Starting phenix.real_space_refine on Sun Dec 29 12:45:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c2h_16390/12_2024/8c2h_16390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2h_16390/12_2024/8c2h_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_16390/12_2024/8c2h_16390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2h_16390/12_2024/8c2h_16390.map" model { file = "/net/cci-nas-00/data/ceres_data/8c2h_16390/12_2024/8c2h_16390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2h_16390/12_2024/8c2h_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.22, per 1000 atoms: 1.01 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: 2.86 Conformation dependent library (CDL) restraints added in 2.2 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: 3.09 Time building geometry restraints manager: 3.15 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: 2.680 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.050 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.630 ------------------------------------------------------------------------------- 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 10222 Z= 0.583 Angle : 1.447 10.807 13785 Z= 0.993 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 *********************** 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 : 1.060 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: 1.2287 time to fit residues: 226.1861 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 : 1.097 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 10222 Z= 0.186 Angle : 0.507 10.021 13785 Z= 0.282 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 *********************** 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 : 1.157 Fit side-chains REVERT: A 542 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5901 (p90) REVERT: B 507 LYS cc_start: 0.6466 (ptpt) cc_final: 0.6223 (ptmm) REVERT: B 566 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6269 (pm20) REVERT: B 590 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7952 (mtt180) REVERT: B 615 ASN cc_start: 0.7341 (m-40) cc_final: 0.6883 (t0) REVERT: B 807 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6560 (tp) REVERT: C 566 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 581 MET cc_start: 0.8996 (mmt) cc_final: 0.8384 (mmt) REVERT: C 590 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8303 (mpp80) REVERT: C 804 LEU cc_start: 0.8025 (tp) cc_final: 0.7805 (tt) REVERT: D 566 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: D 615 ASN cc_start: 0.7517 (m-40) cc_final: 0.7305 (m-40) REVERT: D 623 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7180 (mm-30) REVERT: E 41 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.4878 (ttm-80) REVERT: E 78 LYS cc_start: 0.6967 (tttt) cc_final: 0.6633 (ttpp) REVERT: E 184 PHE cc_start: 0.7507 (m-80) cc_final: 0.7281 (m-10) REVERT: E 202 GLU cc_start: 0.7114 (pt0) cc_final: 0.6904 (mt-10) REVERT: F 99 ARG cc_start: 0.7384 (mmp80) cc_final: 0.6684 (mtt90) REVERT: F 205 GLN cc_start: 0.6055 (mt0) cc_final: 0.5799 (mm-40) REVERT: F 207 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.3934 (tp) REVERT: G 31 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: G 37 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7347 (mtp85) REVERT: H 24 MET cc_start: 0.8513 (tpt) cc_final: 0.7833 (tpt) REVERT: H 37 ARG cc_start: 0.6722 (mtt-85) cc_final: 0.6493 (mtp85) REVERT: H 58 MET cc_start: 0.6510 (tpt) cc_final: 0.5944 (tmm) REVERT: H 99 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.6908 (mmm-85) REVERT: H 172 SER cc_start: 0.6831 (t) cc_final: 0.6577 (p) REVERT: H 208 ARG cc_start: 0.4348 (OUTLIER) cc_final: 0.3793 (ptm160) outliers start: 27 outliers final: 8 residues processed: 151 average time/residue: 1.3373 time to fit residues: 216.4784 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 : 1.054 ------------------------------------------------------------------------------- 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 41 ARG 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 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN E 149 ASN E 160 ASN F 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10222 Z= 0.166 Angle : 0.464 9.410 13785 Z= 0.251 Chirality : 0.036 0.207 1555 Planarity : 0.003 0.030 1663 Dihedral : 12.417 129.715 1591 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.27 % Allowed : 11.01 % 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: 3.46 (0.24), residues: 1219 helix: 3.32 (0.16), residues: 904 sheet: 0.77 (1.01), residues: 40 loop : -1.31 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 177 HIS 0.003 0.001 HIS F 82 PHE 0.016 0.001 PHE C 570 TYR 0.008 0.001 TYR C 519 ARG 0.002 0.000 ARG F 6 *********************** 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 149 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.187 Fit side-chains REVERT: A 542 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6026 (p90) REVERT: A 581 MET cc_start: 0.9080 (mmt) cc_final: 0.8484 (mmt) REVERT: B 507 LYS cc_start: 0.6427 (ptpt) cc_final: 0.6180 (ptmm) REVERT: B 590 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7962 (mtt180) REVERT: B 615 ASN cc_start: 0.7342 (m-40) cc_final: 0.6878 (t0) REVERT: B 807 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6600 (tp) REVERT: C 581 MET cc_start: 0.8981 (mmt) cc_final: 0.8421 (mmt) REVERT: C 590 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8287 (mpp80) REVERT: C 804 LEU cc_start: 0.7989 (tp) cc_final: 0.7750 (tt) REVERT: D 566 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: D 625 MET cc_start: 0.7163 (tpp) cc_final: 0.6952 (mmt) REVERT: D 807 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6526 (tp) REVERT: E 41 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.4997 (ttm-80) REVERT: E 76 VAL cc_start: 0.7132 (t) cc_final: 0.6920 (p) REVERT: E 78 LYS cc_start: 0.6988 (tttt) cc_final: 0.6666 (ttpp) REVERT: E 184 PHE cc_start: 0.7503 (m-80) cc_final: 0.7265 (m-10) REVERT: E 202 GLU cc_start: 0.7080 (pt0) cc_final: 0.6843 (mt-10) REVERT: F 99 ARG cc_start: 0.7402 (mmp80) cc_final: 0.6652 (mtt90) REVERT: F 127 PHE cc_start: 0.5473 (m-10) cc_final: 0.5241 (m-10) REVERT: G 37 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7309 (mtp85) REVERT: H 24 MET cc_start: 0.8488 (tpt) cc_final: 0.7734 (tpt) REVERT: H 37 ARG cc_start: 0.6792 (mtt-85) cc_final: 0.6447 (mtp85) REVERT: H 58 MET cc_start: 0.6509 (tpt) cc_final: 0.6010 (tmm) REVERT: H 67 CYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6706 (m) REVERT: H 99 ARG cc_start: 0.7494 (mmt-90) cc_final: 0.6832 (mmm-85) REVERT: H 208 ARG cc_start: 0.4303 (OUTLIER) cc_final: 0.3821 (ptm160) outliers start: 29 outliers final: 13 residues processed: 143 average time/residue: 1.4506 time to fit residues: 221.2519 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 41 ARG 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 67 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10222 Z= 0.196 Angle : 0.482 9.104 13785 Z= 0.260 Chirality : 0.037 0.209 1555 Planarity : 0.003 0.031 1663 Dihedral : 11.851 118.171 1591 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.27 % Allowed : 12.40 % Favored : 84.33 % 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: 3.40 (0.24), residues: 1219 helix: 3.21 (0.16), residues: 904 sheet: 1.38 (1.45), residues: 20 loop : -0.98 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 64 HIS 0.004 0.001 HIS H 132 PHE 0.017 0.002 PHE C 570 TYR 0.014 0.001 TYR H 200 ARG 0.004 0.000 ARG E 37 *********************** 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 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.105 Fit side-chains REVERT: A 542 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6176 (p90) REVERT: A 581 MET cc_start: 0.9116 (mmt) cc_final: 0.8538 (mmt) REVERT: A 582 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: B 590 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7947 (mtt180) REVERT: B 615 ASN cc_start: 0.7409 (m-40) cc_final: 0.6911 (t0) REVERT: B 807 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6610 (tp) REVERT: C 581 MET cc_start: 0.8971 (mmt) cc_final: 0.8448 (mmt) REVERT: C 590 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8307 (mpp80) REVERT: C 804 LEU cc_start: 0.8018 (tp) cc_final: 0.7789 (tt) REVERT: D 566 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: D 781 SER cc_start: 0.7954 (p) cc_final: 0.7674 (t) REVERT: E 41 ARG cc_start: 0.5363 (OUTLIER) cc_final: 0.4965 (ttm-80) REVERT: E 65 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6693 (mtm-85) REVERT: E 76 VAL cc_start: 0.7027 (t) cc_final: 0.6820 (p) REVERT: E 78 LYS cc_start: 0.6978 (tttt) cc_final: 0.6656 (ttpp) REVERT: E 184 PHE cc_start: 0.7509 (m-80) cc_final: 0.7268 (m-10) REVERT: E 202 GLU cc_start: 0.7092 (pt0) cc_final: 0.6866 (mt-10) REVERT: F 99 ARG cc_start: 0.7401 (mmp80) cc_final: 0.6653 (mtt90) REVERT: G 37 ARG cc_start: 0.7605 (ptp-110) cc_final: 0.7252 (mtp85) REVERT: G 65 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6924 (ptp90) REVERT: H 24 MET cc_start: 0.8452 (tpt) cc_final: 0.7760 (tpt) REVERT: H 37 ARG cc_start: 0.6756 (mtt-85) cc_final: 0.6553 (mtp85) REVERT: H 58 MET cc_start: 0.6451 (tpt) cc_final: 0.6053 (tmm) REVERT: H 99 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.6848 (mmm-85) REVERT: H 132 HIS cc_start: 0.5406 (OUTLIER) cc_final: 0.5120 (p90) REVERT: H 204 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.5817 (t-90) outliers start: 29 outliers final: 12 residues processed: 130 average time/residue: 1.4744 time to fit residues: 204.7421 Evaluate side-chains 130 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 41 ARG 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 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10222 Z= 0.218 Angle : 0.495 10.288 13785 Z= 0.265 Chirality : 0.038 0.209 1555 Planarity : 0.003 0.031 1663 Dihedral : 11.571 114.911 1591 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.37 % Allowed : 12.20 % Favored : 84.42 % 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 (0.23), residues: 1219 helix: 3.14 (0.16), residues: 903 sheet: 1.36 (1.43), residues: 20 loop : -0.83 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 574 HIS 0.009 0.001 HIS H 204 PHE 0.016 0.002 PHE C 570 TYR 0.013 0.001 TYR C 612 ARG 0.003 0.000 ARG E 37 *********************** 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 145 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.331 Fit side-chains REVERT: A 542 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6300 (p90) REVERT: A 581 MET cc_start: 0.9122 (mmt) cc_final: 0.8543 (mmt) REVERT: B 590 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.8006 (mtt180) REVERT: B 615 ASN cc_start: 0.7422 (m-40) cc_final: 0.6898 (t0) REVERT: B 807 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6559 (tp) REVERT: C 581 MET cc_start: 0.8980 (mmt) cc_final: 0.8435 (mmt) REVERT: C 590 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8315 (mpp80) REVERT: C 804 LEU cc_start: 0.8032 (tp) cc_final: 0.7803 (tt) REVERT: D 566 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: D 781 SER cc_start: 0.7953 (p) cc_final: 0.7645 (t) REVERT: E 41 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.5029 (ttm-80) REVERT: E 65 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6656 (mtm-85) REVERT: E 76 VAL cc_start: 0.6992 (t) cc_final: 0.6747 (p) REVERT: E 78 LYS cc_start: 0.6910 (tttt) cc_final: 0.6654 (ttpp) REVERT: E 184 PHE cc_start: 0.7510 (m-80) cc_final: 0.7264 (m-10) REVERT: F 99 ARG cc_start: 0.7412 (mmp80) cc_final: 0.6684 (mtt90) REVERT: G 37 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7278 (mtp85) REVERT: H 24 MET cc_start: 0.8433 (tpt) cc_final: 0.7777 (tpt) REVERT: H 37 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6647 (mtp85) REVERT: H 58 MET cc_start: 0.6422 (tpt) cc_final: 0.6029 (tmm) REVERT: H 99 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.6876 (mmm-85) REVERT: H 204 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.5932 (t-90) REVERT: H 208 ARG cc_start: 0.4242 (OUTLIER) cc_final: 0.3642 (ptm160) outliers start: 30 outliers final: 15 residues processed: 137 average time/residue: 1.5199 time to fit residues: 222.6986 Evaluate side-chains 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 41 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 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 105 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10222 Z= 0.169 Angle : 0.457 11.060 13785 Z= 0.243 Chirality : 0.036 0.195 1555 Planarity : 0.003 0.031 1663 Dihedral : 10.970 109.746 1591 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.27 % Allowed : 12.90 % 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: 3.63 (0.24), residues: 1219 helix: 3.35 (0.16), residues: 903 sheet: 1.34 (1.46), residues: 20 loop : -0.75 (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 0.013 0.001 PHE C 570 TYR 0.009 0.001 TYR C 612 ARG 0.003 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 3.807 Fit side-chains REVERT: A 542 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.6217 (p90) REVERT: A 581 MET cc_start: 0.9097 (mmt) cc_final: 0.8534 (mmt) REVERT: A 582 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: A 590 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: B 590 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8044 (mtt180) REVERT: B 615 ASN cc_start: 0.7455 (m-40) cc_final: 0.6966 (t0) REVERT: B 807 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6581 (tp) REVERT: C 581 MET cc_start: 0.8972 (mmt) cc_final: 0.8454 (mmt) REVERT: C 590 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8322 (mpp80) REVERT: C 804 LEU cc_start: 0.7990 (tp) cc_final: 0.7757 (tt) REVERT: D 566 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: D 781 SER cc_start: 0.7977 (p) cc_final: 0.7647 (t) REVERT: E 41 ARG cc_start: 0.5462 (OUTLIER) cc_final: 0.4938 (ttm-80) REVERT: E 76 VAL cc_start: 0.6948 (t) cc_final: 0.6714 (p) REVERT: E 78 LYS cc_start: 0.6965 (tttt) cc_final: 0.6677 (ttpp) REVERT: E 120 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6507 (mp) REVERT: E 184 PHE cc_start: 0.7514 (m-80) cc_final: 0.7283 (m-10) REVERT: F 99 ARG cc_start: 0.7402 (mmp80) cc_final: 0.6681 (mtt90) REVERT: G 37 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7291 (mtp85) REVERT: H 24 MET cc_start: 0.8425 (tpt) cc_final: 0.7786 (tpt) REVERT: H 37 ARG cc_start: 0.6858 (mtt-85) cc_final: 0.6631 (mtp85) REVERT: H 58 MET cc_start: 0.6420 (tpt) cc_final: 0.6054 (mmm) REVERT: H 99 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.6872 (mmm-85) REVERT: H 208 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3653 (ptm160) outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 1.5438 time to fit residues: 214.4076 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 : 1.111 ------------------------------------------------------------------------------- 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 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 41 ARG Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 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 13 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10222 Z= 0.170 Angle : 0.458 10.541 13785 Z= 0.244 Chirality : 0.036 0.163 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.708 104.550 1591 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.27 % Allowed : 12.80 % Favored : 83.93 % 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: 3.35 (0.16), residues: 904 sheet: 1.19 (1.46), residues: 20 loop : -0.70 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 574 HIS 0.008 0.001 HIS F 204 PHE 0.013 0.001 PHE C 570 TYR 0.010 0.001 TYR C 612 ARG 0.002 0.000 ARG E 37 *********************** 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 : 1.036 Fit side-chains REVERT: A 542 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.6166 (p90) REVERT: A 581 MET cc_start: 0.9095 (mmt) cc_final: 0.8518 (mmt) REVERT: A 582 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: A 590 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8280 (mtp85) REVERT: B 590 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8023 (mtt180) REVERT: B 615 ASN cc_start: 0.7472 (m-40) cc_final: 0.6987 (t0) REVERT: B 807 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6580 (tp) REVERT: C 581 MET cc_start: 0.8976 (mmt) cc_final: 0.8502 (mmt) REVERT: C 590 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8337 (mpp80) REVERT: C 804 LEU cc_start: 0.8001 (tp) cc_final: 0.7766 (tt) REVERT: D 566 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: D 781 SER cc_start: 0.7990 (p) cc_final: 0.7642 (t) REVERT: E 41 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.4974 (ttm-80) REVERT: E 76 VAL cc_start: 0.6907 (t) cc_final: 0.6682 (p) REVERT: E 78 LYS cc_start: 0.6935 (tttt) cc_final: 0.6637 (ttpp) REVERT: E 184 PHE cc_start: 0.7519 (m-80) cc_final: 0.7282 (m-10) REVERT: F 99 ARG cc_start: 0.7398 (mmp80) cc_final: 0.6687 (mtt90) REVERT: G 37 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7301 (mtp85) REVERT: H 24 MET cc_start: 0.8421 (tpt) cc_final: 0.7784 (tpt) REVERT: H 37 ARG cc_start: 0.6841 (mtt-85) cc_final: 0.6606 (mtp85) REVERT: H 58 MET cc_start: 0.6438 (tpt) cc_final: 0.6063 (mmm) REVERT: H 99 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.6878 (mmm-85) REVERT: H 208 ARG cc_start: 0.4272 (OUTLIER) cc_final: 0.3719 (ptm160) outliers start: 29 outliers final: 17 residues processed: 126 average time/residue: 1.4866 time to fit residues: 199.4952 Evaluate side-chains 133 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 41 ARG Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 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 35 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 0.0030 chunk 101 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10222 Z= 0.195 Angle : 0.478 10.093 13785 Z= 0.255 Chirality : 0.037 0.148 1555 Planarity : 0.003 0.030 1663 Dihedral : 10.554 94.587 1591 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.08 % Allowed : 13.00 % Favored : 83.93 % 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: 3.56 (0.24), residues: 1219 helix: 3.29 (0.16), residues: 903 sheet: 1.21 (1.44), residues: 20 loop : -0.76 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.004 0.001 HIS E 204 PHE 0.014 0.001 PHE C 570 TYR 0.012 0.001 TYR C 612 ARG 0.003 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.088 Fit side-chains REVERT: A 581 MET cc_start: 0.9105 (mmt) cc_final: 0.8580 (mmt) REVERT: A 582 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: A 590 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8283 (mtp85) REVERT: B 615 ASN cc_start: 0.7517 (m-40) cc_final: 0.6961 (t0) REVERT: B 807 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6604 (tp) REVERT: C 581 MET cc_start: 0.8986 (mmt) cc_final: 0.8492 (mmt) REVERT: C 590 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8339 (mpp80) REVERT: C 804 LEU cc_start: 0.8006 (tp) cc_final: 0.7773 (tt) REVERT: D 566 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: D 803 MET cc_start: 0.8588 (mtp) cc_final: 0.8325 (mtp) REVERT: E 65 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6675 (mtm-85) REVERT: E 76 VAL cc_start: 0.6838 (t) cc_final: 0.6634 (p) REVERT: E 184 PHE cc_start: 0.7503 (m-80) cc_final: 0.7253 (m-10) REVERT: F 99 ARG cc_start: 0.7409 (mmp80) cc_final: 0.6703 (mtt90) REVERT: G 37 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7321 (mtp85) REVERT: G 120 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6311 (mp) REVERT: H 37 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6620 (mtp85) REVERT: H 58 MET cc_start: 0.6375 (tpt) cc_final: 0.6038 (tmm) REVERT: H 99 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.6931 (mmm-85) REVERT: H 208 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.3821 (ppt-90) outliers start: 27 outliers final: 13 residues processed: 130 average time/residue: 1.4246 time to fit residues: 197.6919 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 204 HIS 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 111 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10222 Z= 0.176 Angle : 0.463 9.437 13785 Z= 0.245 Chirality : 0.036 0.132 1555 Planarity : 0.003 0.030 1663 Dihedral : 9.833 88.457 1583 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.08 % Allowed : 13.00 % Favored : 83.93 % 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: 3.37 (0.16), residues: 903 sheet: 1.22 (1.43), residues: 20 loop : -0.76 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 574 HIS 0.004 0.001 HIS E 204 PHE 0.013 0.001 PHE C 570 TYR 0.011 0.001 TYR C 612 ARG 0.003 0.000 ARG D 624 *********************** 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 137 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.177 Fit side-chains REVERT: A 581 MET cc_start: 0.9089 (mmt) cc_final: 0.8563 (mmt) REVERT: A 582 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: A 590 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8272 (mtp85) REVERT: B 615 ASN cc_start: 0.7464 (m-40) cc_final: 0.6955 (t0) REVERT: B 807 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6578 (tp) REVERT: C 581 MET cc_start: 0.8985 (mmt) cc_final: 0.8465 (mmt) REVERT: C 590 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8329 (mpp80) REVERT: C 804 LEU cc_start: 0.8001 (tp) cc_final: 0.7768 (tt) REVERT: D 566 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: D 803 MET cc_start: 0.8594 (mtp) cc_final: 0.8337 (mtp) REVERT: E 78 LYS cc_start: 0.7098 (ttpp) cc_final: 0.6862 (ttpp) REVERT: E 184 PHE cc_start: 0.7524 (m-80) cc_final: 0.7285 (m-10) REVERT: F 99 ARG cc_start: 0.7404 (mmp80) cc_final: 0.6701 (mtt90) REVERT: G 37 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7290 (mtp85) REVERT: G 120 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6323 (mp) REVERT: H 37 ARG cc_start: 0.6855 (mtt-85) cc_final: 0.6605 (mtp85) REVERT: H 58 MET cc_start: 0.6371 (tpt) cc_final: 0.6058 (mmm) REVERT: H 99 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.6930 (mmm-85) REVERT: H 208 ARG cc_start: 0.4153 (OUTLIER) cc_final: 0.3653 (ppt-90) outliers start: 27 outliers final: 15 residues processed: 127 average time/residue: 1.4571 time to fit residues: 197.9944 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLN 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 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 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 54 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10222 Z= 0.240 Angle : 0.511 9.475 13785 Z= 0.272 Chirality : 0.038 0.146 1555 Planarity : 0.003 0.031 1663 Dihedral : 10.380 85.018 1583 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.88 % Allowed : 13.89 % Favored : 83.23 % 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: 3.39 (0.24), residues: 1219 helix: 3.16 (0.16), residues: 903 sheet: 1.22 (1.43), residues: 20 loop : -0.80 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 64 HIS 0.005 0.001 HIS G 204 PHE 0.015 0.002 PHE C 570 TYR 0.014 0.002 TYR C 612 ARG 0.004 0.000 ARG D 624 ********************** 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 134 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.048 Fit side-chains REVERT: A 581 MET cc_start: 0.9132 (mmt) cc_final: 0.8583 (mmt) REVERT: A 582 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: A 590 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: B 615 ASN cc_start: 0.7532 (m-40) cc_final: 0.6945 (t0) REVERT: B 807 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6579 (tp) REVERT: C 581 MET cc_start: 0.9001 (mmt) cc_final: 0.8493 (mmt) REVERT: C 590 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8353 (mpp80) REVERT: C 804 LEU cc_start: 0.8018 (tp) cc_final: 0.7784 (tt) REVERT: D 566 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: D 803 MET cc_start: 0.8624 (mtp) cc_final: 0.8396 (mtp) REVERT: E 65 ARG cc_start: 0.6958 (mtm-85) cc_final: 0.6503 (mtm-85) REVERT: E 78 LYS cc_start: 0.7071 (ttpp) cc_final: 0.6852 (ttpp) REVERT: E 184 PHE cc_start: 0.7495 (m-80) cc_final: 0.7255 (m-10) REVERT: F 99 ARG cc_start: 0.7411 (mmp80) cc_final: 0.6711 (mtt90) REVERT: G 37 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7329 (mtp85) REVERT: G 120 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6298 (mp) REVERT: H 37 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6605 (mtp85) REVERT: H 58 MET cc_start: 0.6362 (tpt) cc_final: 0.6065 (mmm) REVERT: H 99 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.6942 (mmm-85) REVERT: H 208 ARG cc_start: 0.4148 (OUTLIER) cc_final: 0.3667 (ppt-90) outliers start: 25 outliers final: 15 residues processed: 124 average time/residue: 1.5001 time to fit residues: 198.3062 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLN 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 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 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 88 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109161 restraints weight = 50891.602| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.76 r_work: 0.2500 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10222 Z= 0.153 Angle : 0.455 8.918 13785 Z= 0.240 Chirality : 0.036 0.128 1555 Planarity : 0.003 0.031 1663 Dihedral : 9.785 85.996 1583 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.68 % Allowed : 14.19 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.71 (0.24), residues: 1219 helix: 3.42 (0.16), residues: 903 sheet: 1.29 (1.45), residues: 20 loop : -0.77 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 177 HIS 0.006 0.001 HIS G 204 PHE 0.011 0.001 PHE C 570 TYR 0.009 0.001 TYR F 180 ARG 0.003 0.000 ARG D 624 =============================================================================== Job complete usr+sys time: 3732.35 seconds wall clock time: 68 minutes 25.47 seconds (4105.47 seconds total)