58 MET cc_start: 0.6572 (tpt) cc_final: 0.6133 (tmm) REVERT: H 99 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.7383 (mmm-85) REVERT: H 132 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.5930 (p-80) REVERT: H 208 ARG cc_start: 0.5079 (OUTLIER) cc_final: 0.4265 (ptm160) outliers start: 29 outliers final: 14 residues processed: 134 average time/residue: 1.2910 time to fit residues: 185.2392 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 58 MET 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 132 HIS Chi-restraints excluded: chain H residue 172 SER 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 77 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 582 GLN E 160 ASN F 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105532 restraints weight = 53510.104| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.90 r_work: 0.2432 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10230 Z= 0.179 Angle : 0.533 10.646 13801 Z= 0.286 Chirality : 0.039 0.177 1555 Planarity : 0.003 0.032 1663 Dihedral : 11.313 107.460 1585 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.17 % Allowed : 12.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.24), residues: 1219 helix: 3.06 (0.16), residues: 902 sheet: 1.38 (1.41), residues: 20 loop : -0.86 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 64 HIS 0.004 0.001 HIS E 204 PHE 0.017 0.002 PHE C 570 TYR 0.015 0.002 TYR C 612 ARG 0.006 0.001 ARG H 131 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 785) hydrogen bonds : angle 3.75387 ( 2309) SS BOND : bond 0.00383 ( 8) SS BOND : angle 2.65878 ( 16) covalent geometry : bond 0.00408 (10222) covalent geometry : angle 0.52582 (13785) *********************** 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 139 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.958 Fit side-chains REVERT: A 581 MET cc_start: 0.9360 (mmt) cc_final: 0.8858 (mmt) REVERT: A 590 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8336 (mtp85) REVERT: B 615 ASN cc_start: 0.7873 (m-40) cc_final: 0.7524 (t0) REVERT: B 807 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7100 (tp) REVERT: C 581 MET cc_start: 0.9305 (mmt) cc_final: 0.8807 (mmt) REVERT: C 804 LEU cc_start: 0.8676 (tp) cc_final: 0.8388 (tt) REVERT: D 566 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: E 58 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7275 (tpt) REVERT: E 65 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6991 (mtm-85) REVERT: E 184 PHE cc_start: 0.8092 (m-80) cc_final: 0.7831 (m-10) REVERT: E 202 GLU cc_start: 0.7574 (pt0) cc_final: 0.7129 (mt-10) REVERT: F 99 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7066 (mtt90) REVERT: G 37 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7480 (mtp-110) REVERT: H 37 ARG cc_start: 0.7071 (mtt-85) cc_final: 0.6828 (mtp85) REVERT: H 58 MET cc_start: 0.6598 (tpt) cc_final: 0.6153 (tmm) REVERT: H 99 ARG cc_start: 0.7923 (mmt-90) cc_final: 0.7352 (mmm-85) REVERT: H 208 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4459 (ppt-90) outliers start: 28 outliers final: 16 residues processed: 128 average time/residue: 1.3643 time to fit residues: 186.4901 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 : 1.050 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 0.0870 chunk 101 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN F 204 HIS H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107954 restraints weight = 53949.590| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.93 r_work: 0.2472 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10230 Z= 0.126 Angle : 0.468 10.352 13801 Z= 0.250 Chirality : 0.036 0.160 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.674 105.388 1585 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.27 % Allowed : 12.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.24), residues: 1219 helix: 3.28 (0.16), residues: 903 sheet: 1.33 (1.45), residues: 20 loop : -0.82 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 177 HIS 0.004 0.001 HIS H 204 PHE 0.013 0.001 PHE C 570 TYR 0.010 0.001 TYR C 612 ARG 0.004 0.000 ARG D 624 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 785) hydrogen bonds : angle 3.54147 ( 2309) SS BOND : bond 0.00273 ( 8) SS BOND : angle 2.52354 ( 16) covalent geometry : bond 0.00270 (10222) covalent geometry : angle 0.46059 (13785) *********************** 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 137 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.064 Fit side-chains REVERT: A 581 MET cc_start: 0.9298 (mmt) cc_final: 0.8808 (mmt) REVERT: A 590 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8328 (mtp85) REVERT: B 615 ASN cc_start: 0.7823 (m-40) cc_final: 0.7491 (t0) REVERT: B 807 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7047 (tp) REVERT: C 581 MET cc_start: 0.9275 (mmt) cc_final: 0.8764 (mmt) REVERT: C 804 LEU cc_start: 0.8633 (tp) cc_final: 0.8344 (tt) REVERT: D 566 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: D 625 MET cc_start: 0.7526 (tpp) cc_final: 0.7164 (mmt) REVERT: E 10 MET cc_start: 0.7851 (tpt) cc_final: 0.7545 (tpp) REVERT: E 58 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7274 (tpt) REVERT: E 184 PHE cc_start: 0.8032 (m-80) cc_final: 0.7770 (m-10) REVERT: E 202 GLU cc_start: 0.7553 (pt0) cc_final: 0.7131 (mt-10) REVERT: F 99 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7023 (mtt90) REVERT: G 37 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7283 (mtp85) REVERT: H 37 ARG cc_start: 0.7049 (mtt-85) cc_final: 0.6801 (mtp85) REVERT: H 58 MET cc_start: 0.6555 (tpt) cc_final: 0.6150 (mmm) REVERT: H 99 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7343 (mmm-85) REVERT: H 132 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.5945 (p-80) REVERT: H 208 ARG cc_start: 0.5200 (OUTLIER) cc_final: 0.4405 (ppt-90) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 1.3721 time to fit residues: 184.9223 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 519 TYR 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 58 MET 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 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 132 HIS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 204 HIS 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 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN F 204 HIS H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108968 restraints weight = 56436.387| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 6.05 r_work: 0.2486 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 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 = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10230 Z= 0.120 Angle : 0.461 10.129 13801 Z= 0.246 Chirality : 0.036 0.146 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.262 99.064 1583 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.24), residues: 1219 helix: 3.37 (0.16), residues: 903 sheet: 1.25 (1.46), residues: 20 loop : -0.82 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 177 HIS 0.003 0.001 HIS E 204 PHE 0.012 0.001 PHE C 570 TYR 0.010 0.001 TYR C 519 ARG 0.004 0.000 ARG H 131 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 785) hydrogen bonds : angle 3.49483 ( 2309) SS BOND : bond 0.00278 ( 8) SS BOND : angle 2.43845 ( 16) covalent geometry : bond 0.00252 (10222) covalent geometry : angle 0.45376 (13785) *********************** 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 134 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.001 Fit side-chains REVERT: A 581 MET cc_start: 0.9294 (mmt) cc_final: 0.8792 (mmt) REVERT: A 590 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8344 (mtp85) REVERT: B 590 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (mtm-85) REVERT: B 615 ASN cc_start: 0.7849 (m-40) cc_final: 0.7504 (t0) REVERT: B 807 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7033 (tp) REVERT: C 581 MET cc_start: 0.9276 (mmt) cc_final: 0.8837 (mmt) REVERT: C 804 LEU cc_start: 0.8632 (tp) cc_final: 0.8347 (tt) REVERT: C 807 LEU cc_start: 0.8021 (tp) cc_final: 0.7809 (tm) REVERT: D 566 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: D 625 MET cc_start: 0.7521 (tpp) cc_final: 0.7147 (mmt) REVERT: E 10 MET cc_start: 0.7800 (tpt) cc_final: 0.7570 (tpp) REVERT: E 58 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7257 (tpt) REVERT: E 184 PHE cc_start: 0.8023 (m-80) cc_final: 0.7770 (m-10) REVERT: E 202 GLU cc_start: 0.7541 (pt0) cc_final: 0.7124 (mt-10) REVERT: F 99 ARG cc_start: 0.7782 (mmp80) cc_final: 0.7034 (mtt90) REVERT: F 126 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6425 (tp30) REVERT: G 37 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7313 (mtp85) REVERT: H 37 ARG cc_start: 0.7044 (mtt-85) cc_final: 0.6793 (mtp85) REVERT: H 58 MET cc_start: 0.6440 (tpt) cc_final: 0.6139 (mmm) REVERT: H 65 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7744 (mpp-170) REVERT: H 99 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7376 (mmm-85) REVERT: H 208 ARG cc_start: 0.5134 (OUTLIER) cc_final: 0.4388 (ppt-90) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 1.3647 time to fit residues: 179.1569 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 590 ARG 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 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 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 132 HIS 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 82 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108248 restraints weight = 60390.145| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 6.13 r_work: 0.2466 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 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 = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10230 Z= 0.127 Angle : 0.472 9.919 13801 Z= 0.250 Chirality : 0.036 0.140 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.126 91.704 1583 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.88 % Allowed : 13.59 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.24), residues: 1219 helix: 3.34 (0.16), residues: 903 sheet: 1.25 (1.45), residues: 20 loop : -0.84 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 574 HIS 0.009 0.001 HIS H 132 PHE 0.013 0.001 PHE C 570 TYR 0.010 0.001 TYR C 612 ARG 0.003 0.000 ARG D 624 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 785) hydrogen bonds : angle 3.51754 ( 2309) SS BOND : bond 0.00261 ( 8) SS BOND : angle 2.47042 ( 16) covalent geometry : bond 0.00272 (10222) covalent geometry : angle 0.46443 (13785) *********************** 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 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.115 Fit side-chains REVERT: A 581 MET cc_start: 0.9300 (mmt) cc_final: 0.8803 (mmt) REVERT: A 590 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8326 (mtp85) REVERT: B 590 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8276 (mtm-85) REVERT: B 615 ASN cc_start: 0.7810 (m-40) cc_final: 0.7448 (t0) REVERT: B 807 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7003 (tp) REVERT: C 581 MET cc_start: 0.9275 (mmt) cc_final: 0.8831 (mmt) REVERT: C 804 LEU cc_start: 0.8598 (tp) cc_final: 0.8313 (tt) REVERT: D 566 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: D 625 MET cc_start: 0.7460 (tpp) cc_final: 0.7091 (mmt) REVERT: E 10 MET cc_start: 0.7759 (tpt) cc_final: 0.7528 (tpp) REVERT: E 58 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7229 (tpt) REVERT: E 65 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6776 (mtm-85) REVERT: E 184 PHE cc_start: 0.8000 (m-80) cc_final: 0.7735 (m-10) REVERT: E 202 GLU cc_start: 0.7509 (pt0) cc_final: 0.7095 (mt-10) REVERT: F 99 ARG cc_start: 0.7709 (mmp80) cc_final: 0.6942 (mtt90) REVERT: F 126 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6479 (tp30) REVERT: G 37 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7289 (mtp85) REVERT: H 37 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6762 (mtp85) REVERT: H 58 MET cc_start: 0.6429 (tpt) cc_final: 0.6115 (mmm) REVERT: H 65 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7734 (mpp-170) REVERT: H 99 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7320 (mmm-85) REVERT: H 208 ARG cc_start: 0.5125 (OUTLIER) cc_final: 0.4368 (ppt-90) outliers start: 25 outliers final: 15 residues processed: 123 average time/residue: 1.3860 time to fit residues: 181.9282 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 590 ARG 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 58 MET 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 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 204 HIS 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 64 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN G 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 = 0.3596 r_free = 0.3596 target = 0.142581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108756 restraints weight = 45038.628| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.51 r_work: 0.2489 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10230 Z= 0.118 Angle : 0.461 9.780 13801 Z= 0.245 Chirality : 0.036 0.133 1555 Planarity : 0.003 0.030 1663 Dihedral : 9.915 87.225 1583 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.98 % Allowed : 13.69 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.24), residues: 1219 helix: 3.40 (0.16), residues: 903 sheet: 1.26 (1.45), residues: 20 loop : -0.85 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 177 HIS 0.003 0.001 HIS E 204 PHE 0.012 0.001 PHE C 570 TYR 0.012 0.001 TYR E 173 ARG 0.003 0.000 ARG D 624 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 785) hydrogen bonds : angle 3.48391 ( 2309) SS BOND : bond 0.00239 ( 8) SS BOND : angle 2.49234 ( 16) covalent geometry : bond 0.00247 (10222) covalent geometry : angle 0.45317 (13785) ********************** 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 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.094 Fit side-chains REVERT: A 581 MET cc_start: 0.9280 (mmt) cc_final: 0.8792 (mmt) REVERT: A 590 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8306 (mtp85) REVERT: B 590 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8249 (mtm-85) REVERT: B 615 ASN cc_start: 0.7802 (m-40) cc_final: 0.7450 (t0) REVERT: B 807 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6990 (tp) REVERT: C 581 MET cc_start: 0.9268 (mmt) cc_final: 0.8825 (mmt) REVERT: C 804 LEU cc_start: 0.8596 (tp) cc_final: 0.8307 (tt) REVERT: C 807 LEU cc_start: 0.8003 (tp) cc_final: 0.7786 (tm) REVERT: D 566 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: D 625 MET cc_start: 0.7460 (tpp) cc_final: 0.7091 (mmt) REVERT: E 10 MET cc_start: 0.7763 (tpt) cc_final: 0.7532 (tpp) REVERT: E 58 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7217 (tpt) REVERT: E 184 PHE cc_start: 0.7985 (m-80) cc_final: 0.7724 (m-10) REVERT: E 202 GLU cc_start: 0.7505 (pt0) cc_final: 0.7081 (mt-10) REVERT: F 99 ARG cc_start: 0.7700 (mmp80) cc_final: 0.6940 (mtt90) REVERT: F 126 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6476 (tp30) REVERT: G 37 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7300 (mtp85) REVERT: H 37 ARG cc_start: 0.7027 (mtt-85) cc_final: 0.6753 (mtp85) REVERT: H 58 MET cc_start: 0.6417 (tpt) cc_final: 0.6105 (mmm) REVERT: H 65 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7723 (mpp-170) REVERT: H 99 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.7319 (mmm-85) REVERT: H 208 ARG cc_start: 0.5186 (OUTLIER) cc_final: 0.4450 (ppt-90) outliers start: 26 outliers final: 14 residues processed: 124 average time/residue: 1.3314 time to fit residues: 176.5288 Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 590 ARG 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 160 ASN 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 = 0.3590 r_free = 0.3590 target = 0.142055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108239 restraints weight = 59771.233| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 6.08 r_work: 0.2482 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 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 = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10230 Z= 0.124 Angle : 0.469 9.448 13801 Z= 0.249 Chirality : 0.036 0.132 1555 Planarity : 0.003 0.030 1663 Dihedral : 9.754 85.480 1583 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.24), residues: 1219 helix: 3.36 (0.16), residues: 903 sheet: 1.22 (1.45), residues: 20 loop : -0.84 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 574 HIS 0.005 0.001 HIS H 132 PHE 0.012 0.001 PHE C 570 TYR 0.013 0.001 TYR E 173 ARG 0.003 0.000 ARG D 624 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 785) hydrogen bonds : angle 3.51774 ( 2309) SS BOND : bond 0.00252 ( 8) SS BOND : angle 2.39912 ( 16) covalent geometry : bond 0.00263 (10222) covalent geometry : angle 0.46163 (13785) =============================================================================== Job complete usr+sys time: 7239.98 seconds wall clock time: 125 minutes 16.72 seconds (7516.72 seconds total)